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Sarthak Malhotra, , Swagata Karmakar,
Published: 28 September 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00059

Abstract:
Coal fly ash dumps represent contaminated sites that pollute the environment and affect the health of living organisms. Vegetation development at ash dumps is an ecological solution to minimize the environmental threats of ash, however low content of nutrients, organic matter and moisture pose a challenge for plant growth at the dumps. Bacterial indole acetic acid (IAA) facilitates plant recruitment and growth, more crucially in degraded ecosystems. Bacteria with different levels of IAA determine the plant-bacterial interactions as pathogenesis or symbiosis, therefore, form microbial functional types. Understanding plant-soil feedback and identifying environmental predictors of bacterial IAA producers at ash dump would help in improving biostimulation strategies for vegetation development. Therefore, to evolve a nature-based solution for vegetational restoration of ash dumps, we analyzed the role of geochemical factors, host species and age of dump on the assembly of rhizobacterial IAA functional types of naturally colonizing grasses (Saccharum ravennae and Cynodon dactylon). Analyses showed that the rhizosphere effect on geochemical traits was distinct in the dumps, irrespective of the host plant and age of the dumps. The rhizobacterial communities from the dumps produce relatively high mean IAA levels and harbor a high micro-diversity of IAA producers as compared with the region as a whole (non-rhizosphere or bulk ash). Canonical correspondence analysis showed that the host species and specific nutrients i.e. NO3-N, PO4-P, Fe, and Na are the significant predictors of bacterial IAA functional types. S. ravennae and C. dactylon provided evidence of driving assembly of different IAA functional types in their rhizosphere via enrichment of NO3-N and PO4-P, respectively. The identification of environmental predictors of rhizobacterial IAA functional types of S. ravennae and C. dactylon has provided basic guidelines to improve the biostimulation strategies to accelerate vegetation restoration at the ash dumps. Both controlled and field experiments involving grass species with supplementation of specific nutrients would be required to develop an effective biostimulation strategy for the on-field application.
Published: 26 September 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00060

Abstract:
Agriculture is fundamental for human survival through food production and is performed in ecosystems that, while simplified, still operate along ecological principles and retain complexity. Agricultural plants are thus part of ecological systems, and interact in complex ways with the surrounding terrestrial, soil and aquatic habitats. We discuss three case studies that demonstrate how agricultural solutions to pest and weed control, if they overlook important ecological and evolutionary factors, cause ’surprises‘: i) the fast emergence of resistence against the crop-inserted Bt-toxin in South Africa, ii) the ecological changes generated by Bt-cotton landscapes in China, and iii) the decline of the monarch butterfly, Danaus plexippus, in North America. The recognition that we work with complex systems is in itself important, as it should limit the belief in reductionist solutions. Agricultural practices lacking eco-evolutionary understanding result in ’surprises’ like resistance evolution both in weeds and pest insects, risking the reappearance of the “pesticide treadmill” – with increased use of toxic pesticides as the follow-up. We recommend prioritization of research that counteracts the tendencies of reductionist approaches. These may be beneficial on a short term, but with trade-off costs on a medium- to long term. Such costs include loss of biodiversity, ecosystem services, long-term soil productivity, pollution and reduced food quality.
Muhammad A. Aslam, , Claudio O. Stöckle, Stewart S. Higgins, Fayyaz Ul Hassan, Rifat Hayat
Published: 25 September 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00057

Abstract:
Wheat (Triticum aestivum) production in the rainfed area of Pothwar Pakistan is extremely vulnerable to high temperature. The expected increase in temperature due to global warming should result in shorter crop life cycles, and thus lower biomass and grain yield. Two major factors control wheat phenological development: temperature and photoperiod. To evaluate wheat development in response to these factors, we conducted experiments that created diverse temperature and daylength conditions by adjusting the crop sowing time. The study was conducted during 2013-14 and 2014-15 using five spring wheat genotypes, four sowing times, at three sites under rainfed management in Pothwar, Pakistan. Wheat crops experienced more cold days with early sowing, but later sowing dates resulted in higher temperatures, especially from anthesis to maturity. These treatments produced large differences in phenology, biomass production, and yield. To investigate whether growing degree days (GDD) and photoperiod algorithms could predict wheat phenology under these changing conditions, GDD was calculated based on the method proposed by Wang and Engel while photoperiod followed the approach introduced in the APSIM crop growth model. GDD was calculated separately and in combination with photoperiod from germination to anthesis. For the grain filling period, only GDD was calculated. The observed and predicted number of days to anthesis and maturity were in good agreement, showing that the combination of GDD and photoperiod algorithms provided good estimations of spring wheat phenology under variable temperature and daylength conditions.
Richard Egelkamp, , Robert Hertel,
Published: 12 September 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00056

Abstract:
Nitriles are a diverse group of organic compounds with –C≡N as functional group. Most nitriles are slightly cytotoxic but some cause severe toxic effects. More than 120 naturally occurring nitriles without considering cyanogenic glycosides are present in terrestrial and marine habitats, especially in plant components such as almonds or other fruit pits. The most common group of naturally occurring nitriles are cyanogenic glycosides, which can be found in more than 100 plant families as well as in fungi, bacteria, and animals. This group of molecules can be chemically or enzymatically hydrolyzed, leading to the release of highly toxic hydrogen cyanide and thereby act as natural defense compound (Fleming, 1999). For detoxification, two enzymatic pathways for the degradation of nitriles are known. The first one involves nitrilases (EC 3.5.5.1), a subgroup of the carbon-nitrogen hydrolase superfamily, which degrade nitriles directly to carboxylic acids and ammonia. The second one is a bi-enzymatic pathway using nitrile hydratases (NHases; EC 4.2.1.84) for the degradation of nitriles to amides and amidases (EC 3.5.1.4) for the subsequent degradation to carboxylic acids and ammonia (Gong et al., 2012). The enzymatic hydrolysis of nitriles proceeds under mild reaction conditions, whereas the chemical hydrolysis is dependent on acidic or alkaline conditions and high temperatures. The latter also results in the production of large quantities of byproducts and inorganic waste (Clouthier and Pelletier, 2012; Vergne-Vaxelaire et al., 2013). Consequently, nitrile-converting enzymes are of increasing industrial importance with respect to green chemistry. A constantly increasing number of nitrile-derived amides [e.g., acrylamides or carboxylic acids (e.g., glycolic acid)] are produced with these enzymes (Schmid et al., 2001; Panova et al., 2007). In addition, nitrilases can be used for the treatment of nitrile-polluted wastewater (Li et al., 2016) and other environmentally-friendly bioremediation processes (Gong et al., 2012). Here, we report data on the taxonomic composition of an enrichment culture with acetonitrile as nitrogen source. In addition, we present eight individual bacterial draft genome sequences of isolates obtained from this enrichment. The genome content of these isolates was analyzed with respect to genes responsible for the nitrile-degrading phenotype. Genome and average nucleotide identity analysis indicated that the isolated bacterial strains are affiliated to the species Rhodococcus erythropolis, Flavobacterium sp., Variovorax boronicumulans, Pseudomonas sp., and Pseudomonas kilonensis. Compost (100 g, pH 7.5) of the Experimental Botanical Garden Göttingen, Germany (51°33′22.6″N 9°57′16.2″E) was suspended in 500 ml H2O and filtered with a 2.7 μm GF/D glass fiber filter (Whatman, Little Chalfont, UK). Enrichment and control cultures were each initiated with 750 μl of the resulting filtrate. Enrichment cultures were grown in 40 ml M9 medium (Atlas, 2010) with ATCC trace mineral supplement (LGC Standards, Teddington, UK), 10 mM glucose as carbon source and 25 mM acetonitrile as sole nitrogen source at 25°C for 4 days. Control cultures were grown in same medium but the medium contained 18.7 mM NH4Cl instead of acetonitrile. The enrichment culture was streaked on solid M9 medium with 25 mM acetonitrile as sole nitrogen source and incubated at 25°C. The obtained 33 colonies showed four distinct colony morphologies, and were picked and purified over five rounds of incubation. Growth in the absence of an added nitrogen source was not recorded. Genomic DNA of the liquid cultures and the specific isolates was extracted using the MasterPure complete DNA and RNA purification kit (Epicentre, Madison, WI, USA), while DNA isolation of the compost sample was done with the PowerMax soil DNA isolation kit (MO BIO Laboratories, Carlsbad, CA, USA). The bacterial composition was determined by amplicon-based analysis of the V3-V4 region of the 16S rRNA gene using the bacterial primers S-D-Bact-0341-b-S-17 and S-D-Bact-0785-a-A-21 (Klindworth et al., 2013) with adapters for Illumina MiSeq sequencing (Illumina, San Diego, CA, USA). The PCR reaction mixture (50 μl) contained 10 μl 5-fold Phusion GC buffer, 200 μM of each of the four dNTPs, 2.5 μl DMSO, 0.2 μM of each primer, 200 μM MgCl2, 1 U of Phusion polymerase (Thermo Fisher Scientific, Waltham, MA, USA), and 25 ng of isolated DNA as template. The following cycling scheme was used: initial denaturation at 98°C for 1 min and 25 cycles of denaturation at 98°C for 45 s, annealing at 60°C for 45 s, and extension at 72°C for 30 s, followed by a final extension at 72°C for 5 min. PCR reactions were performed in triplicate for each sample. The resulting PCR products were pooled in equal amounts and purified using the NucleoMag 96 PCR kit (Macherey-Nagel, Düren, Germany) as recommended by the manufacturer. Quantification of the PCR products was performed using the Quant-iT dsDNA HS assay kit and a Qubit fluorometer as recommended by the manufacturer (Invitrogen, Carlsbad, CA, USA). Indexing of the PCR products was performed with Nextera XT DNA library prep kit as described by the supplier (Illumina). Sequencing was performed with the Illumina MiSeq platform using the dual index paired-end approach (2 × 300 bp) and v3 chemistry. The 16S rRNA genes of specific isolates were amplified with the primer pair 08f (5′-AGAGTTTGATCCTGGC-3′) and 1504r (5′-TACCTTGTTACGACTT-3′). The previously mentioned cycling scheme was modified to an annealing temperature of 40°C and an extension time of 45 s. Sanger sequencing of the PCR products was done by Seqlab (Göttingen, Germany). Demultiplexing and clipping of sequence adapters from raw amplicon sequences were performed by employing CASAVA data analysis software (Illumina). Paired-end sequences were merged using PEAR v0.9.10 with default parameters (Zhang et al., 2014). Subsequently, sequences with an average quality score lower than 20 and containing unresolved bases were removed with the split_libraries_fastq.py script of QIIME 1.9.1 (Caporaso et al., 2010). Non-clipped reverse and forward primer sequences were removed by employing cutadapt 1.12 with default settings (Martin, 2011). USEARCH version 9.2.64 was used following the UNOISE pipeline (Edgar, 2010). In detail, reads shorter than 380 bp were removed, dereplicated, and denoised with the UNOISE2 algorithm of USEARCH resulting in zero-radius operational taxonomic units (zOTUs). Additionally, chimeric sequences were removed using UCHIME2 in reference mode against the SILVA SSU database release 128 (Yilmaz et al., 2014). All quality-filtered sequences were mapped to chimera-free OTUs and a zOTU table was created using USEARCH. Taxonomic classification of the picked reference sequences (zOTUs) was performed with parallel_assign_taxonomy_blast.py against the same SILVA database. Extrinsic domain OTUs, chloroplasts, and unclassified OTUs were removed from the dataset by employing filter_otu_table.py. Sample comparisons were performed at same surveying effort, utilizing the lowest number of sequences by random subsampling (31,000 reads per sample). Genome sequencing was performed using an Illumina MiSeq system with the Nextera XT DNA library prep kit as recommended by the manufacturer (Illumina). Paired-end reads were quality-trimmed with Trimmomatic version 0.36 (Bolger et al., 2014) and verified with FastQC version 0.11.5 (Andrews, 2010). Assembly and first coverage calculation was performed with SPAdes version 3.9.0 (Bankevich et al., 2012). All contigs >500 bp and with a coverage >5 were annotated using Prokka version 1.11 (Seemann, 2014). Final coverage was calculated with Bowtie 2 version 2.2.9 (Langmead and Salzberg, 2012). A BLASTn search (Altschul et al., 1990) was performed against the NCBI non-redundant database to verify assembled contigs. For taxonomic assignment, the full-length 16S rRNA gene sequences of all isolated organisms were searched against the NCBI database. Combination of these data with an analysis of the tetra-nucleotide signatures (Tetra) and the average nucleotide identities (ANI) performed with JSpeciesWS (Richter et al., 2016) as well as in silico DNA-DNA hybridization results calculated with the online tool GGDC 2.1 (Meier-Kolthoff et al., 2013) were employed for taxonomic classification of the isolates. Putative nitrilases, NHases, and amidases were compared with the non-redundant protein database of the NCBI using BLASTp (Altschul et al., 1990). The hit with the highest score is given in Table 1. Table 1. Genome data and similarities of putative nitrile-degrading enzymes encoded by the genomes of the isolates. Enrichment of the compost sample with M9 minimal medium containing acetonitrile as sole nitrogen source resulted in microbial growth, indicating the presence of acetonitrile-degrading organisms. The bacterial diversity and composition of the compost sample and the enrichment culture were determined via amplicon-based 16S rRNA gene analysis. The compost sample used as starting material for enrichment comprised 520 zOTUs, which were reduced to 63 during enrichment (Supplementary Table S1). The dominant bacterial genera after enrichment were Aeromonas (33%) and Pseudomonas (55%) with similar abundances in the control sample (Figure 1A). In the enrichment culture the relative abundances of Flavobacterium and Bacillus were 5 and 2%, respectively, and in the control culture 2 and 0.4%, respectively. Chryseobacterium, Paenibacillus, Pedobacter, and Sphingobacterium varied between 1.1 and 1.3% in the control culture, but showed relative abundances below 0.1% in the acetonitrile-containing enrichment. In contrast, Variovorax (3%) was only detected in the acetonitrile enrichment culture in significant amounts. We performed isolation experiments from enrichment cultures on solid media with acetonitrile as sole nitrogen source. A total of 33 isolates (Figure 1B) were recovered of which eight isolates (ACN1 to ACN8, Table 1) showed a different 16S rRNA gene sequence. All isolates were able to grow with acetonitrile as sole nitrogen source in axenic culture. No growth was observed in the absence of an added nitrogen source. The genomes of all eight isolates were sequenced and analyzed with the focus on genes potentially involved in nitrile-degradation (Table 1). Based on average nucleotide identity, tetra-nucleotide signatures and in silico DNA-DNA hybridization, the eight isolates were affiliated to the genera Flavobacterium, Pseudomonas, Rhodococcus and Variovorax. Besides Rhodococcus all isolated strains belonged to genera detected during 16S rRNA gene analysis of the bacterial community in the enrichment culture. Figure 1. (A) Community composition of acetonitrile-enrichment and control culture and (B) 16S rRNA gene analysis of 33 acetonitrile-degrading isolates; “Others” refers to genera with an abundance of <1%. M9, control; ACN, acetonitril enrichment. In contrast to all other isolates, only slight traces of Rhodococcus could be found during 16S rRNA gene analysis. Nevertheless, this isolate was obtained multiple times from the enrichment, indicating its ability to degrade acetonitrile. The reason for the discrepancy between 16S rRNA gene analysis of the community and the isolation results may be due to non-optimal media conditions for Rhodococcus in the enrichment culture, leading to low abundance. Genome sequencing of R. erythropolis ACN1 and quality-filtering resulted in 2,641,652 paired-end reads resulting in a draft genome of 7.24 Mbp with a 93.9-fold coverage. Similarity searches for putative genes involved in nitrile-degradation revealed two genes (BKP42_65670 and BKP42_65680), coding for one of the two putative NHase subunits. These enzymes are known to be responsible for nitrile degradation in various R. erythropolis strains (Kaufmann et al., 1999; Brandão et al., 2003; Vejvoda et al., 2007; Kamble et al., 2013). The deduced protein sequences showed highest identity to the alpha subunit of Rhodococcus sp. N-774 (Ikehata et al., 1989) and the beta subunit of R. erythropolis deep-sea strain 122-AN065 (Brandão et al., 2003). The deduced acetamidases (BKP42_40660 and BKP42_26750) are most similar to acetamidases of R. erythropolis and Rhodococcus sp. 311R (Ehsani et al., 2015). The two aliphatic amidases of the isolated strain (BKP42_54900 and BKP42_64640) most resemble an acylamide amidohydrolase from Gordonia desulfuricans and an amidase of Rhodococcus sp. R312 (Fournand et al., 1998). An additional amidase (BKP42_65660) is most similar to an amidase of Rhodococcus sp. N-774 (Table 1). Members of the genus Variovorax were prime candidates for active nitrile degradation, as the genus appeared only in significant abundances in the bacterial community after enrichment with acetonitrile. With the isolation of ACN3 identified as V. boronicumulans a member of this genus was recovered. Sequencing and assembly of 3,471,160 paired-end reads resulted in a draft genome of 7.14 Mbp (131-fold coverage). Although V. boronicumulans is a species described just recently (Miwa et al., 2008), evidence for nitrile degradation by this microorganism was reported before (Zhang et al., 2012; Liu et al., 2013). A search for genes encoding putative nitrile-degrading enzymes resulted in the identification of genes for two possible degradation pathways, the first one via a nitrilase (BKP43_17560) and the second one via an NHase (BKP43_58000 and BKP43_58010) and amidase (BKP43_28100). The most similar enzymes to the nitrilase, alpha and beta subunits of NHase, and the aliphatic amidase are an amidohydrolase, NHase subunits and acylamide amidohydrolase of another V. boronicumulans strain, respectively (Table 1). With a relative abundance of over 50%, Pseudomonas is the major genus of the bacterial community in the acetonitrile enrichment culture. Several Pseudomonas species such as P. chlorographis and P. fluorescens are able to use nitriles as nitrogen source and harbor genes encoding nitrilases, or NHases and amidases (Nagasawa et al., 1987; Kiziak et al., 2005; Howden et al., 2009). The presence of these genes could be due to the plant habitat of some Pseudomonas species, which is rich in different and unusual nitriles like indole-3-carbonyl nitrile (Rajniak et al., 2015). Isolates ACN4 and ACN7 were affiliated to P. kilonensis, a species described in 2001 (Sikorski et al., 2001). Sequencing of the ACN4 genome resulted in 2,239,346 paired-end reads, an average coverage of 96.7-fold, and a draft genome of 6.55 Mbp. Genes encoding a putative nitrilase (BSF43_29400) and amidase (BSF43_35090) were detected, which showed highest identity to a Pseudomonas nitrilase and a putative acylamide amidohydrolase of P. sp. Root401 (Bai et al., 2015), respectively. The genome assembly of isolate ACN7 was based on 2,049,404 paired-end reads and resulted in a draft genome of 6.49 Mbp and a 74.9-fold coverage. The GC-content is 61.0%. The draft genome encodes a nitrilase (BSG18_13010) and an amidase (BSG18_29450) similar to a nitrilase of P. sp. Ep R1 (Chiellini et al., 2014) and an acylamide amidohydrolase of P. sp. Root401, respectively. The two Pseudomonas isolates ACN5 and ACN8 could not be assigned to a specific Pseudomonas species. The genome of ACN5 (6.69 Mbp, 61.3-fold coverage) was assembled from 1,350,588 paired-end reads. Potential genes for two nitrilases, one NHase and two amidases were predicted in the ACN5 genome. The aliphatic nitrilase (BSF40_48900) showed highest similarity to a nitrilase of Pseudomonas sp. UW4 (Duan et al., 2013), while the other nitrilase (BSF40_42250) most resembles a nitrilase of Pseudomonas sp. GM48 (Brown et al., 2012). The NHase alpha and beta subunits (BSF40_24660 and BSF40_24650) are related to the corresponding ones of Pseudomonas and P. sp. UW4. The predicted amidases (BSF40_24670 and BSF40_59650) are similar to an amidase of P. sp. GM33 and GM49 (Brown et al., 2012). For the assembly of the ACN8 genome, 1,505,826 paired-end reads were used, resulting in a draft genome of 6.34 Mbp and 66.0-fold coverage. Genes for two nitrilases (BSF44_34690 and BSF44_52950) were predicted, which resemble two different nitrilases from P. fluorescens. Furthermore, two genes encoding putative amidases (BSF44_36240 and BSF44_50390) similar to an amidase of P. composti and P. sp. GM74 (Brown et al., 2012) were detected. The two isolates ACN2 and ACN6 from the acetonitrile enrichment culture were affiliated to the Gram-negative genus Flavobacterium. A total of 1,503,824 paired-end reads were used for the assembly of the ACN2 genome, resulting in a draft genome of 5.40 Mbp with an average coverage of 72.7-fold. ACN6 genome assembly of 2,409,950 paired-end reads yielded a draft genome of 5.13 Mbp with average coverage of 120.4-fold. Genes encoding putative nitrile-degrading enzymes were not detected in both draft genomes. As the nitrile degrading capacity of both strains was independently verified multiple times by growth experiments with acetonitrile as sole nitrogen source, the presence of so far unknown genes and pathways for nitrile utilization is indicated. In addition, the ability to overcome the nitrogen limitation via nitrogen fixation from air was experimentally excluded as no growth could be monitored in liquid M9 medium without any added nitrogen source. Furthermore, typical genes for nitrogen fixation such as dinitrogenases and dinitrogenase reductases were not identified in the genome sequences. Thus, two explanations are possible for the discrepancy between the observed phenotype of both strains and the lack of putative genes for nitrile degradation. First, genes responsible for nitrile degradation could not be annotated as they are located in contig gaps, as both genomes are still in the draft state. This is unlikely as most contig gaps are due to repetitive regions longer than the read length of the used sequencing technology (Whiteford et al., 2005; Chaisson et al., 2015). Second, genes for new types of nitrile degradation enzymes are present. The only other available study on nitrile degradation by Flavobacteria reports weak degradation of 3-cyanopyridine by F. aquatile IFO 3772, F. suaveolens IFO 3752 and F. rigense IAM 1238 (Kato et al., 2000), but genes responsible for the observed phenotype were not reported and genomes of the three strains are not available. Thus, further analyses are required to unravel the basis of the nitrile-degrading phenotype of the flavobacterial isolates. The here presented data revealed the potential of specifically designed enrichment experiments for the isolation of organisms with a desired metabolic activity like nitrile degradation. Our study provided new candidates to cover the industrial demand for new nitrile-degrading biocatalysts as part of a green chemistry. While for the isolates R. erythropolis ACN1, V. boronicumulans ACN2, P. kilonensis ACN4 and ACN7 as well as P. sp. ACN5 and ACN8 nitrilases and/or NHases and amidases could be annotated, the nitrile-degrading pathway of F. sp ACN2 and ACN6 remains to be unraveled. The draft genome sequences of all eight organisms have been deposited at GenBank with the following accession numbers: R. erythropolis ACN1, MRCL00000000; F. sp. ACN2, MRCM00000000; V. boronicumulans ACN3, MRCN00000000; P. kilonensis ACN4, MRCO00000000; P. sp. ACN5, MRCP00000000; F. sp. ACN6, MRCQ00000000; P. kilonensis ACN7, MRCR00000000; P. sp. ACN8, MRCS00000000. Raw sequence data of all genomes are available at the NCBI SRA archive and linked to the respective BioSamples. The sequences of the 16S rRNA gene analysis are linked to the BioSamples SAMN07278921 (inoculum), SAMN0278947 (control) and SAMN07278950 (acetonitrile enrichment). Strains have been submitted to the DSMZ German Collection of Microorganism and Cell Cultures and are available on request. RD and RH conceived the study. RE performed the experiments. 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Food Chem. 60, 153–159. doi: 10.1021/jf203232u PubMed Abstract | CrossRef Full Text | Google Scholar Zhang, J., Kobert, K., Flouri, T., and Stamatakis, A. (2014). PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30, 614–620. doi: 10.1093/bioinformatics/btt593 PubMed Abstract | CrossRef Full Text | Google Scholar Keywords: acetonitrile, nitrilase, nitrile hydratase, amidase, Flavobacterium, Pseudomonas, Rhodococcus, Variovorax Citation: Egelkamp R, Schneider D, Hertel R and Daniel R (2017) Nitrile-Degrading Bacteria Isolated from Compost. Front. Environ. Sci. 5:56. doi: 10.3389/fenvs.2017.00056 Received: 25 July 2017; Accepted: 24 August 2017; Published: 12 September 2017. Edited by: Reviewed by: Copyright © 2017 Egelkamp, Schneider, Hertel and Daniel. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. *Correspondence: Rolf Daniel, [email protected]
, , Elizabeth R. Allen, Elizabeth M. Whitefield, Nichole M. Embertson, Vincent P. Jones, Brooke R. Saari, , Gabrielle E. Roesch-McNally, Beatrice Van Horne, et al.
Published: 31 August 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00052

