Applied and Environmental Microbiology

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ISSN / EISSN : 0099-2240 / 1098-5336
Published by: American Society for Microbiology (10.1128)
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Yue Chen, Lei Qiao, Xiaofan Song, Li Ma, Xina Dou, Chunlan Xu
Applied and Environmental Microbiology; https://doi.org/10.1128/aem.01636-21

Abstract:
Composite microecological agents have received widespread attention due to their advantageous properties, including safety, multi-effects, and low cost. This study was conducted to evaluate the protective effects of selenium (Se) nanoparticle-enriched Lactococcus lactis NZ9000 ( L. lactis NZ9000-SeNPs) against enterotoxigenic Escherichia coli K88 (ETEC K88)-induced intestinal barrier damage in C57BL/6 mice. Oral administration of L. lactis NZ9000-SeNPs significantly increased the villi height and the number of goblet cells in the ileum, and reduced the levels of serum and ileal interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), and interferon-γ (IFN-γ), and increased the activities of thioredoxin reductase (TrxR) and glutathione peroxidase (GSH-Px) compared with the ETEC K88-infected group not treated with L. lactis NZ9000-SeNPs. In addition, L. lactis NZ9000-SeNPs significantly attenuated the reduction of the expression levels of occludin and claudin-1, dysbiosis of the gut microbiome, and the activation of toll-like receptor (TLR)/nuclear factor-kappa (NF-κB)-mediated signaling pathway induced by ETEC K88. These findings suggested that L. lactis NZ9000-SeNPs may be a promising and safe Se supplement for food or feed additives. Importance The beneficial effects of microecological agents have been widely proven. Se, which is nutritionally essential trace element for human and animals, is incorporated into selenoproteins that have a wide range of pleiotropic effects, ranging from antioxidant and anti-inflammatory effects. However, the sodium selenite, a common addition form of Se in feed and food, has disadvantages such as strong toxicity and low bioavailability. We investigated the protective effects of L. lactis NZ9000-SeNPs against ETEC K88-induced intestinal barrier injury in C57BL/6 mice. Our results show that L. lactis NZ9000-SeNPs effectively alleviate ETEC-K88-induced intestinal barrier dysfunction. This study highlights the importance of developing a promising and safe Se supplement for the substation of sodium selenite applied in food, feed and biomedicine.
Pengfei Zhai, Landan Shi, Guowei Zhong, Jihong Jiang, Jingwen Zhou, Xin Chen, Guokai Dong, Lei Zhang, Rongpeng Li,
Applied and Environmental Microbiology; https://doi.org/10.1128/aem.01120-21

Abstract:
An efficient reactive oxygen species (ROS) detoxification system is vital for the survival of the pathogenic fungus Aspergillus fumigatus within the host high ROS environment of the host. Therefore, identifying and targeting factors essential for oxidative stress response is one approach to develop novel treatments for fungal infections. Oxidation resistance 1 (Oxr1) protein is essential for protection against oxidative stress in mammals, but its functions in pathogenic fungi remain unknown. The present study aimed to characterize the role of an Oxr1 homolog in A. fumigatus . The results indicated that the OxrA protein plays an important role in oxidative stress resistance by regulating the catalase function in A. fumigatus , and overexpression of catalase can rescue the phenotype associated with OxrA deficiency. Importantly, the deficiency of oxrA decreased the virulence of A. fumigatus and altered the host immune response. Using the Aspergillus -induced lung infection model, we demonstrated that the ΔoxrA mutant strain induced less tissue damage along with decreased levels of LDH and albumin release. Additionally, the ΔoxrA mutant caused inflammation at a lower degree, along with a markedly reduced influx of neutrophils to the lungs and a decreased secretion of cytokine usually associated with recruitment of neutrophils in mice. These results characterize for the role of OxrA in A. fumigatus , as a core regulator of oxidative stress resistance and fungal pathogenesis. Importance Knowledge of reactive oxygen species (ROS) detoxification in fungal pathogens is useful in the design of new antifungal drugs and could aid in the study of oxidative stress resistance mechanisms. In this study, we demonstrate that OxrA protein localize to the mitochondria and function to protect against oxidative damage. We demonstrate that OxrA contributes to oxidative stress resistance by regulating catalase function, and overexpression of catalase (CatA or CatB) can rescue the phenotype that is associated with OxrA deficiency. Remarkably, a loss of OxrA attenuated the fungal virulence in a mouse model of invasive pulmonary aspergillosis and altered the host immune response. Therefore, our finding indicates that inhibition of OxrA might be an effective approach for alleviating A. fumigatus infection. The present study is, to the best of our knowledge, a pioneer in reporting the vital role of Oxr1 protein in pathogenic fungi.
Shunli Hu, Guiping Liu, Long Zhang, Yufeng Gan, Baozhan Wang, Shiri Freilich,
Applied and Environmental Microbiology; https://doi.org/10.1128/aem.01562-21