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In order for agricultural systems to successfully mitigate and adapt to climate change there is a need to coordinate and prioritize next steps for research and extension. This includes focusing on “win-win” management practices that simultaneously provide short-term benefits to farmers and improve the sustainability and resiliency of agricultural systems with respect to climate change. In the Northwest U.S., a collaborative process has been used to engage individuals spanning the research-practice continuum. This collaborative approach was utilized at a 2016 workshop titled “Agriculture in a Changing Climate,” that included a broad range of participants including university faculty and students, crop and livestock producers, and individuals representing state, tribal and federal government agencies, industry, nonprofit organizations, and conservation districts. The Northwest U.S. encompasses a range of agro-ecological systems and diverse geographic and climatic contexts. Regional research and science communication efforts for climate change and agriculture have a strong history of engaging diverse stakeholders. These features of the Northwest U.S. provide a foundation for the collaborative research and extension prioritization presented here. We focus on identifying research and extension actions that can be taken over the next five years in four areas identified as important areas by conference organizers and participants: (1) cropping systems, (2) livestock systems, (3) decision support systems to support consideration of climate change in agricultural management decisions; and (4) partnerships among researchers and stakeholders. We couple insights from the workshop and a review of current literature to articulate current scientific understanding, and priorities recommended by workshop participants that target existing knowledge gaps, challenges, and opportunities. Priorities defined at the Agriculture in a Changing Climate workshop highlight the need for ongoing investment in interdisciplinary research integrating social, economic and biophysical sciences, strategic collaborations, and knowledge sharing to develop actionable science that can support informed decision-making in the agriculture sector as the climate changes.
Published: 29 August 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00055

Abstract:
A commentary onEvaluating the Role of Seagrass in Cenozoic CO2 Variationsby Brandano, M., Cuffaro, M., Gaglianone, G., Pettricca, P., Stagno, V., and Mateu-Vicens, G. (2016). Front. Environ. Sci. 4:72. doi: 10.3389/fenvs.2016.00072 Brandano et al. (2016) sought to quantify the role of seagrasses in removing atmospheric CO2 during the past 65 million years. To date, this estimate has been missing from the literature. Moreover, as the authors point out, there has so far been little attention paid to the role of calcium carbonate formation (CaCO3; inorganic carbon precipitated by calcifying organisms) in seagrass carbon budgets; much of the literature has focused on organic carbon only. The authors conclude that seagrasses have had globally-significant impacts on atmospheric CO2 fluxes throughout the Cenozoic era. While we appreciate the ambitious nature and difficulty of the study, we argue that the authors have made fundamental misconceptions about the contribution of carbonate production (calcification) and sequestration to ocean carbon budgets. The authors have not accounted for the fact that calcification increases pCO2 (by depleting CO32- and therefore reducing alkalinity), which facilitates the return of CO2 to the atmosphere (Frankignoulle et al., 1994). Specifically, for every mole of CaCO3 precipitated as carbonate, the process also consumes 2 moles of HCO3- and releases 1 mole of CO2: However, the stoichiometry of this reaction is complicated by buffering effects in seawater (Frankignoulle et al., 1995), leading to less than 1 mole of CO2 being released to the atmosphere. This ratio is ~0.63 under current atmospheric CO2 concentrations (known as the “rule of the 0.6”; Ware et al., 1992), but is predicted to increase at higher atmospheric CO2 concentrations (Suzuki, 1998), with unaddressed implications for the CO2 atmospheric fluxes since the Cenozoic reported by Brandano et al. (2016) (their Figure 4). Hence, carbonate production results in CO2 release, but the authors do not account for this. Instead, the authors treat carbonate production as resulting in net CO2 sequestration, which they add to the CO2sink capacity of seagrasses, when in reality it needs to be treated as a CO2source. Previous studies have pointed out that although Posidonia meadows (as well as other seagrass species; Mazarrasa et al., 2015) host significant CaCO3 stocks and accumulation rates, it has been shown that calcification represents a global CO2 source to the atmosphere (Smith and Gattuso, 2009), and therefore seagrass meadows (all species) could represent a significant net CO2 source (Mateo and Serrano, 2012; Serrano et al., 2012). A global estimate for the entire Mediterranean indicates that calcification in P. oceanica meadows could be responsible for the emission of 0.7 to 4.2 Tg C year−1 to the atmosphere (Mateo and Serrano, 2012). Indeed, they conclude that the net carbon balance between the organic carbon (CO2 sink) and the inorganic carbon (CO2 source) pools in Tyrrhenian P. oceanica meadows could range from −7.4 to +3.9 Tg C year−1. Coral reefs are also not considered natural atmospheric CO2 sinks because production and respiration are balanced (i.e., there is no net accumulation of organic carbon) and as a result of high calcification rates in many reef systems, they are considered a net source of CO2 to the atmosphere (e.g., Ware et al., 1992; Gattuso et al., 1995). We acknowledge the complexity of estimating the CO2 sequestration capacity of ecosystems over geological time scales, and the multiple assumptions on which such type of estimates are based. However, we feel that their analysis is weakened by not taking proper account of the chemistry of carbonate formation and that accordingly the values they report must represent an overestimate of the true rates of draw-down of CO2. PM led the paper. All authors contributed to the writing. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. PM was supported by an Australian Research Council DECRA Fellowship (DE130101084) and a Linkage Project (LP160100242). OS was supported by the CSIRO Flagship Marine and Coastal Carbon Biogeochemical Cluster and an ARC DECRA Fellowship DE170101524. DM is supported by an ARC DECRA Fellowship (DE150100581). CD is supported by baseline funding from KAUST. Brandano, M., Cuffaro, M., Gaglianone, G., Pettricca, P., Stagno, V., and Mateu-Vicens, G. (2016). Evaluating the role of seagrass in Cenozoic CO2 variations. Front. Environ. Sci. 4:72. doi: 10.3389/fenvs.2016.00072 CrossRef Full Text | Google Scholar Frankignoulle, M., Canon, C., and Gattuso, J. P. (1994). Marine calcification as a source of carbon dioxide: positive feedback of increasing atmospheric CO2. Limnol. Oceanogr. 39, 458–462. doi: 10.4319/lo.1994.39.2.0458 CrossRef Full Text | Google Scholar Frankignoulle, M., Pichon, M., and Gattuso, J. P. (1995). “Aquatic calcification as a source of carbon dioxide,” in Proceedings of the NATO ARW on Carbon Sequestration in the Biosphere, Vol. 133., ed A. Beran (Elsevier), 265–271. Google Scholar Gattuso, J. P., Pichon, M., and Frankignoulle, M. (1995). Biological control of air-sea CO2 fluxes: effect of photosynthetic and calcifying marine organisms and ecosystems. Mar. Ecol. Prog. Ser. 129, 307–312. doi: 10.3354/meps129307 CrossRef Full Text | Google Scholar Mateo, M. A., and Serrano, O. (2012). The Carbon Sink Associated to Posidonia oceanica. Gland; Málaga, IUCN. Mazarrasa, I., Marba, N., Lovelock, C., E., Serrano, O., Lavery, P. S., Fourqurean, J. W., et al. (2015). Seagrass meadows as a globally significant carbonate reservoir. Biogeosciences 12, 4993–5003. doi: 10.5194/bg-12-4993-2015 CrossRef Full Text | Google Scholar Serrano, O., Mateo, M., A., Renom, P., and Julia, R. (2012). Characterization of soils beneath a Posidonia oceanica meadow. Geoderma 185, 26–36. doi: 10.1016/j.geoderma.2012.03.020 CrossRef Full Text | Google Scholar Smith, S. V., and Gattuso, J. P. (2009). Coral Reefs. Gland: IUCN. Google Scholar Suzuki, A. (1998). Combined effects of photosynthesis and calcification on the partial pressure of carbon dioxide in seawater. J. Oceanogr. 54, 1–7. doi: 10.1007/BF02744376 CrossRef Full Text | Google Scholar Ware, J. R., Smith, S. V., and Reaka-Kudla, M. L. (1992). Coral reefs: sources or sinks of atmospheric CO2? Coral Reefs 11, 127–130. doi: 10.1007/BF00255465 CrossRef Full Text | Google Scholar Keywords: seagrass, CO2, biosequestration, ecosystem, coast, carbonate, blue carbon, calcification Citation: Macreadie PI, Serrano O, Duarte CM, Beardall J and Maher D (2017) Commentary: Evaluating the Role of Seagrass in Cenozoic CO2 Variations. Front. Environ. Sci. 5:55. doi: 10.3389/fenvs.2017.00055 Received: 07 December 2016; Accepted: 18 August 2017; Published: 29 August 2017. Edited by: Reviewed by: Copyright © 2017 Macreadie, Serrano, Duarte, Beardall and Maher. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. *Correspondence: Peter I. Macreadie, [email protected]
Published: 29 August 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00054

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We propose and illustrate multi-scale integrated analysis of societal and ecosystem metabolism (MuSIASEM) as a tool to bring nexus thinking into practice. MuSIASEM studies the relations over the structural and functional components of social-ecological systems that determine the entanglement of water, energy and food flows in a complex metabolic pattern. MuSIASEM simultaneously considers various dimensions and multiple scales of analysis and therefore avoids the predicament of quantitative analysis based on reductionism (one dimension and one scale at the time). The different functional elements of society (the parts) are characterized using the concept of ‘processor’, that is, a profile of expected inputs and outputs associated with the expression of a specific function. The processors of the functional elements of the social-ecological system can be scaled-up to describe the metabolic pattern of the system as a whole, and scaled-down by considering the characteristics of its lower-level parts – i.e. the different processors associated with the structural elements required to express the specific function. An analysis of functional elements provides insight in the socio-economic factors that pose internal constraints on the development of the system. An analysis of structural elements makes it possible to study the compatibility of the system with external constraints (availability of natural resources and ecological services) in spatial terms. The usefulness of the approach is illustrated in relation to the use of charcoal in a rural village of Laos.
, Henry W. Loescher, Margaux S. Dillon
Published: 21 August 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00049

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The present paper is a preliminary analysis of the funding, organizational culture, environmental and innovation challenges that are currently faced by Environmental Research Infrastructures (ERI) and private enterprises working together. We contend there is a strong case for building creative collaboration models across these sectors that also require to new management tools to effectively generate economically-driven solutions to the global society at large in the face of climate change. To that end, public/private stakeholders that are likely to partner to address climate change also face new frontiers in how they will structurally and organizationally work together. We explore these issues around changing political, scientific, commercial environments; partnerships models; barriers in bridging these communities; and the role of formal project management processes. There is no one solution to fit all conditions that can bring together a specific public / private enterprise that incorporates a research infrastructure. However, we have provided two examples of collaborative models of public/private enterprises to highlight how these issues can be addressed, and to foster future dynamic and creative solutions to this problem.
, Shuang Wang, Jiaping Luan, Min Yu
Published: 21 August 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00046

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The forest ecosystem is the largest land vegetation type, which plays the role of unreplacement with its unique value. And in the landscape scale, the research on forest landscape pattern has become the current hot spot, wherein the study of forest canopy structure is very important. They determines the process and the strength of forests energy flow, which influences the adjustments of ecosystem for climate and species diversity to some extent. The extraction of influencing factors of canopy structure and the analysis of the vegetation distribution pattern are especially important. To solve the problems, remote sensing technology, which is superior to other technical means because of its fine timeliness and large-scale monitoring, is applied to the study. Taking Lingkong Mountain as the study area, the paper uses the remote sensing image to analyze the forest distribution pattern and obtains the spatial characteristics of canopy structure distribution, and DEM data are as the basic data to extract the influencing factors of canopy structure. In this paper, pattern of trees distribution is further analyzed by using terrain parameters, spatial analysis tools and surface processes quantitative simulation. The Hydrological Analysis tool is used to build distributed hydrological model, and corresponding algorithm is applied to determine surface water flow path, rivers network and basin boundary. Results show that forest vegetation distribution of dominant tree species present plaque on the landscape scale and their distribution have spatial heterogeneity which is related to terrain factors closely. After the overlay analysis of aspect, slope and forest distribution pattern respectively, the most suitable area for stand growth and the better living condition are obtained.
Published: 17 August 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00051

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The Intergovernmental Panel on Climate Change (IPCC) fourth assessment report confirmed that climate change is unequivocal. It is coming to us faster with larger impacts and bigger risks than even most climate scientists expected as recently as a few years ago. One particular worry is the disastrous consequence to agriculture and food security sectors in many parts of the world, particularly in developing countries. Adaptation is the only option to reduce the impacts of climate change on the agriculture sector. However, before planning adaptation policy or strategies to climate change, it is important to assess the impacts of climate change at regional and local scale. In this study the impacts of climate change on rain-fed maize (Zea Mays) production in the southern and western highlands sub-agro ecological zones of Tanzania are evaluated. High resolution climate simulations from the Coordinated Regional Climate Downscaling Experiment _Regional Climate Models (CORDEX_RCMs) were used as input into the Decision Support System for Agro-technological Transfer (DSSAT) to simulate maize yields in the historical climate condition (1971-2000), current (2010-2039), mid (2040-2069) and end (2070-2099) centuries. Daily rainfall, solar radiations, minimum and maximum temperatures for the historical (1971-2000) climate condition and future climate conditions (2010-2099) under two Representative Concentration Pathways (RCPs) RCP4.5 and RCP 8.5 were used to drive DSSAT. The impacts of climate change were assessed by comparing the average maize yields in historical climate condition against the average of simulated maize yields in the current, mid and end centuries under RCP4.5 and RCP8.5. Results indicated that maize yields will decline in future climate condition. High decreases in maize yield over the Southern and southwestern sub ecological zones are expected in the end centuries under RCP 8.5. The main reason for decline in maize yields during future climate is the increase in temperatures that shorten the length of growing seasons. Therefore it is recommended that more studies need to be carried out that addresses on how farmers may adapt the impacts of projected increase in temperatures on maize crop production.
Published: 8 August 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00048

Abstract:
The nexus approach helps in recognizing the link between water, energy and food production systems, emphasizing the need to manage them in a more integrated way. The socio‑ecosystem (SES) approach, however, goes beyond that, by incorporating the regulation and supporting services in the management equation. Changes in ecosystem integrity affect the delivery of ecosystem services to society, which affects local people’s well-being, creating a feedback mechanism regarding management strategies. The SES approach makes explicit the “human‑bio‑physical” nature of our interaction with ecosystems, highlighting the need for a more integrated and interconnected social‑ecological research perspective. In addition, the SES approach makes more explicit the multi-scale character of the ecological processes that structure and maintain social‑ecological systems. Water dynamics have an important role in shaping ecosystem’s structure and functioning, as well as determining the systems capacity for delivering provisioning services. The tropical dry-deciduous forest, is particularly useful in studying water-food-energy trade-off interactions. Recently, a category 5 hurricane landed in the study area (Mexico’s Pacific coast), triggering various social and ecological problems. This event is challenging the current forest management strategies in the region. The extreme hydrometeorological event created an excellent opportunity to test and promote the SES approach for more integrated food‑water‑energy research. By using the SES approach within our long-term socio-ecological research project, it was easier to identify opportunities for tackling trade‑offs between maintaining the transformation of the system and a more sustainable alternative: promoting the maintenance of the ecosystem’s integrity and its capacity to deliver provisioning and regulating services.
, Nihel Ben Gamra, Marine Periot, Marie Roumagnac, Perrine Zeller, , Annick Méjean, Olivier Ploux,
Published: 25 July 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00043

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Microcystin (MC) is a common and widespread toxin which represents a health hazard to humans and animals. MC toxin concentrations are monitored by various direct or proxy techniques (HPLC, LC-MS/MS, ELISA, PPIA), however, these techniques do not discriminate producing species from non-producing ones. In order to simultaneously provide the identity and activity of cyanotoxin producing species in freshwater lakes, we applied simple, and fully detailed, whole cell fluorescent in situ hybridization enhanced by tyramid signal amplification (TSA-FISH). DNA oligonucleotide probes MICR3 and MCYA were targeting 16S rRNA and mcyA-mRNA, respectively. The mcyA gene is coding for the MC synthetase enzyme involved in MC synthesis. Controls were acquired with the general eubacterial 16S rRNA probe EUB338, for TSA-FISH assay, and standard HPLC and LC-MS/MS as standard methods for the measurements of MC concentration. Results obtained from monoclonal strains and natural samples demonstrated a specific identification of Microcystis species and were able to discriminate MC producing from non-producing ones. In addition, the MCYA probe allowed the specific detection of MC-synthetase mRNA within Planktothrix isothrix (Oscillatoriale) filaments. Two kinds of mcyA-mRNA labeling were observed in these cells, spots like and plasmid like, which illustrates the well-known plasticity of microbial genome to adapt to environmental stresses. We demonstrated that a simple TSA-FISH assay allows acquiring rapidly dual information of the presence and abundance of potentially toxic species, while identifying species actively producing MC-synthetase mRNA, a proxy of MC toxin. This technique has the potential to be developed into an effective environmental monitoring tool. In addition, detail visualization of cellular mRNAs is powerful for the acquisition of ecological and biomolecular studies of toxic cyanobacteria.
, Dmitry Beletsky, Raisa Beletsky, Krista Wigginton, Brendan W. Locke,
Published: 19 July 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00045

Abstract:
Most plastic pollution originates on land. As such, freshwater bodies serve as conduits for the transport of plastic litter to the ocean. Understanding the concentrations and fluxes of plastic litter in freshwater ecosystems is critical to our understanding of the global plastic litter budget and underpins the success of future management strategies. We conducted a replicated field survey of surface plastic concentrations in four lakes in the North American Great Lakes system, the largest contiguous freshwater system on the planet. We then modeled plastic transport to resolve spatial and temporal variability of plastic distribution in one of the Great Lakes, Lake Erie. Triplicate surface samples were collected at 38 stations in mid-summer of 2014. Plastic particles >106 µm in size were quantified. Concentrations were highest near populated urban areas and their water infrastructure. In the highest concentration trawl, nearly 2 million fragments km-2 were found in the Detroit River—dwarfing previous reports of Great Lakes plastic abundances by over 4-fold. Yet, the accuracy of single trawl counts was challenged: within-station plastic abundances varied 0- to 3-fold between replicate trawls. In the smallest size class (106-1000 µm), false positive rates of 12-24% were determined analytically for plastic versus non-plastic, while false negative rates averaged ~18%. Though predicted to form in summer by the existing Lake Erie circulation model, our transport model did not predict a permanent surface “Lake Erie Garbage Patch” in its central basin—a trend supported by field survey data. Rather, general eastward transport with recirculation in the major basins was predicted. Further, modeled plastic residence times were drastically influenced by plastic buoyancy. Neutrally buoyant plastics—those with the same density as the ambient water—were flushed several times slower than plastics floating at the water’s surface and exceeded the hydraulic residence time of the lake. It is likely that the ecosystem impacts of plastic litter persist in the Great Lakes longer than assumed based on lake flushing rates. This study furthers our understanding of plastic pollution in the Great Lakes, a model freshwater system to study the movement of plastic from anthropogenic sources to environmental sinks.
Published: 1 January 2013
Frontiers in Environmental Science, Volume 1; https://doi.org/10.3389/fenvs.2013.00003

Abstract:
Several cultures emphasize that one should live in harmony with the environment, avoiding those human activities that substantially interfere with natural processes, including air pollution. Undoubtedly, the atmosphere is a principal environmental component, representing a crucial part of the entire climate system (Ayers, 2005). It behaves as a colloidal medium because it contains not only gases but also suspended particles and clouds. In ancient times the term “air pollution” was represented by smoke and soot. For example, Horatius (classical poet 65 B.C.—8 A.D.) wrote that Roman buildings became more and more dark from smoke. According to Xenophon (434–359 B.C.) and Lucretius (98–55 B.C.), harmful smoke of lead mines in Attica were damaging to peoples' health. Since then, a huge amount of historical information and a large body of literature on this field has become available. It mainly concerns air pollution sources, air pollutants content, health effects, engineering, and policy (Kelly, 2003; Schwartz, 2004; Dockery and Stone, 2007; Miller et al., 2007; Wilson et al., 2007; Fullerton et al., 2008; Krzyzanowski, 2008; Brook et al., 2009; Mohai et al., 2011). Nowadays, air pollution is an international problem with several impacts on living organisms (Akimoto, 2003). Many open questions still remain, such as the measurement and monitoring of air pollution, including the exploration of new technologies and methods like remote sensing and in-situ observations. For example, the investigation of air pollution over megacities by means of satellites observations has recently become a central topic of interest within the air pollution community (Van der A et al., 2008; Kar et al., 2010; Xue et al., 2010; Hilboll et al., 2013). Air pollution also impacts historic and modern buildings and materials, affecting sites of cultural heritage by damaging structural materials of monuments, statues, and even paintings. For example, substances such as sulfur dioxide, nitrogen compounds, ozone, and particulates can lead to material corrosion (Tzanis et al., 2011). In addition, it is of great importance to collect new data on hazardous and toxic substances, gaseous and particulate air pollutants. Among the two hundred toxic air pollutants, particular interest needs to be paid to those that are prevalent in specific regions, such as benzene and formaldehyde in the United States (Suh et al., 2000; Osthoff et al., 2008). Both, indoor and outdoor air pollution has been found to cause serious health effects, such as respiratory problems, including asthma, human eye, and skin irritation, and others. To this day, however, the effects of bioaerosol pollution at the workplace and at home remain unclear (Ziemke et al., 2000; Trasande and Thurston, 2005; Bernstein et al., 2008). New algorithms are being developed for the association of air pollution to other geophysical parameters such as solar and terrestrial radiation field in order to study the interplay of air pollution with long- and shortwave radiation. As an example, the solar radiation reaching the Earth's surface affects the terrestrial environment, thus changes in air pollution and cloudiness may substantially affect atmospheric transmission leading to a decline (dimming effect) or increase (brightening effect) in solar irradiance at the surface. These changes may significantly affect surface climate and consequently, the state of ecosystems (Wild et al., 2005). To investigate the spatio-temporal variability of air pollution on a local, regional, and global scale, new tools are being developed. In this context, the detection, tracking and understanding of pollutant transport on various spatial scales are of both local and global interest. Specifically, in rural and remote areas, where no ground-based monitoring network of the air pollution is available, the use of satellite data can provide an estimation of the regional distribution of pollutants, in order to assess the impact of specific events (e.g., biomass burning or dust storm outbreaks) (Lee et al., 2007). Over the last decade the role of the non-linear dynamics to the spatio-temporal variability of air pollution has still not been resolved (Varotsos, 2005; Varotsos et al., 2012, 2013). Air pollution, as most geophysical properties such as air turbulence, air temperature, humidity, precipitation, and ozone, obeys non-linear laws, which usually generate spatio-temporal, non-stationarities and thus instead of the application of the conventional analyses (i.e., Fourier analysis), new analytical techniques (i.e., detrended fluctuation analysis) capable to eliminate the non-stationarities in the data should be utilized. The role of air pollution in climate change dynamics is a question that must be urgently addressed. For example, the importance of air pollution and greenhouse warming vs. aerosol cooling needs to be discussed with air pollution cooling, dominated by aerosol content, expected to decline relative to greenhouse gas forcing in the future. The main reason is a much shorter lifetime of aerosols compared to that of most greenhouse gases (Andreae et al., 2005). In order to improve air pollution modeling and mitigation, modern research should take into consideration the implications of alternative formulations of air pollution modeling as well as integrated assessment models for further mitigation measures (Varotsos and Kirk-Davidoff, 2006; Amann et al., 2011). Current and future air pollution and ozone variability in the troposphere and stratosphere need to be addressed. For example, the recognition of the stratospheric ozone depletion and the increase of the tropospheric ozone amount has led to intensive theoretical and experimental research of the ozonesphere over the last three decades. Nevertheless, important problems still remain and need to be urgently addressed, including the non-linear behavior of the relevant chemical and dynamical mechanisms. In...
Published: 1 January 2013
Frontiers in Environmental Science, Volume 1; https://doi.org/10.3389/fenvs.2013.00002

Abstract:
Environmental pollution is one of the major threats to the biota and public health. The growing world population produces increasing amounts of toxins which accumulate in water, air, and soil. Especially in developing countries indiscriminate disposal of industrial and municipal wastes, vehicle emissions and improper application of pesticides and fertilizers in agriculture are main factors for increasing pollution (Lone et al., 2008). Persistent organic pollutants (POP) arise from accidental spillage or untreated emissions (Gao et al., 2008; Harrad, 2010; Zhou et al., 2013). In order to protect the environment and the public, permissive limits have been defined for many organic and inorganic toxins by national and international agencies (WHO, 2008). Limits for various pollutants can vary between countries and are sometimes adapted, e.g., when new research results indicate a health hazard at lower concentrations than previously assumed. The recommendation of the Federal Health Office in Germany for the concentration of nitrate in drinking water from 1986 was replaced by the recommendation of the Drinking Water Commission in 2003, which defines the permissive limit at 50 mg L−1 (Grummt, 2007). The bigger problem is that defined limits are not always observed, especially in developing countries. e.g., the WHO standard for arsenic in ground water is 10 μg L−1; this value is exceeded manifold in East Punjab, Pakistan, where concentrations of 32–1900 μg L−1 have been found (Farooqi et al., 2007). For some health hazards no firm limits can be defined. The doses for exposure of humans to radioactivity have been devised with respect to the natural exposure to radiation from the Earth (such as from radon and uranium) and ionizing radiation from outer space. The average exposure on Earth is ≈0.01 mSv/day, but in some areas it may be 5-fold higher. Astronauts in the International Space Station are exposed to ≈1 mSv/day. High-dose radiation of > 150 mSv causes often serious immediate effects on humans (Bonner, 2003). At low doses the effects of radiation result from the interaction of the radiation with the cellular DNA. The higher the radiation, the higher is the chance for DNA defects and mutations which may eventually lead to cancer (Tubiana et al., 2009). Consequently, decreasing the exposure reduces the health risk, but there is no firm lower limit; even a single hit can modify the DNA. As an example, lung cancer mortality was studied in 1415 Swedish iron miners who were exposed to short-lived derivatives of radon close to the currently accepted occupational limit. 50 deaths from lung cancer were observed between 1951 and 1976, in contrast to 12.8 expected (Radford and St. Clair Renard, 1984). When defining standards for pollutants, other environmental factors need to be considered. Especially organic substances can change under the influence of pH in water or when exposed to intense solar radiation. These products may or may not have a different toxicity. Things are even more complicated with mixtures of different pollutants. When doing a chemical analysis of ground, drinking or waste water, the laboratory work soon exceeds the economical limits, since it is not possible to test for the thousands of potentially damaging chemicals. e.g., 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD), also known as dioxin had not been synthesized for commercial purposes except as a test chemical for research. Therefore, there was no routine testing until it caused the Seveso poisoning in Italy (Geyer et al., 1986). So, how can we judge whether or not a given toxin—or even worse—a mixture of pollutants exceeds the safe threshold. Since it is unethical to test this on humans, plants and animals such as fish are being used to determine safe thresholds (Klauck et al., 2013). In order to avoid animal tests and to automate, facilitate and standardize environmental monitoring we have developed a biotest based on on-line computerized image analysis of the movement parameters in swimming microorganisms (Tahedl and Häder, 2000). A number of end points, such as the cell morphology, motility, swimming velocity and orientation of the flagellates with respect to the gravity vector of the Earth are being determined in thousands of cells providing sensitive, fast, inexpensive and reliable tests of the biological safety for the biota in aquatic habitats (Ahmed and Häder, 2010). This Ecotox test system has been used to monitor water treatment plants in Germany (Streb et al., 2006), detect toxins in industrial and municipal effluents in Pakistan (Azizullah et al., 2011) or the pollution level in lakes and rivers in Argentina and Egypt (Ahmed, 2010) as well as the effects of gamma-ray radiation in Japan (Sakashita et al., 2002). Frontiers in Environmental Toxicity is envisioned as a platform to present novel approaches for monitoring environmental safety, detecting and mitigating potential pollution, preventing accidental or intentional release of toxic substances into the environment which, alone or in conjunction with other pollutants and the prevailing environmental factors, threaten the biota in water, soil, and air. These immense tasks will be important for a future world with growing populations, changing environmental conditions and technological as well as demographic developments. Ahmed, H. (2010). Biomonitoring of Aquatic Ecosystems, Dept. Biology. Ph.D. thesis, Friedrich-Alexander-Universität, Erlangen- Nürnberg. Ahmed, H., and Häder, D.-P. (2010). Rapid ecotoxicological bioassay of nickel and cadmium using motility and photosynthetic parameters of Euglena gracilis. Env. Exp. Bot. 69, 68–75. doi: 10.1016/j.envexpbot.2010.02.009 CrossRef Full Text Azizullah, A., Richter, P., and Häder, D.-P. (2011). Ecotoxicological evaluation of wastewater samples from Gadoon Amazai Industrial Estate (GAIE), Swabi, Pakistan. Int. J....
Published: 1 January 2013
Frontiers in Environmental Science, Volume 1; https://doi.org/10.3389/fenvs.2013.00001

Abstract:
Climate change has been at the forefront of environmental concerns for over a quarter of a century. The sequence of reports published by the Intergovernmental Panel on Climate Change (IPCC, 1990, 1996, 2001, 2007, 2013) has been instrumental in bringing climate issues to the attention of the public and policy-makers alike. In 1992, the United Nations Conference on Environment and Development (UNCED-1992, Rio de Janeiro, Brazil) identified climate change as one of the major environmental challenges facing humankind and the Framework Convention on Climate Change (FCCC) was ratified on this occasion, thereby acknowledging the concerns of governments related to the impacts and risks to environmental resources, local to national economies, and society resulting from a changing climate. The two other major UN conventions drafted at UNCED-1992, namely the biodiversity and the desertification conventions, have never received the attention that the FCCC has, particularly since the Kyoto Protocol, aimed at reducing anthropogenic carbon emissions into the atmosphere, was signed in 1997. Despite much criticism as to the slow pace of negotiations and the limited success in the implementation of the Protocol, it remains to this day a unique attempt to address the greenhouse-gas problem at the global scale. The issues of climate change have led to heated debates, both within academia as well as between scientists and a large community of skeptics. While the sources of skepticism range from simple denial to organized “anti-global warming” lobbies, the opposition to what is considered to be a consensus view on anthropogenic climate change has had a beneficial side-effect in terms of encouraging improved research and communication. Large efforts have been deployed to improve the knowledge base on the functioning of the climate system, observations of the Earth system, numerical modeling techniques, and data handling and analysis. Despite large scientific progress in the last two decades, many domains of uncertainty still remain as to the functioning of the climate system. The reduction of these uncertainties would be unlikely to radically change the fairly robust conclusion that contemporary climate change is to a significant degree driven by anthropogenic emissions of greenhouse gases. However, furthering our understanding of climate-relevant processes would improve not only the predictive capability of climate models at space and time scales useful to decision-making, but also help reduce criticisms when communicating on climate issues. The outstanding issues that need continued scientific focus are today collectively termed as “grand challenges,” since many of these issues have been addressed over many years by many research teams, but still have large uncertainties associated with them. The World Climate Research Program (WCRP), one of the flagship domains of the World Meteorological Organization (WMO) has identified a number of these challenges that are currently receiving enhanced scientific attention that will be outlined in the next section. Indeed, the CLIVAR (Climate predictability and variability) program of the WCRP has proposed the definition that “A Grand Challenge is both highly specific and highly focused identifying a specific barrier preventing progress in a critical area of climate science.” In addition to the fundamental science issues identified by the WCRP, two further issues are identified as grand challenges in this paper, namely those associated improved communication of science, and those linked to access to environmental and socio-economic data for research purposes. The current state of knowledge of the climate system and its functioning contains a range of uncertainties inherent to most complex non-linear systems. These need to be further addressed by the research community in order to enhance the confidence in the understanding and prediction of the system (Asrar and Hurrell, 2013). The outstanding areas identified by the WCRP as “grand challenges” requiring particular attention, are briefly outlined below. The potential impacts of sea-level rise on coastal cities through permanent flooding or greater vulnerability to storm surges, as well as on the increasing risks of salt intrusion into ground water and the collateral effects on the fertility of agricultural soils, for example, have been widely reported in the IPCC (2007) reports. While earlier assessments of sea-level rise as a function of a warming climate seemed to be fairly robust, there is today much greater uncertainty; current estimates of sea-level rise range from 20 cm by 2100 (Meehl et al., 2007) to 2 m or more (Vermeer and Rahmstorf, 2009). One of the principal reasons for this increased uncertainty in sea-level projections is related to the behavior of the Greenland ice sheet that has been showing signs of accelerated melting and calving at a scale that was unanticipated a decade ago. Ocean processes linked to the thermohaline circulation and the contribution of modes of climate variability such as the North Atlantic Oscillation require further understanding in order to enable more refined estimates of changes in sea-level at the regional scale and thereby to prepare for appropriate adaptation strategies. The major changes currently observed notably on the Arctic sea-ice and on the Greenland ice sheet are part of a two-way interaction between climate and the high-latitude cryosphere that can lead to amplification of warming and higher rates of sea-level rise than hitherto anticipated. Permafrost beneath large ice-sheets could increasingly melt as surface waters infiltrate to the base of the ice sheet. As the permafrost recedes, melt-waters could enter into porous bedrock regions that would reduce the amount of water flowing into the oceans, and thereby confound gravity-based estimates of the contribution of ice melting to sea-level rise. Thawing permafrost in...
, , Stephen Machado, Erin Brooks, Jodi L. Johnson-Maynard, Lauren E. Young, Frank L. Young, Ian Leslie, Ayana Glover, , et al.
Published: 29 May 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00023

Abstract:
Ecological instability and low resource use efficiencies are concerns for the long-term productivity of conventional cereal monoculture systems, particularly those threatened by projected climate change. Crop intensification, diversification, reduced tillage, and variable N management are among strategies proposed to mitigate and adapt to climate shifts in the inland Pacific Northwest (iPNW). Our objectives were to assess these strategies across iPNW agroecological zones and time for their impacts on 1) winter wheat (Triticum aestivum L.) productivity, 2) crop sequence productivity and 3) N fertilizer use efficiency. Region-wide analysis indicated that WW yields increased with increasing annual precipitation, prior to maximizing at 520 mm yr-1 and subsequently declining when annual precipitation was not adjusted for available soil water holding capacity. While fallow periods were effective at mitigating low nitrogen (N) fertilization efficiencies under low precipitation, efficiencies declined as annual precipitation exceeded 500 mm yr-1. Variability in the response of WW yields to annual precipitation and N fertilization among locations and within sites supports precision N management implementation across the region. In years receiving less than 350 mm precipitation yr-1, WW yields declined when preceded by crops rather than summer fallow. Nevertheless, WW yields were greater when preceded by pulses and oilseeds rather than wheat across a range of yield potentials, and when under conservation tillage practices at low yield potentials. Despite the yield penalty associated with eliminating fallow prior to WW, cropping system level productivity was not affected by intensification, diversification, or conservation tillage. However, increased fertilizer N inputs, lower fertilizer N use efficiencies, and more yield variance may offset and limit the economic feasibility of intensified and diversified cropping systems.
, Carol Franco, Caitlin Quarrington
Published: 17 May 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00021

Abstract:
One-third of food produced for human consumption is lost or wasted globally, which amounts to about 1.3 billion tons per year. An updated review of global food loss and waste (FLW) is presented, as well as the related environmental, social and economic impacts, based on existing data and peer-reviewed literature. The authors reflect on the different food waste patterns and challenges faced by diverse regions around the world. The scale of FLW throughout the food value chain is analyzed, from agricultural production down to household consumption and disposal. FLW represent a waste of resources used in each production stage, such as land, water and energy; FLW also contributes to unnecessary increase of greenhouse gas (GHG) emissions. The environmental and socio-economic impacts of FLW are analyzed based on reviewed life cycle assessments. Providing insights into key concepts around FLW, this article highlights the scale of the problem at a global and regional level. It also reflects on the main challenges for implementing strategies to reduce FLW and the implications for policy-making.
, Jizhou Duan, Ian R. Jenkinson
Published: 15 May 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00022

Abstract:
A Book Review on
Biofilms in Bioremediation: Current Research and Emerging Technologies
Gavin Lear (Caister: Academic Press), 2016, 252 pages, ISBN: 978-1-910190-29-6 and cover page given in Figure 1. This book treats the roles of biofilms in bioremediation. Biofilms, here taken to include flocs, comprise physical structures that support ecosystems of microorganisms. In turn, the microorganisms construct and engineer these biofilms, forming microbial communities (Flemming and Wingender, 2010). Biofilms are organized as stable communities of mono- or multi-specific cells of bacteria with or without eukaryotes, attached to each other and surfaces in different environments (Costerton, 1995). In the last few years, many novel, organic compounds have been developed, and are released into the environment. They include heavy metals, polyaromatic hydrocarbons, polychlorinated biphenyls, pesticides, chemical fertilizers, detergents, paints, disinfectants, lubricants, antibiotics, and nanoparticles. Many of them are toxic to humans and other organisms. Managing the effects of these pollutants is a challenge to sustainable development globally. Using biofilms as a tool in bioremediation of such potentially harmful affects can allow new technologies to remain environmentally sustainable if integrated methods of use are correctly developed and applied. Such technology, using microorganisms and their products to degrade and clean up a large variety of pollutants are advantageous, and they need to be integrated into protocols that minimize: disruption of land or wildlife in the treated region; noise and dust; release of harsh chemicals. Numerous studies have been made on how biofilms relate to disease and industries, but less focus has been given to the biofilms related to the environment. One striking example, however, relates to current cleaning of the major oil spill by Exxon Oil on the shorelines of Prince William Sound, Alaska, back in 1989 (Bragg et al., 1994; Atlas and Hazen, 2011). Consortia of genetically modified microbes have been deployed to detoxify pollutants. Such biofilm research in the natural environment of soil, sand, and sediments has revealed the potential of biofilms in treating pollutants. Figure 1. Book covering page. The book consists of 13 chapters providing up-to-date information on biofilms in bioremediation of different environmental pollutants. Chapters 2, 3, and 4 explain the basic biofilm concepts particularly as related to: (1) bioremediation; (2) biofilm survival strategies through changes in their extracellular matrix when challenged by pollutants; (3) cellular biochemistry; (4) cellular social interactions; (5) exchange of metabolites; (6) signaling molecules; (7) genetic control of chemotactic responses by bacteria to pollutants. Chapters 1, 8, and 10 describe approaches for successful bioremediation, highlighting polycyclic aromatic hydrocarbons (PAH), pesticides and hydrocarbon degradation. Chapter 9 describes the removal of Chromium (VI) from industrial wastewater using a bacterial biofilm. Chapters 6 and 7 describe microscopic and molecular methods for monitoring bioremediation. Chapter 5 treats biosensors applied to detect bioavailability of contaminants and pollutants. Chapter 11 describes the engineering of permeable reactive barriers (PRB) within contaminated aquifers to manage migration of mobile pollutants. Chapter 12 investigates the formation of Pseudoalteromonas bacterial biofilm in fish farms These biofilms produce extracellular proteases, which remove excess proteinaceous material from sediment and sludge, thus maintaining good water quality. How biofilm-associated cells of Pseudoalteromonas stutzeri promote naphthalene degradation is also explained. Chapter 13A deals with the potential role of microbial biofilm in enhancing phytoremediation linked to phenol degradation, and further explain the role of microbial biofilm in development of duckweed populations. Chapter 13B describes how microbial biofilms are applied to enhance phytoremediation of contaminants in soil and water through Phragmites australis rhizospheres. While the book describes well the basic principles of biofilm in the degradation of organic pollutants, there would have been room for more elaboration about removal of pollutants and manipulation of biofilms for bioremediation under different condition. In the place of Chapter 12, for example, it would have been good to see inclusion of molecular approaches and analysis of biofilms in soil water. Commonly these microbial biofilms work in natural environments, but some modifications can promote microbial degradation of pollutant more rapidly. Better understanding of microbial biochemistry, physiology, and genetics will help further develop microbial processes to focus bioremediation better on particular functional problems. New post-genomics technologies such as metabolomics represent a rapidly emerging field that is likely to enhance understanding of biological mechanisms. Metabolomics applied in bioremediation studies, will help elucidate mineralization process, while pathways using isotope distribution analysis, molecular connectivity analysis, and metabolic foot-printing analysis, may all improve targeted biodegradation processes using metabolic engineering. In short, the field of bioremediation has much to gain from this emerging area. In short, this book clearly explains the potential roles of biofilms in bioremediating soils, sediments, and aquifers containing both organic and inorganic pollutants. It also brings together descriptions of recent tools and information about microbial biofilms applied to degradation and phytoremediation of industrial waste. In addition, it describes the significance of permeable, reactive barriers for the treatment of mobile pollutants. The book will help the microbiologist, the biotechnologist, and the environmental engineer to develop and integrate more sustainable technologies for bioremediation of industrial wastes. It will be useful or even indispensable to teachers, students, and researchers in the life sciences, particularly of industrial biotechnology and environmental microbiology. SK is the primary author and initiator of this book review, while JD and IJ have both contributed to writing this review at SK's request. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. This work was supported by the Program of Visiting Research Scientist of the Chinese Academy of Sciences (Grant No. Y3KY02013L) and PIFI project of Chinese Academy of Science (Grant No. 2016VBC077). Authors are also thankful to Key Laboratory of Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of Science Qingdao, China for providing facility, space, and resources for this work. Atlas, R. M., and Hazen, T. C. (2011). Oil biodegradation and bioremediation: a tale of the two worst spills in U.S. history. Environ. Sci. Technol. 45, 6709–6715. doi: 10.1021/es2013227 PubMed Abstract | CrossRef Full Text | Google Scholar Bragg, J. R., Prince, R. C., and Harner, E. J. (1994). Effectiveness of bioremediation for the Exxon Valdez oil spill. Nature 368, 413–418. Google Scholar Costerton, J. W. (1995). Overview of microbial biofilms. J. Ind. Microbiol. 15, 137–140. PubMed Abstract | Google Scholar Flemming, H.-C., and Wingender, J. (2010). The biofilm matrix. Nature 8, 623–633. doi: 10.1038/nrmicro2415 PubMed Abstract | CrossRef Full Text | Google Scholar Keywords: biofilm, bioremediation, microbe, sustainable, technology Citation: Karn SK, Duan J and Jenkinson IR (2017) Book Review: Role of Biofilms in Bioremediation. Front. Environ. Sci. 5:22. doi: 10.3389/fenvs.2017.00022 Received: 26 February 2017; Accepted: 28 April 2017; Published: 15 May 2017. Edited and reviewed by: Qiang Wang, Institute of Hydrobiology (CAS), China Copyright © 2017 Karn, Duan and Jenkinson. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. *Correspondence: Santosh Kr. Karn, [email protected]
, Lizzi Andersen, Denis A. Angers, Martial Bernoux, Michel Brossard, , Rob N. J. Comans, Joop Harmsen, Knut Jonassen, Frank Lamé, et al.
Published: 12 July 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00041

Abstract:
Soil is a key compartment for climate regulation as a source of greenhouse gases (GHGs) emissions and as a sink of carbon. Thus, soil carbon sequestration strategies should be considered alongside reduction strategies for other greenhouse gas emissions. Taking this into account, several international and European policies on climate change are now acknowledging the importance of soils, which means that proper, comparable and reliable information is needed to report on carbon stocks and GHGs emissions from soil. It also implies a need for consensus on the adoption and verification of mitigation options that soil can provide. Where consensus is a key aspect, formal standards and guidelines come into play. This paper describes the existing ISO soil quality standards that can be used in this context, and calls for new ones to be developed through (international) collaboration. Available standards cover the relevant basic soil parameters including carbon and nitrogen content but do not yet consider the dynamics of those elements. Such methods have to be developed together with guidelines consistent with the scale to be investigated and the specific use of the collected data. We argue that this standardization strategy will improve the reliability of the reporting procedures and results of the different climate models that rely on soil quality data.
, Torsten Prinz, Silvia R. Ziller, , , João A. A. Meira-Neto, Tillmann K. Buttschardt
Published: 11 July 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00044

Abstract:
Remote sensing by Unmanned Aerial Systems (UAS) is a dynamic evolving technology. UAS are particularly useful in environmental monitoring and management because they have the capability to provide data at high temporal and spatial resolutions. Moreover, data acquisition costs are lower than those of conventional methods such as extensive ground sampling, manned airplanes, or satellites. Small fixed-wing UAS in particular offer further potential benefits as they extend the operational coverage of the area under study at lower operator risks and accelerate data deployment times. Taking these aspects into account, UAS might be an effective tool to support management of invasive plant based on early detection and regular monitoring. A straightforward UAS approach to map invasive plant species is presented in this study with the intention of providing ready-to-use field maps essential for action-oriented management. Our UAS utilizes low-cost sensors, free-of-charge software for mission planning and an affordable, commercial aerial platform to reduce operational costs, reducing expenses with personnel while increasing overall efficiency. We illustrate our approach using a real example of invasion by Acacia mangium in a Brazilian Savanna ecosystem. A. mangium was correctly identified with an overall accuracy of 82.7% from the analysis of imagery. This approach provides land management authorities and practitioners with new prospects for environmental restoration in areas where invasive plant species are present.
Navdeep Kaur,
Published: 5 July 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00042

Abstract:
Rice is an important cereal crop responsible for world’s food security. The sensitivity of rice plants towards a range of abiotic stresses is a prime challenge for its overall growth and productivity. Among these, salinity is a major stress which results in a significant loss of global rice yield annually. For finding straightforward and strict future solutions in order to assure the food security to growing world population, understanding of the various salt stress tolerance mechanisms in rice is of paramount importance. Plants combat the effects of salt stress through various mechanisms that operate at different levels. Diverse strategies have been adopted for understanding and unraveling the key components involved in these complex mechanisms. In classical studies, identification of salt tolerant cultivars and the genetic markers linked to salt tolerance and breeding approaches have been give emphasis for developing salt tolerance in rice. However, only limited success has been achieved in these approaches as salt tolerance is a complex process and is governed by multiple factors. Hence, for better understanding of salt tolerance mechanisms, a comprehensive approach involving physiological, biochemical and molecular studies is much warranted. Modern experimental and genetic resources have provided a momentum in this direction. Integrating the knowledge of classical and modern research in understanding of salt stress adaptive pathways will facilitate for designing effective strategies to combat salt stress. Hence, the present review focuses on the interdependency of classical and modern approaches and their integration for better understanding of salt stress tolerance mechanisms in rice.
, Bulbul Ahmed, Jamie R. Nuñez, Bin Cao, Paul D. Majors, ,
Published: 29 June 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00030

Abstract:
In this study, we developed a two-dimensional mathematical model to predict substrate utilization and metabolite production rates in Shewanella oneidensis MR-1 biofilm in the presence and absence of uranium (U). In our model, lactate and fumarate are used as the electron donor and the electron acceptor, respectively. The model includes the production of extracellular polymeric substances (EPS). The EPS bound to the cell surface and distributed in the biofilm were considered bound EPS (bEPS) and loosely associated EPS (laEPS), respectively. COMSOL® Multiphysics finite element analysis software was used to solve the model numerically (model file provided in the Supplementary Material). The input variables of the model were the lactate, fumarate, cell and EPS concentrations, half saturation constant for fumarate, and diffusion coefficients of the substrates and metabolites. To estimate unknown parameters and calibrate the model, we used a custom designed biofilm reactor placed inside a nuclear magnetic resonance (NMR) microimaging and spectroscopy system and measured substrate utilization and metabolite production rates. From these data we estimated the yield coefficients, maximum substrate utilization rate, half saturation constant for lactate, stoichiometric ratio of fumarate and acetate to lactate and stoichiometric ratio of succinate to fumarate. These parameters are critical to predicting the activity of biofilms and are not available in the literature. Lastly, the model was used to predict uranium immobilization in S. oneidensis MR-1 biofilms by considering reduction and adsorption processes in the cells and in the EPS. We found that the majority of immobilization was due to cells, and that EPS was less efficient at immobilizing U. Furthermore, most of the immobilization occurred within the top 10 μm of the biofilm. To the best of our knowledge, this research is one of the first biofilm immobilization mathematical models based on experimental observation. It has the ability to predict the relative contributions to U immobilization of laEPS, bEPS, and cells.
Published: 29 June 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00036

Abstract:
Food quality is highly dynamic within lake ecosystems and varies spatially and temporally over the growing season. Consumers may need to continuously adjust their metabolism in response to this variation in dietary nutrient content. However, the rate of metabolic responses to changes in food nutrient content has received little direct study. Here, we examine responses in two metabolic phosphorus (P) pools, ribonucleic acids (RNA), and adenosine triphosphate (ATP) along with body mass and body P content in Daphnia magna exposed to chronic and acute dietary P-limitation. First, we examined food quality effects on animals consuming different food carbon (C):P quality over a 14 day period. Then, we raised daphnids on one food quality for 4 days, switched them to contrasting dietary treatments, and measured changes in their metabolic responses at shorter time-scales (over 48 h). Animal P, RNA, and ATP content all changed through ontogeny with adults containing relatively less of these pools with increasing body mass. Irrespective of age, Daphnia consuming high C:P diets had lower body %P, %RNA, %ATP, and mass compared to animals eating low C:P diets. Diet switching experiments revealed diet dependent changes in body %P, %RNA, %ATP, and animal mass within 48 hours. We found that Daphnia switched from low to high C:P diets had some metabolic buffering capacity with decreases in body %P occurring after 24 h but mass remaining similar to initial diet conditions for 36 h after the diet switch. Switching Daphnia from low to high C:P diets caused a decrease in the RNA:P ratio after 48 h. Daphnia switched from high to low C:P diets increased their body P, RNA, and ATP content within 8-24 h. This switch from high to low C:P diets also led to increased RNA:P ratios in animal bodies. Overall, our study revealed that consumer P metabolism reflects both current and past diet due to more dynamic and rapid changes in P biochemistry than total body mass. This metabolic flexibility is likely linked to resource integration in D. magna, which reduces the negative effects of short-term or variable exposure to nutrient-deficient foods.
Sarah K. Hathaway, Nicholas A. Bartolerio, Luis F. Rodríguez, Angela D. Kent,
Published: 28 June 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00035

Abstract:
Nitrate can be removed from wastewater streams, including subsurface agricultural drainage systems, using woodchip bioreactors to promote microbial denitrification. However, the variations in water flow in these systems could make reliable performance from this microbially-mediated process a challenge. In the current work, the effects of fluctuating water levels on nitrate removal, denitrifying activity, and microbial community composition in laboratory-scale bioreactors were investigated. The performance was sensitive to changing water level. An average of 31% nitrate was removed at high water level and 59% at low water level, despite flow adjustments to maintain a constant theoretical hydraulic retention time. The potential activity, as assessed through denitrifying enzyme assays, averaged 0.0008 mg N2O-N/h/dry g woodchip and did not show statistically significant differences between reactors, sampling depths, or operational conditions. In the denitrifying enzyme assays, nitrate removal consistently exceeded nitrous oxide production. The denitrifying bacterial communities were not significantly different from each other, regardless of water level, meaning that the denitrifying bacterial community did not change in response to disturbance. The overall bacterial communities, however, became more distinct between the two reactors when one reactor was operated with periodic disturbances of changing water height, and showed a stronger effect at the most severely disturbed location. The communities were not distinguishable, though, when comparing the same location under high and low water levels, indicating that the communities in the disturbed reactor were adapted to fluctuating conditions rather than to high or low water level. Overall, these results describe a biological treatment process and microbial community that is resistant to disturbance via water level fluctuations.
Cecilia Polizzi, Felipe Alatriste-Mondragón,
Published: 28 June 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00037

Abstract:
Mathematical modelling of anaerobic digestion is widely acknowledged as a powerful tool to improve the understanding of the process and to support full-scale plant design, operation and optimization. In this work, a modified version of the IWA-ADM1 model is proposed to simulate the anaerobic digestion of tannery primary sludge and fleshing, with special emphasis on the disintegration formulation. Multiple batch tests were performed at different inoculum/substrate VS-mass ratio, in order to evaluate the biodegradability of the two substrates and to provide experimental data for modelling purposes. Beside the necessary adjustments of substrates’ COD fractionation, the structure modifications of the model focused on the disintegration and hydrolysis. The Contois Monod-based model was adopted to describe disintegration kinetics and the results were compared to the traditionally adopted first-order kinetic. The fate of particulate matter generated from biomass lysis was also questioned and a new model variable was introduced to account for cellular lysis products. Finally, a further modification differentiated substrate particulate matter into a readily and a slowly hydrolysable fraction. Batch tests confirmed that tannery primary sludge and fleshing are suitable substrates for anaerobic digestion, exhibiting specific methane productions of: 0.26±0.06 and 0.47±0.05 Nm3Kg-1VS, respectively. Modelling results showed that the proposed modifications were crucial for successful simulation of experimental data referring to fleshing, whereas did not have a significant effect on the results related to primary sludge degradation. This work is the first application of an IWA-ADM1-based model to anaerobic digestion of tannery waste.
, Zhenyang Peng, Chan Yu, Biting Li, Astrid R. Jacobson,
Published: 28 June 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00039

Abstract:
Groundwater contamination by oocysts of the waterborne pathogen Cryptosporidium parvum is a significant cause of animal and human disease worldwide. Although research has been undertaken in the past to determine how specific physical and chemical properties of soils affect the risk of groundwater contamination by C. parvum, there is as yetno clear conclusion concerning the range of mobility of C. parvum that one should expect in field soils. In this context, the key objective of this research was to determine the magnitude of C. parvum transport in a number of soils, under conditions in which fast and preferential transport has been successfully prevented. C. parvum oocysts were applied at the surface of different soils and subjected to artificial rainfall. Apparently for the first time, quantitative PCR was used to detect and enumerate oocysts in the soil columns and in the leachates. The transport of oocysts by infiltrating water, and the considerable retention of oocysts in soil was demonstrated for all soils, although differences in the degree of transport were observed with soils of different types. More oocysts were found in leachates from sandy loam soils than in leachates from loamy sand soils and the retention of oocysts in different soils did not significantly differ. The interaction of various processes of the hydrologic system and biogeochemical mechanisms contributed to the transport of oocysts through the soil matrix. Results suggest that the interplay of clay, organic matter, and Ca2+ facilitates and mediates the transfer of organic matter from mineral surfaces to oocysts surface, resulting in the enhanced breakthrough of oocysts through matrices of sandy loam soils compared to those of loamy sand soils. Although the number of occysts that penetrate the soil matrix account for only a small percentage of initial inputs, they still pose a significant threat to human health, especially in groundwater systems with a water table not too distant from the soil surface.
, Michael L. Reed, Rebecca A. Wilkes, Tracy Youngster, Matthew A. Kukurugya, Valerie Katz, Clayton R. S. Sasaki
Published: 20 June 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00034

Abstract:
Previous studies have reported adverse effects of glyphosate on crop-beneficial soil bacterial species, including several soil Pseudomonas species. Of particular interest is the elucidation of the metabolic consequences of glyphosate toxicity in these species. Here we investigated the growth and metabolic responses of soil Pseudomonas species grown on succinate, a common root exudate, and glyphosate at different concentrations. We conducted our experiments with one agricultural soil isolate, P. fluorescens RA12, and three model species, P. putida KT2440, P. putida S12, and P. protegens Pf-5. Our results demonstrated both species- and strain-dependent growth responses to glyphosate. Following exposure to a range of glyphosate concentrations (up to 5 mM), the growth rate of both P. protegens Pf-5 and P. fluorescens RA12 remained unchanged whereas the two P. putida strains exhibited from 0 to 100% growth inhibition. We employed a 13C-assisted metabolomics approach using liquid chromatography-mass spectrometry to monitor disruptions in metabolic homeostasis and fluxes. Profiling of the whole-cell metabolome captured deviations in metabolite levels involved in the tricarboxylic acid cycle, ribonucleotide biosynthesis, and protein biosynthesis. Altered metabolite levels specifically in the biosynthetic pathway of aromatic amino acids (AAs), the target of toxicity for glyphosate in plants, implied the same toxicity target in the soil bacterium. Kinetic flux experiments with 13C-labeled succinate revealed that biosynthetic fluxes of the aromatic AAs were not inhibited in P. fluorescens Pf-5 in the presence of low and high glyphosate doses but these fluxes were inhibited by up to 60% in P. putida KT2440, even at sub-lethal glyphosate exposure. Notably, the greatest inhibition was found for the aromatic AA tryptophan, an important precursor to secondary metabolites. When the growth medium was supplemented with aromatic AAs, P. putida S12 exposed to a lethal dose of glyphosate completely recovered in terms of both growth rate and selected metabolite levels. Collectively, our findings led us to conclude that the glyphosate-induced specific disruption of de novo biosynthesis of aromatic AAs accompanied by widespread metabolic disruptions was responsible for dose-dependent adverse effects of glyphosate on sensitive soil Pseudomonas species.
, Sarah F. Trainor,
Published: 22 June 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00033

Abstract:
The gap between science and practice is widely recognized as a major concern in the production and application of decision-relevant science. This research analyzed the roles and network connections of scientists, service providers, and decision makers engaged in climate science and adaptation practice in Alaska, where rapid climate change is already apparent. Our findings identify key actors as well as significant differences in the level of bonding ties between network members who perceive similarity in their social identities, bridging ties between network members across different social groups, and control of information across roles – all of which inform recommendations for adaptive capacity and the co-production of usable knowledge. We also find that some individuals engage in multiple roles in the network suggesting that conceptualizing science policy interactions with the traditional categories of science producers and consumers oversimplifies how experts engage with climate science, services, and decision making. Our research reinforces the notion that the development and application of knowledge is a networked phenomenon and highlights the importance of centralized individuals capable of playing multiple roles in their networks for effective translation of knowledge into action.
Correction
Published: 23 June 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00038

Abstract:
A corrigendum onValidation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessmentby Elbrecht, V., and Leese, F. (2017). Front. Environ. Sci. 5:11. doi: 10.3389/fenvs.2017.00011 In the original article, the reference for Bista et al. (2017) was incorrectly written as “Carvalho, G. R., Walsh, K., Seymour, M., Hajibabaei, M., Lallias, D., Christmas, M., et al. (2017). Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nat. Commun. 8, 1–11. doi: 10.1038/ncomms14087.” It should be “Bista, I., Carvalho, G. R., Walsh, K., Seymour, M., Hajibabaei, M., Lallias, D., et al. (2017). Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nat. Commun. 8, 1–11. doi: 10.1038/ncomms14087.” In the original article, there was a mistake in Table 2 as published. “Ephemeroptera” and taxa abundance (8) are missing in the table. The corrected Table appears below. The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. Table 2. Number of species recovered with the newly developed primers and data on 16S and Folmer primers from previous tests (Elbrecht and Leese, 2015; Elbrecht et al., 2016). The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Elbrecht, V., and Leese, F. (2015). Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass—sequence relationships with an innovative metabarcoding protocol. PLoS ONE 10:e0130324. doi: 10.1371/journal.pone.0130324 PubMed Abstract | CrossRef Full Text | Google Scholar Elbrecht, V., Taberlet, P., Dejean, T., Valentini, A., Usseglio-Polatera, P., Beisel, J.-N., et al. (2016). Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects. PeerJ 4, e1966–e1912. doi: 10.7717/peerj.1966 PubMed Abstract | CrossRef Full Text | Google Scholar Keywords: DNA barcoding, primer development, primer evaluation, primer bias, ecosystem assessment, in silico PCR, invertebrates Citation: Elbrecht V and Leese F (2017) Corrigendum: Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment. Front. Environ. Sci. 5:38. doi: 10.3389/fenvs.2017.00038 Received: 04 May 2017; Accepted: 13 June 2017; Published: 23 June 2017. Edited and reviewed by: Michael M. Douglas, University of Western Australia, Australia Copyright © 2017 Elbrecht and Leese. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. *Correspondence: Vasco Elbrecht, [email protected]
, , Natalie Mladenov, Karen Johannesson, , Prosun Bhattacharya, , Joseph Weeks, Madhubhashini Galkaduwa,
Published: 23 June 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00029

Abstract:
HIGHLIGHTS • Manganese and arsenic concentrations are elevated in Murshidabad groundwater. • Manganese release appears to be independent of dissolved organic matter quality. • Mineral precipitation and dissolution reactions impact fate of manganese. • Arsenic concentrations are related to dissolved organic matter quantity and quality. The prevalence of manganese (Mn) in Southeast Asian drinking water has recently become a topic of discussion, particularly when concurrent with elevated arsenic (As). Although Mn groundwater geochemistry has been studied, the link between dissolved organic matter (DOM) quality and Mn release is less understood. This work evaluates characteristics of DOM, redox chemistry, and the distribution of Mn within Murshidabad, West Bengal, India. Shallow aquifer samples were analyzed for cations, anions, dissolved organic carbon, and DOM properties using 3-dimensional fluorescence excitation emission matrices followed by parallel factor modeling analyses. Two biogeochemical regimes are apparent, separated geographically by the river Bhagirathi. East of the river, where Eh and nitrate (NO3) values are low, humic-like DOM coexists with high dissolved Mn, As, and Fe. West of the river, lower dissolved As and Fe concentrations are coupled with more protein-like DOM and higher NO3 and Eh values. Dissolved Mn concentrations are elevated in both regions. Based on the distribution of available electron acceptors, it is hypothesized that groundwater east of the Bhagirathi, which is more reducing and enriched in dissolved Fe and Mn but depleted in NO3, is chemically dominated by Mn(IV)/Fe(III) reduction processes. West of the river where NO3 is abundant yet dissolved Fe is absent, NO3 and Mn(IV) likely buffer redox conditions such that Eh values are not sufficiently reducing to release Fe into the dissolved phase. The co-occurrence of humic-like DOM with dissolved As, Fe, and Mn in the more reducing aquifers may reflect complex formation between humic DOM and metals, as well as electron shuttling processes involving humic DOM, which may enhance metal(loid) release. Saturation indices of rhodochrosite (MnCO3) suggest that precipitation is thermodynamically favorable in a greater proportion of the more reducing sites, however humic DOM–Mn complexes may be inhibiting MnCO3 precipitation. Where dissolved arsenic concentrations are low, it is postulated that Mn(IV) reduction is oxidizing As(III) to As(V), increasing the potential for re-adsorption of As(V) onto relatively stable, un-reduced or newly precipitated Fe-oxides. Manganese release appears to be independent of DOM quality, as it persists in both humic and protein-like DOM environments.
Rosaria Mulé, Giorgio Sabella, Lavinia Robba,
Published: 26 June 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00032

Abstract:
Safeguarding crop productivity by protecting crops from pest attacks entails the wide use of plant protection products that provide a quick, easy and cheap solution. The objective of this study is to understand the effects of insecticides used in agriculture on non-target butterflies, specifically on the families Lycaenidae, Nymphalidae, Hesperiidae and Papilionidae. To achieve this goal, a formal systematic review was performed according to European Food Safety Authority (EFSA) guidelines, by entering a combination of keywords on 3 online databases. Three reviewers independently extracted information on study characteristics and quality. The main results were collected and grouped by the insecticide used, butterflies species and family, and endpoints. The output was valuable but heterogeneous as the endpoints and methodologies of the studies reviewed were different. Few experimental studies on the effects of insecticides on the most common butterfly families have been published. Naled and permethrin are the most commonly used insecticides in the experiments, whilst the target organisms of these studies are Vanessa cardui, Danaus plexippus, Heliconius charitonius, belonging to the Nymphalidae family, and Eumaeus atala, belonging to the Lycaenidae family; the effects were evaluated on all developmental stages, with special attention to the larval phase. This systematic review highlights the need for more studies on the effects of chemical insecticides on non-target Lepidoptera in light of their ecological importance and the extensive use of these chemical products.
, Henry Neufeldt, Mary Njenga, Abayneh Derero, Geoffrey M. Ndegwa, Athanase Mukuralinda, Philip Dobie, Ramni Jamnadass, Jeremias Mowo
Published: 14 June 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00031

Abstract:
The production of charcoal is an important socio-economic activity in sub-Saharan Africa (SSA). Charcoal production is one of the leading drivers of rural land-use changes in SSA, although the intensity of impacts on the multi-functionality of landscapes varies considerably. Within a given landscape, charcoal production is closely interconnected to agriculture production both as major livelihoods, while both critically depend on the same ecosystem services. The interactions between charcoal and agricultural production systems can lead to positive synergies of impacts, but will more often than not result in trade-offs and even vicious cycles. Such sustainability outcomes vary from one site to another due to the heterogeneity of contexts, including agricultural production systems that affect the adoption of technologies and practices. Trade-offs or cases of vicious cycles occur when one-off resource exploitation of natural trees for charcoal production for short-term economic gains permanently impairs ecosystem functions. Given the fact that charcoal, as an important energy source for the growing urban populations and an essential livelihood for the rural populations, cannot be readily substituted in SSA, there must be policies to support charcoal production. Policies should encourage sustainable technologies and practices, either by establishing plantations or by encouraging regeneration, whichever is more suitable for the local environment. To guide context-specific interventions, this paper presents a new perspective - the charcoal-agriculture nexus - aimed at facilitating the understanding of the socio-economic and ecological interactions of charcoal and agriculture production. The nexus especially highlights two dimensions of the socio-ecological contexts: charcoal value chains and tenure systems. Combinations of the two are assumed to underlie varied socio-economic and ecological sustainability outcomes by conditioning incentive mechanisms to affect the adoption of technologies and practices in charcoal and agriculture productions. Contrasting sustainability outcomes from East Africa are presented and discussed through the lens of the charcoal-agriculture nexus. The paper then concludes by emphasizing the importance of taking into account the two-dimensional socio-ecological contexts into effective policy interventions to turn charcoal-agriculture interactions into synergies.
, , , Maarten C. Braakhekke, Detlef P. van Vuuren
Published: 14 June 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00028

Abstract:
Global demand for charcoal is increasing mainly due to urban population in developing countries. More than half the global population now lives in cities, and urban-dwellers are restricted to charcoal use because of easiness of production, access, transport, and tradition. Increasing demand for charcoal, however, may lead to increasing impacts on forests, food and water resources, and may even create additional pressures on the climate system. Here we assess how different charcoal scenarios based on the Shared Socio-economic Pathways (SSP) relate to potential biomass supply. For this, we use the energy model TIMER to project the demand for fuelwood and charcoal for different socio-economic pathways for urban and rural populations, globally and for four tropical regions (Central America, South America, Africa and Indonesia). Second, we assess whether the biomass demands for each scenario can be met with current and projected forest biomass estimated with remote sensing and modeled Net Primary Productivity (NPP) using a Dynamic Global Vegetation Model (LPJ-GUESS). Currently one third of residential energy use is based on traditional bioenergy, including charcoal. Globally, biomass needs by urban households by 2100 under the most sustainable scenario, SSP1, are of 14.4 mi ton biomass for charcoal plus 17.1 mi ton biomass for fuelwood (31.5 mi ton biomass in total). Under SSP3, the least sustainable scenario, we project a need of 205 mi tons biomass for charcoal plus 243.8 mi ton biomass for fuelwood by 2100 (total of 450 mi ton biomass). Africa and South America contribute the most for this biomass demand, however, all areas are able to meet the demand. We find that the future of the charcoal sector is not dire. Charcoal represents a small fraction of the energy requirements, but its biomass demands are disproportionate and in some regions require a large fraction of forest. This could be because of large growing populations moving to urban areas, conversion rates, production inefficiencies, and regions that despite available alternative energy sources still use a substantial amount of charcoal. We present a framework that combines Integrated Assessment Models and local conditions to assess whether a sustainable sector can be achieved.
, Charles Meshack
Published: 8 June 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00027

Abstract:
Charcoal is the main cooking fuel for urban populations in many African countries. Urbanisation and population growth are driving an increase in demand for charcoal, whilst deforestation reduces biomass stocks. Given increasing demand for charcoal, and decreasing availability of biomass, policies are urgently needed that ensure secure energy supplies for urban households and reduce deforestation. There is potential for charcoal to be produced sustainably in natural woodlands, but this requires supportive policies. Previous research has identified policy issues that have contributed to the charcoal sector remaining informal and environmentally destructive. In this paper, we describe how national policies in Tanzania on energy, forests, agriculture, land, and water, consider charcoal, and the degree to which they do, and do not, support sustainable charcoal production. The paper identifies policy gaps and a cross-sector tendency to marginalise natural forest management. By adopting a nexus approach, the paper highlights the inter-connections between sustainable charcoal production, ecosystem services, and trade-offs in the allocation of land, labour, and net primary production. In conclusion, sustainable charcoal production has been marginalised in multiple national policies. As a result, potential benefits of sustainable charcoal production are lost to multiple sectors.
, Lathadevi Chintapenta, Amy Cannon, Kenneth Hannum
Published: 7 June 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00026

Abstract:
The presence of heavy metals, excess nutrients, and microbial contaminants in aquatic systems of coastal Delaware has become a public concern as human population increases and land development continues. Delaware's coastal lagoons have been subjected to problems commonly shared by other coastal Mid-Atlantic states: turbidity, sedimentation, eutrophication, periodic hypoxic/anoxic conditions, toxic substances, and high bacterial levels. The cumulative impact of pollutants from run-off and point sources has degraded water quality, reduced the diversity and abundance of various fish species, invertebrates, and submerged aquatic vegetation. The effects are especially pronounced within the manmade dead end canal systems. In this article, we present selected case studies conducted in the Delaware Inland Bays. Due to the ecological services provided by bivalves, our studies in Delaware Inland Bays are geared towards oysters with special focus on the microbial loads followed by the water quality assessments of the bay. The relationships between oysters (Crassostrea virginica), microbial loads and nutrient levels in the water were investigated. The heavy metal levels monitored near the waste water treatment plant in the inland bays are marginally higher than the recommended EPA limits Also, our studies confirmed that aerobic bacteria and Vibrionaceae levels are salinity dependent. Total bacteria in oysters increased when nitrate and total suspended solids increased in the waters. Studies such as these are important because every year millions of Americans consume raw oysters. Data collected over the last ten years from our studies may be used to build a predictive index of conditions that are favorable for the proliferation of human pathogenic bacteria. Results from this study will benefit the local community by helping them understand the importance of oyster aquaculture and safe consumption of oysters while making them appreciate their ecological and commercial values. This will also be of tremendous help to the commercial shellfish aquaculture farms to predict poor conditions to prevent oysters’ consumption when bacterial levels are high in water.
Yusuke Shiratori, Takeo Yamakawa, Mio Sakamoto, Hinomi Yoshida, , Quang Tuyen Tran, ,
Published: 26 May 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00025

Abstract:
Fuel-flexible solid oxide fuel cell (SOFC) technologies are presently under study in a Vietnam-Japan international joint research project. The purpose of this project is to develop and demonstrate an SOFC-incorporated energy circulation system for the sustainable development of the Mekong Delta region. Lab-scale methane fermentation experiments in this study with a mixture of biomass feedstock collected in the Mekong Delta (shrimp pond sludge, bagasse, and molasses from sugar production) recorded biogas production yield over 400 L kgVS−1 with H2S concentration below 50 ppm level. This real biogas was directly supplied to an SOFC without any fuel processing such as desulfurization, methane enrichment and pre-reforming, and stable power generation was achieved by applying paper-structured catalyst (PSC) technology.
, Louise Karlberg
Published: 24 May 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00024

Abstract:
The ‘water-energy-food (WEF) nexus’ has become an increasingly popular way to frame the challenges associated with reconciling improvements in human wellbeing and aspirations for better lives with sustainable management of natural resources and ecosystems. Yet the nexus is complex, requiring effective engagement between expert and non-expert stakeholders in order to understand biophysical inter-linkages between resources and resource flows and social interactions between different actors in the socio-ecological system and landscape. This can be a substantial challenge due to varying levels of knowledge and understanding amongst actors with divergent, and often entrenched, interests. This paper presents insights on how participatory scenario-building processes can create space for dialogue amongst stakeholders with differing knowledge, experience, priorities and political perspectives. Drawing on completed and on-going research applying a ‘nexus toolkit’ in Ethiopia and Rwanda respectively, we contribute to a generalized conceptual framework for addressing, communicating, and assessing the water-energy-food nexus, with a particular focus on how to utilize the nexus concept in practice. We find that participatory scenario-building processes that facilitate engagement beyond technical aspects to include social, economic and political concerns provide a valuable space for discussing and negotiating development pathways that are sustainable both biophysically and socio-economically. In addition, the involvement of stakeholders throughout the project process greatly enhances the quality and legitimacy of results. Furthermore, we suggest that by building capacity amongst stakeholders to maintain a quantitative ‘nexus toolkit’, it has a better chance of informing decision-making and for supporting the development of more technically refined analyses of alternative decisions and management strategies.
, Rüdiger M. Schmelz,
Published: 15 May 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00020

Abstract:
Enchytraeidae (Oligochaeta, Annelida) are often considered to be typical forestliving organisms, but they are regularly found in agroecosystems of the temperate regions of the world. Although less known than their larger relatives, the earthworms, these saprophagous organisms play similar roles in agricultural soils (but at a smaller scale), e.g., influencing soil structure and organic matter dynamics via microbial communities, and having a central place in soil food webs. Their diversity is rarely studied or often underestimated due to difficulties in distinguishing the species. New genetic techniques reveal that even in anthropogenically highly influenced soils, more than ten species per site can be found. Because of their close contact with the soil pore water, a high ingestion rate and a thin cuticle, they often react very sensitively to a broad range of pesticides. Firstly we provide a short overview of the diversity and abundance of enchytraeid communities in agroecosystems. Afterwards, we explore the available data on enchytraeid sensitivity towards pesticides at different levels of biological organization, focusing on pesticides used in (mainly) European agroecosystems. Starting with non-standardized studies on the effects of pesticides on the sub-individual level, we compile the results of standard laboratory tests performed following OECD and ISO guidelines as well as those of higher-tier studies (i.e., semi-field and field tests). The number of comparable test data is still limited, because tests with enchytraeids are not a regulatory requirement in the European Union. While focusing on the effects of pesticides, attention is also given to their interactions with environmental stressors (e.g., climate change). In conclusion, we recommend to increase the use of enchytraeids in pesticide risk assessment because of their diversity and functional importance as well as their increasingly simplified use in (mostly standardized) tests at all levels of biological organization.
, Maria Engelke, , Elena Lesnikov, Jan Köser, Thilo Eickhorst,
Published: 10 May 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00019

Abstract:
Silver nanoparticles (AgNP) are integrated into various products due to their antimicrobial characteristics and hence, the application of AgNP is increasing. During production, use and disposal AgNP are emitted and enter the environment via several pathways. Soils are considered a major sink of AgNP. The aim of the present study was to determine the toxic effect of AgNP on Folsomia candida reproduction to illustrate potential impact on terrestrial ecosystems. The AgNP-dependent reduction of F. candida reproduction was studied in RefeSol 01-A, LUFA 2.2 and OECD soil at 0.3 µg – 50 mg Ag kg-1. To simulate realistic exposure pathways, effects on F. candida reproduction after the application of AgNP via sewage sludge and after aging this treatment in the soil for up to 140 days were studied using environmentally relevant concentrations. The OECD representative AgNP, NM-300K, and AgNO3, as a metal salt reference, were used in all experiments. The generated data demonstrate that the presence of AgNP in the soil in the low mg Ag kg-1 concentration range results in significant, but concentration independent inhibition of F. candida reproduction in RefeSol 01-A and LUFA 2.2. Significant inhibition of F. candida reproduction due to AgNP was also observed for soil amended with AgNP treated sludge. An increase in inhibition with aging of the AgNP in the soil was evident. In conclusion, our results demonstrate that, at environmentally relevant concentrations, AgNP adsorption to sludge and subsequent aging in soil lead to a toxic effect on soil invertebrates.
, , Rana El-Sabaawi, Halvor M. Halvorson, , , Richard J. Vogt,
Published: 8 May 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00018

Abstract:
The theories developed in ecological stoichiometry are fundamentally based on traits. On the one hand, traits directly linked to cell/body stoichiometry, such as nutrient uptake and storage traits, as well as the associated trade-offs, have the potential to shape ecological interactions such as competition and predation within ecosystems. On the other hand, traits that indirectly influence and are influenced by nutritional requirements, such as cell/body size and growth rate, are tightly linked to organismal stoichiometry. Despite their physiological and ecological relevance, traits are seldom explicitly integrated in the framework of ecological stoichiometry and, currently, the major challenge is to connect ecological stoichiometry traits with functional traits considered in trait-based ecology. Here, we therefore explore and synthesize existing insights, to develop novel connections between ecological stoichiometry and trait-based ecology. By reviewing key traits and their elemental requirements and illustrating community and ecosystem consequences of variation in elemental balances of traits, we show that unifying the framework of ecological stoichiometry with trait-based ecology sheds light on the interplay between elements and functional traits. Linking elements with functions furthers our understanding of the complex connections between subcellular processes, species interactions, and ultimately ecosystem dynamics.
Published: 28 April 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00017

Abstract:
A Book Review on
The Real Cost of Fracking: How America's Shale Gas Boom is Threatening Our Families, Pets, and Food
Michelle Bamberger and Robert Oswald (Boston, MA: Beacon Press Books), 2014, 248 pages, ISBN-10: 0807081418; ISBN-13: 978-0807081419. The Real Cost of Fracking by Michelle Bamberger and Robert Oswald examines the impacts and risks of hydraulic fracturing and shale gas extraction on our environment and health, food supply, and pets. Written by a veterinarian and a pharmacologist, the book combines scientific studies and data with anecdotal experiences to make a strong case that individuals and communities are at risk. The authors describe how they began to investigate the impacts of hydraulic fracking because many of their neighbors in upstate New York had leased their property to drilling companies. The issue was contentious in the community. In the course of their research, they heard from many individuals about the effects of gas drilling on the health and well-being of their animals and families, and felt that these voices should be heard. Highly readable and well-organized, the book is divided into three sections: families and their pets; fracking, farming, and our food supply; and environmental justice. In interviews included in each section, families living in areas with shale gas activities describe the wide-ranging impacts on their lives. A thoughtful epilog asks the question: “Where do we go from here?” and provides some steps that we can take to protect our health. The introduction discusses the precautionary principle, which requires exercise of caution in the absence of data to conclusive show the safety of an activity, such as fracking. The authors say that the industry follows the reverse: fracking can proceed, unless there is definitive proof that it causes harm, thus “…putting the burden of proof on the victim” (p. 9). Much of the book's emphasis is on impacts to animals and children, “inadvertent sentinels” for risks from environmental pollutants due to “their higher metabolic rates and immature neurologic and detoxifying systems” (p. 10). The first chapter explains that animals are even more vulnerable than children as they remain at home or outside, thus “increasing exposure times” (p. 19), and most families cannot afford alternative water or food supplies for their animals to replace a contaminated source. The second section deals with the impacts of fracking on farming and our food supply, and questions the “safety of food raised near such operations” (p. 97). Gas wells and the extraction activities are often intermixed with food production processes. The authors discuss the toxic chemicals and radioactive compounds from drilling waste, volatile organic compounds, and other hazards, and because animals are usually slaughtered before chemical testing, conclude that that “we really don't know” (p. 101) whether our food and water are safe. The third section deals with issues of environmental justice and shows the difficulty in gaining recourse after environmental damage or harm to health has occurred. The stories recount how “drilling has pitted neighbor against neighbor” (p. 153). But while that may be true in some locations, the authors describe a small community where “we experienced a different dynamic, one that provides hope and inspiration” (p. 153) as neighbors pulled together to supply one another with water as they faced problems of contaminated water, and inadequate help from government or industry. The overarching message of the book is that the stunning lack of information on multiple levels makes decision-making virtually impossible. For example, settlements of lawsuits involving health impacts typically include non-disclosure agreement requirements. Thus, a veterinarian may suspect an animal has encountered a contaminant, but the practitioner has no right to information on the suspected chemical. Not only is there no transparency, there is no recourse. While there is a lack of data on multiple levels, the anecdotal data and interviews shows that there is indeed danger—people and animals are getting sick—and we need to act. The epilog addresses what next steps are necessary, including collection of longer term data and lifecycle assessments of the fracking process, and the need for better regulation: “the solution is better regulations and better enforcement of unconventional fossil fuel extraction in the states that allow this process” (p. 180). It is significant to note that the key messages embedded in this work are in line with the Food and Agriculture Organization of the United Nations' Sustainable Development Goals, a list of 17 universally-relevant goals “integrating the three dimensions of sustainability—social, economic and environmental1.” In particular, the seventh goal of “affordable and clean energy” explains that “food systems, which currently consume 30 percent of the world's energy, will gradually need to decouple from fossil fuel dependence to deliver more food with less and cleaner energy2.” Additionally, goal six discusses increasing food production while using less water. This is import to highlight as we consider the demonstrably large water quantities required for unconventional gas extraction. In a similar vein to the Sustainable Development Goals, Bamberger and Oswald's work sheds light on the complexity of the food-energy-water nexus, and shows how the specific impacts of hydraulic fracturing affect our food and water sources, the health of our families, and our agricultural systems and animal health. Bamberger and Oswald provide a novel and groundbreaking examination of the effects of fracking on those who cannot speak for themselves, our farm and household animals, who act as the “canaries in the coal mine.” The authors reach the disturbing conclusion that despite common assertions to the contrary, there is indeed evidence of direct links between unconventional drilling and health problems. The dangers are made that much more immediate through the telling of real stories of loss and harm. This extremely important work should be read by anyone who is interested in the effects of unconventional gas extraction on our families and animals, food supply, and environment. The author confirms being the sole contributor of this work and approved it for publication. The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. 1. ^United Nations http://www.fao.org/sustainable-development-goals/goals/en/ 2. ^ www.fao.org/3/a-i4997e.pdf Keywords: hydraulic fracturing, shale gas, precautionary principle, environmental exposure, toxicology of pollutants Citation: Aczel MR (2017) Book Review: The Real Cost of Fracking: How America's Shale Gas Boom Is Threatening Our Families, Pets, and Food. Front. Environ. Sci. 5:17. doi: 10.3389/fenvs.2017.00017 Received: 13 February 2017; Accepted: 12 April 2017; Published: 28 April 2017. Edited by: Reviewed by: Copyright © 2017 Aczel. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. *Correspondence: Miriam R. Aczel, [email protected]
, M. N. Bari, , M. M. M. Kabir, S. Afrin, M. A. U. Zaman, S. S. Haque, J. L. Willers
Published: 1 May 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00016

Abstract:
Currently rice protection from insect pests solely depends on chemical pesticides which have tremendous impact on biodiversity, environment, animal and human health. To reduce their impact from our society we need to cut pesticide use from agricultural practices. To address this issue, we did experiment in order to identify realistic solutions that could help farmers to build sustainable crop protection system and minimum use of insecticides and thus minimizes the impact of pesticides in environment. Innovations developed jointly by farmers and researchers and evaluated for their potential to be adopted by more farmers. In this paper we tested four management practices jointly with farmers in smallholder farmer’s field in order to select best one. Four management practices were used namely, T1 = Prophylactic use of insecticide where insecticide was applied in rice field at every 15 days interval without judging the infestation level; T2 = Perching and simultaneously used sweeping and need base insecticide application; T3 = Perching only; and T4 = Farmer’s own practices. The results revealed that routine application of insecticides for crop protection is not mandatory which is commonly found at use in rice farmers. In our experiment, where prophylactic method or farmers used 3-4 times insecticides without judging the insect pests infestation level, the similar pest population was found when compared to the field where insecticide was not applied. Our management system reduced 75% insecticides use even the field was infested with insect pest. Predatory insects were higher than that of insecticide applied field. Refrain insecticide application up to 30-40 days after transplanting enhanced higher predatory population which might check the pest population in rice field. Our experimental results shows that proper manner of ecologically management system cut pesticide use without any yield penalty indicating T2 management system minimizes pest damage by increasing natural enemies and improves environment quality.
, Joshua H. Viers,
Published: 21 April 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00015

Abstract:
Vineyards shape important economic, cultural, and ecological systems in many temperate biomes. Like other agricultural systems, they can be multifunctional landscapes that not only produce grapes, but also for example serve as wildlife habitat, sequester carbon, and are places of rich traditions. However, research and management practices often focus mostly on individual, specific ecosystem services, without considering multifunctionality. Therefore, we set out to meet four research objectives: (1) evaluate how frequently the ecosystem services approach has been applied in vineyard systems; (2) identify which individual ecosystem services have been most frequently studied in vineyard systems, (3) summarize knowledge on the key ecosystem services identified in (2), and (4) illustrate approaches to multifunctionality in vineyards to inform more holistic land management. For research objective (1), we identified 45 publications that used the term “ecosystem services” in relation to vineyards, but found that only seven fully apply the ecosystem service concept to their research. For research objective (2), we operationalized the Common International Classification of Ecosystem Services (CICES) for 27 ecosystem services in vineyards, in order to consider provisioning, regulating, and cultural services through an analysis of more than 4,000 scientific papers that mentioned individual services. We found the six most frequently studied ecosystem services included (1) cultivated crop, (2) filtration, sequestration, storage and accumulation by the vineyards, (3) pest control and (4) disease control, (5) heritage, cultural and (6) scientific services. For research objective (3), we found that research on these six single ecosystem services is highly developed, but relationships between single ecosystem services are less studied. Therefore, we suggest that greater adoption of the ecosystem services approach could help scientists and practitioners to acknowledge the multifunctionality of the agricultural system and gain a holistic perspective that supports more sustainable land management.
, Alison H. Kingston-Smith, Mauro Centritto
Published: 20 April 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00013

Abstract:
Editorial on the Research TopicAbiotic Stresses in Agroecology: A Challenge for Whole Plant Physiology Abiotic stresses in agroecology are caused by climatic factors (e.g., temperature and precipitation extremes), pollutants (e.g., heavy metals, gaseous pollutants) and salinity. In the context of global change, climatic factors become particularly important. The alarming, progressive alterations in climate caused by rising levels of carbon dioxide (CO2) and other greenhouse gases in the atmosphere are linked to well-known consequences of climate change; increase in average global temperature and the melting of the polar ice caps (IPCC, 2014). In addition to these global problems, increased frequencies and severities of extreme events including heat waves, drought periods or waterlogging have significant impacts at local and regional levels (Schär et al., 2004; IPCC, 2012; Kelley et al., 2015; Knutti et al., 2016). Such events may strongly influence crop yields and the quality of agricultural products. The effects of stresses imposed by these factors individually and in combination are relevant in the context of agroecology and in developing new agricultural concepts taking into account soil quality, biodiversity, sustainability as well as social and economic aspects (Tomich et al., 2011; Lai, 2015). This Research Topic focuses on the impacts of abiotic stress at the whole plant level, the mechanisms involved in the stress responses and the potential to increase stress tolerance in field crops and trees. Elevated CO2 in the atmosphere caused by human activities is the major driver for global climate change that affects ambient temperature and precipitation patterns on global and regional scales, and water availability in soils as well as the frequency and severity of extreme events (IPCC, 2012, 2014). Atmospheric CO2 may also directly influence primary metabolism and thereby plant growth and productivity as reported by Long et al. (2006), Centritto et al. (2011), Hasegawa et al. (2013), Haworth et al., Haworth et al., Martinez-Lüscher et al. Free-air CO2 enrichment (FACE) facilities have been used to establish the impact of elevated CO2 on the efficiency of radiation, water and nitrogen utilization, overall crop yields (Dugas and Pinter, 1994; Long et al., 2006), and the interactions between sink structures (Hasegawa et al., 2013). In this Research Topic, Martinez-Lüscher et al. investigated interactions between elevated CO2 levels, ambient temperature and water availability in grapevine (Vitis vinifera L.) phenology from bud break to fruit maturation, while Haworth et al. addressed interactions between elevated CO2, stomatal control and photosynthetic performance. Haworth et al. argue that because of the tendency in free-air CO2 (FACE) experiments to publish more of significant results and less of nonsignificant results, the meta-analyses of results of such studies might lead to overestimation of the physiological impacts of rising CO2 levels in the atmosphere. Therefore while the direction and significance of impacts reported in individual studies are not questioned by these considerations (Haworth et al.), caution is recommended when extrapolating such findings to world-wide productivity, especially as the interactions between atmospheric CO2 levels and other environmental factors (e.g., temperature, water availability) and the physiological mechanisms behind these interactions remain to be further elucidated. Water availability in the soil and water relations of plants are key parameters predicted to be influenced by global climate change through altered regional precipitation patterns. This subject was addressed in several papers (Jian et al.; Kunert et al.; Martinez-Lüscher et al.; Polania et al.; Zarrouk et al.). Drought effects on root architecture and nodule properties in legumes with symbiotic nitrogen fixation as well as the possibilities for genetic improvements were reviewed by Kunert et al. Extended drought periods not only affect the development and physiological functions of roots and vegetative shoots, but also influence redistribution of nutrients to pods and seeds of maturing beans (Polania et al.) or to ripening grape berries (Zarrouk et al.). From these reports it is evident that source/sink relationships are highly relevant in plants exposed to drought and perturbation affects the quantity and quality of yield. Salt stress is an important consideration in many regions (especially coastal zones) and while not directly related to global climatic change, there are some similarities to drought stress and interactions with other abiotic stress factors (Wang et al., 2003; Munns and Tester, 2008), for example microRNAs were found to be important for the germination of rapeseed (Brassica napus L.) seeds under drought or salt stress (Jian et al.). Transport processes across membranes are important for subcellular compartmentation (e.g., sequestration into the vacuole) as well as for long-distance transport processes (e.g., release into the root xylem followed by acropetal transport in the transpiration stream). A salt-specific mechanism was investigated in soybean (Glycine max (L.) Merr.) by Wei et al. These authors found that a Cl/H+ antiporter (GmCLC1) contributed to salt tolerance and was involved in the retention of Cl ions in the roots and in decreasing the release to the shoot. Besides the steady increase in average temperature caused by the elevated CO2 concentration in the air, more frequent and more severe extreme events including heat waves and also cold phases have been predicted by climate models (Schär et al., 2004; IPCC, 2012). Elevated temperature may influence photosynthetic performance (e.g., via decreased Rubisco activase activity as reported by Scafaro et al., 2016), stomatal regulation (Reynolds-Henne et al., 2010; Feller and Vaseva, 2014), floret fertility (Prasad et al.) or ripening berries (Zarrouk et al.). These effects, which are all related to the source/sink network, have been clearly documented, but the overall effects of heat on various plant species and the mechanisms behind these effects are not yet well understood. A perspective paper on limitations to grassland productivity by low temperature was contributed by Wingler and Hennessy to this Research Topic and addresses issues of seasonality, breeding and epigenetic changes. The risk for freezing damage in woody perennial plants was evaluated in the context of global climate change in an opinion paper contributed by Arora and Taulavuori. These authors refer to cold acclimation prior to the cold season, dormancy and deacclimation (including the risk of premature deacclimation) and discuss physiological processes involved as well as their regulation. Cytokinin may play an important role in the perception of environmental stresses (Argueso et al., 2009). Two papers in this Research topic are focused on the role of cytokinin in the response of plants to abiotic stresses (Golan et al.; Paul et al.). Transgenic Arabidopsis plants characterized by an overproduction of cytokinin were found to be less drought-susceptible and to be more productive under drought than control plants (Golan et al.). The avoidance of premature senescence in these drought-stressed plants and the mechanisms involved in the beneficial cytokinin effects were investigated. Paul et al. presented good evidence that cytokinin is important for the maintenance of meristematic functions in plants subjected to abiotic stress and that this protective effect in poplar (Populus × canescens (Aiton) Sm.) is important during the summer as well as during winter. The response of plants to various abiotic stresses or to combinations of stresses is of practical relevance, since environmental disturbances are often characterized by coincidence of several factors (e.g., drought and elevated temperature) (Wang et al., 2003). Responses of plants to various stresses and combinations of stresses were addressed in several papers of this Research Topic (Gangadhar et al.; Martinez-Lüscher et al.; Zarrouk et al.). Gangadhar et al. characterized the functions of the thermo-tolerance gene StnsLTP1 in enhancing the activation of the antioxidant defense system, thus contributing to tolerance to multiple abiotic stresses in potato. Kopecky et al. explored the evolution of polyploidy within the fescue [Festuca pratensis subsp. apennina (De Not.) Hegi] species and how this knowledge can contribute to improved stress tolerance in Festulolium cultivars to produce climate change resilient grasses. As mentioned by these authors as well as by others, the elucidation of breeding strategies is a key aspect to support farmers in a changing climate with more frequent and more severe extreme events (Humphreys et al., 2014). All aspects presented in this Research Topic are relevant in the context of the impact of abiotic stress, but not all relevant aspects could be included in this Research Topic. The following aspects remain to be addressed or further emphasized in the future: (a) Additional abiotic stresses not included here (e.g., pollution, unbalanced nutrient supply). (b) Timing of stress phases (starting time, duration, single phase or multiple phases). (c) Interplay between various abiotic stresses including the mechanisms behind the interactions. (d) Further integration of processes at the whole-plant level including recovery phases. (e) Separation of species-specific and more general effects. (f) Identification of key proteins/genes for breeding (potential for improvements). (g) Biophysical limits of crops to climatic extremes. UF, AHK-S, and MC co-wrote this editorial based on the various contributions to this Research Topic. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. We thank all authors of contributions to this Research Topic for preparing high-quality manuscripts under a tight time schedule and the reviewers for critically evaluating the papers and for further improving them with their questions, comments, and suggestions. 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P., Mohtadi, S., Cane, M. A., Seager, R., and Kushnir, Y. (2015). Climate change in the fertile crescent and implications of the recent syrian drought. Proc. Natl. Acad. Sci. U.S.A. 112, 3241–3246. doi: 10.1073/pnas.1421533112 PubMed Abstract | CrossRef Full Text | Google Scholar Knutti, R., Rogelj, J., Sedláček, J., and Fischer, E. M. (2016). A scientific critique of the two-degree climate change target. Nat. Geosci. 9, 13–19. doi: 10.1038/NGEO2595 CrossRef Full Text | Google Scholar Lai, R. (2015). Restoring soil quality to mitigate soil degradation. Sustainability 7, 5875–5895. doi: 10.3390/su7055875 CrossRef Full Text | Google Scholar Long, S. P., Ainsworth, E. A., Leakey, A. D., Nösberger, J., and Ort, D. R. (2006). Food for thought: lower-than-expected crop yield stimulation with rising CO2 concentrations. Science 312, 1918–1921. doi: 10.1126/science.1114722 PubMed Abstract | CrossRef Full Text | Google Scholar Munns, R., and Tester, M. (2008). Mechanisms of salinity tolerance. 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Nature 427, 332–336. doi: 10.1038/nature02300 PubMed Abstract | CrossRef Full Text | Google Scholar Tomich, T. P., Brodt, S., Ferris, H., Galt, R., Horwath, W. R., Kebreab, E., et al. (2011). Agroecology: a review from a global-change perspective. Annu. Rev. Environ. Resour. 36, 193–222. doi: 10.1146/annurev-environ-012110-121302 CrossRef Full Text | Google Scholar Wang, W. X., Vinocur, B., and Altman, A. (2003). Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 218, 1–14. doi: 10.1007/s00425-003-1105-5 PubMed Abstract | CrossRef Full Text | Google Scholar Keywords: climate change, salt, temperature, water availability, whole plant physiology Citation: Feller U, Kingston-Smith AH and Centritto M (2017) Editorial: Abiotic Stresses in Agroecology: A Challenge for Whole Plant Physiology. Front. Environ. Sci. 5:13. doi: 10.3389/fenvs.2017.00013 Received: 31 January 2017; Accepted: 27 March 2017; Published: 20 April 2017. Edited and reviewed by: P. K. Ramachandran Nair, University of Florida, USA Copyright © 2017 Feller, Kingston-Smith and Centritto. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. *Correspondence: Urs Feller, [email protected]
, Amanda T. Rugenski, John L. Sabo, , James J. Elser
Published: 18 April 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00014

Abstract:
The growth rate hypothesis predicts that organisms with higher maximum growth rates will also have higher body percent phosphorus (P) due to the increased demand for ribosomal RNA production needed to sustain rapid growth. However, this hypothesis was formulated for invertebrates growing at the same temperature. Within a biologically relevant temperature range, increased temperatures can lead to more rapid growth, suggesting that organisms in warmer environments might also contain more P per gram of dry mass. However, since higher growth rates at higher temperature can be supported by more rapid protein synthesis per ribosome rather than increased ribosome investment, increasing temperature might not lead to a positive relationship between growth and percent P. We tested the growth rate hypothesis by examining two genera of Neotropical stream grazers, the leptophlebiid mayfly Thraulodes and the bufonid toad tadpole Rhinella. We measured the body percent P of field-collected Thraulodes as well as the stoichiometry of periphyton resources in six Panamanian streams over an elevational gradient spanning approximately 1100 m and 7 °C in mean annual temperature. We also measured Thraulodes growth rates using in situ growth chambers in two of these streams. Finally, we conducted temperature manipulation experiments with both Thraulodes and Rhinella at the highest and lowest elevation sites and measured differences in percent P and growth rates. Thraulodes body percent P increased with temperature across the six streams, and average specific growth rate was higher in the warmer lowland stream. In the temperature manipulation experiments, both taxa exhibited higher growth rate and body percent P in the lowland experiments regardless of experimental temperature, but growth rate and body percent P of individuals were not correlated. Although we found that Thraulodes from warmer streams grew more rapidly and had higher body percent P, our experimental results suggest that the growth rate hypothesis does not apply across temperatures. Instead, our results indicate that factors other than temperature drive variation in organismal percent P among sites.
Published: 10 April 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00011

Abstract:
A central challenge in the present era of biodiversity loss is to assess and manage human impacts on freshwater ecosystems. Macroinvertebrates are an important group for bioassessment as many taxa show specific responses to environmental conditions. However, generating accurate macroinvertebrate inventories based on larval morphology is difficult and error-prone. Here, DNA metabarcoding provides new opportunities. Its potential to accurately identify invertebrates in bulk samples to the species level, has been demonstrated in several case studies. However, DNA based identification is often limited by primer bias, potentially leading to taxa in the sample remaining undetected. Thus, the success of DNA metabarcoding as an emerging technique for bioassessment critically relies on carefully evaluating primers. We used the R package PrimerMiner to obtain and process cytochrome c oxidase I (COI) sequence data for the 15 most globally relevant freshwater invertebrate groups for stream assessment. Using these sequence alignments, we developed four primer combinations optimized for freshwater macrozoobenthos. All primers were evaluated by sequencing ten mock community samples, each consisting of 52 freshwater invertebrate taxa. Additionally, popular metabarcoding primers from the literature and the developed primers were tested in silico against the 15 relevant invertebrate groups. The developed primers varied in amplification efficiency and the number of detected taxa, yet all detected more taxa than standard ‘Folmer’ barcoding primers. Two new primer combinations showed more consistent amplification than a previously tested ribosomal marker (16S) and detected all 42 insect taxa present in the mock community samples. In silico evaluation revealed critical design flaws in some commonly used primers from the literature. We demonstrate a reliable strategy to develop optimized primers using the tool PrimerMiner. The developed primers detected almost all taxa present in the mock samples, and we argue that high base degeneracy is necessary to decrease primer bias as confirmed by experimental results and in silico primer evaluation. We further demonstrate that some primers currently used in metabarcoding studies may not be suitable for amplification of freshwater macroinvertebrates. Therefore, careful primer evaluation and more region / ecosystem specific primers are needed before DNA metabarcoding can be used for routine bioassessment of freshwater ecosystems.
Published: 10 April 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00012

Abstract:
The number of published researching works related with applications of nanomaterials in agriculture is increasing every year. Most of such works focus on the synthesis of nanodevices, their characteristics as nanocarriers for controlled release of active substances, and their interaction (either positive or negative) with plants or microorganisms under controlled conditions. Important knowledge has been gained about the uptake and distribution of nanomaterials in plants, although there are still gaps regarding internalization inside plant cells. Nanoparticle traits and plant species greatly affect the interaction, and nanodevices can enter and move through different pathways (apoplast vs. symplast), what influences their effectiveness and their final fate. Depending on the effect we are expecting for a nanocarrier, the application method might be critical. However, in order to get that research used in the field, some problems must be addressed. First, the cost for escalating the production of nanodevices must be affordable with the current production cost of agricultural goods. Second, we need to be sure that a technology is safe before spreading it into the environment. Third, consumers will distrust a technology unfamiliar for them in the same way that happened with transgenic crops. We need to broaden our horizons and start looking for real practical approaches, filling the main gaps that hamper our jump from laboratory research into field applications.
J. Bas Nelemans, René P. A. van Wijngaarden, Ivo Roessink,
Published: 28 March 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00010

Abstract:
A field trial was set up to simulate a field margin environment to analyze sub-lethal effects of the herbicide metsulfuron-methyl on several endpoints of non-target terrestrial plants (NTTPs). Both vegetative and reproductive endpoints were evaluated. The experiment was conducted in an experimentally established field strip with sown species. The treatments consisted of 5 dosages and a control: 0, 0.0097, 0.0193, 0.058, 0.174 and 0.348 gram active ingredient per hectare (g a.i./ha). The plant cover, number of (flowering) individuals per species and fruit collection were performed and estimated weekly for a period of 4 months. At the end of the growing season, the total dry biomass per species was obtained and the collected fruits were weighted, counted and sieved to obtain the seeds. The seeds were counted and weighted as well, before they were used in a germination experiment to test the seed emergence of the F1 generation. The herbicide only affected the biomass of Matricaria recutita at the treatment levels tested (0.058 g a.i./ha and higher). Field dosages of 0.174 and 0.348 g a.i./ha differed significantly in the endpoint “plant cover” compared to lower dosages and controls. The F1 generations of Sinapis alba, Centaurea cyanus and Phacelia tanacetifolia were particularly affected at field dosages of 0.0193 g a.i./ha and higher, showing significantly lower seed germination rates. This would imply that spray drift of metsulfuron-methyl might lead to shifts in species compositions and succession in vegetation in off-crop areas adjacent to arable fields. Conducting germination experiments is necessary to investigate a herbicide's effect on the full life cycle of plants.
Published: 15 March 2017
Frontiers in Environmental Science, Volume 5; https://doi.org/10.3389/fenvs.2017.00008

Abstract:
Low precipitation enhances transmission of influenza viruses, which cause seasonal epidemics during the winter in northern and southern hemispheres. El Niño southern oscillation (ENSO) which modulates global precipitation is a multicomponent signal that is composed of sub-annual to multi-decadal oscillations. The dynamics of oscillatory components of ENSO and influenza are characterized, and causal relationship of annual oscillatory components is determined. Seasonality of influenza was determined in five geographical areas of north and south hemispheres. Monthly influenza time series of these regions and of ENSO were decomposed to oscillatory components. The oscillatory components were characterized in time-frequency and phase space domains. Periodicities of the oscillatory components of ENSO and influenza range from sub-annual to multidecadal. Time-dependent intrinsic correlations of instantaneous amplitude and frequencies of annual oscillatory components of ENSO and influenza are > 0.9. The dynamics of ENSO and influenza, which are dissipative with multifractal chaotic attractors, transit from quasi-periodic to chaotic regimes. Five most severe peaks of epidemic, which include 2009–2010 pandemic, occurred during chaos. ENSO and influenza dynamics are phase coherent, but there is unidirectional causal effect of ENSO on influenza. Amplitude and frequency modulations of annual oscillatory components of ENSO and influenza are strongly coupled. Chaotic dynamics of ENSO determines the timing and severity of influenza epidemics. Monitoring of ENSO dynamics will aid public health surveillance of influenza epidemics.
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