Abstract:
Rac -dichlorprop, a commonly used phenoxyalkanoic acid herbicide, is frequently detected in environments and poses threats to environmental safety and human health. Microbial consortia are thought to play key roles in Rac -dichlorprop degradation. However, the compositions of the microbial consortia involved in Rac -dichlorprop degradation remain largely unknown. In this study, DNA-stable isotope probing and metagenomics analysis were integrated to reveal the key microbial consortium responsible for Rac -dichlorprop degradation in a Rac -dichlorprop-degrading enrichment. OTU340 ( Sphingobium sp.) and OTU348 ( Sphingopyxis sp.) were significantly enriched in the 13 C- Rac -dichlorprop-labeled heavy DNA fractions. A Rac -dichlorprop degrader, Sphingobium sp. L3, was isolated from the enrichment by traditional enrichment method but with additional supplementation of the antibiotic ciprofloxacin, which was instructed by metagenomics analysis of the associations between Rac -dichlorprop-degraders and antibiotic resistance genes. As revealed by functional profiling of the metagenomes of the heavy DNA, the genes rdpA and sdpA , involved in the initial degradation of the ( R )- and ( S )-enantiomers of dichlorprop respectively, were mostly taxonomically assigned to Sphingobium species, indicating that Sphingopyxis species might harbor novel dichlorprop degrading genes. In addition, taxonomically diverse bacterial genera such as Dyella , Sphingomonas , Pseudomonas , and Achromobacter were presumed to synergistically cooperate with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of Rac -dichlorprop. Importance Understanding of the key microbial consortium involved in the degradation of the phenoxyalkanoic acid herbicide of Rac -dichlorprop is pivotal for design of synergistic consortia used for enhanced bioremediation of herbicide-contaminated sites. However, the composition of microbial consortium and the interactions between community members during the biodegradation of Rac -dichlorprop are unclear. In this study, DNA-SIP and metagenomics analysis were integrated to reveal that the metabolite 2,4-dichlorophenol degraders Dyella , Sphingomonas , Pseudomonas , and Achromobacter synergistically cooperated with the key degraders Sphingobium / Sphingopyxis for enhanced degradation of Rac -dichlorprop. Our study provides new insights into the synergistic degradation of Rac -dichlorprop at the community level and implies the existence of novel degrading genes for Rac -dichlorprop in nature.
Chelsea L. Murphy, R. Yang, T. Decker, C. Cavalliere, V. Andreev, N. Bircher, J. Cornell, R. Dohmen, C. J. Pratt, A. Grinnell, et al.
Applied and Environmental Microbiology; https://doi.org/10.1128/aem.01706-21

Abstract:
Cultured Myxococcota are predominantly aerobic soil inhabitants, characterized by their highly coordinated predation and cellular differentiation capacities. Little is currently known regarding yet-uncultured Myxococcota from anaerobic, non-soil habitats. We analyzed genomes representing one novel order (o__JAFGXQ01) and one novel family (f__JAFGIB01) in the Myxococcota from an anoxic freshwater spring (Zodletone spring) in Oklahoma, USA. Compared to their soil counterparts, anaerobic Myxococcota possess smaller genomes, and a smaller number of genes encoding biosynthetic gene clusters (BGCs), peptidases, one- and two-component signal transduction systems, and transcriptional regulators. Detailed analysis of thirteen distinct pathways/processes crucial to predation and cellular differentiation revealed severely curtailed machineries, with the notable absence of homologs for key transcription factors (e.g. FruA and MrpC), outer membrane exchange receptor (TraA), and the majority of sporulation-specific and A-motility-specific genes. Further, machine-learning approaches based on a set of 634 genes informative of social lifestyle predicted a non-social behavior for Zodletone Myxococcota. Metabolically, Zodletone Myxococcota genomes lacked aerobic respiratory capacities, but encoded genes suggestive of fermentation, dissimilatory nitrite reduction, and dissimilatory sulfate-reduction (in f_JAFGIB01) for energy acquisition. We propose that predation and cellular differentiation represent a niche adaptation strategy that evolved circa 500 Mya in response to the rise of soil as a distinct habitat on earth. Importance The Myxococcota is a phylogenetically coherent bacterial lineage that exhibits unique social traits. Cultured Myxococcota are predominantly aerobic soil-dwelling microorganisms that are capable of predation and fruiting body formation. However, multiple yet-uncultured lineages within the Myxococcota have been encountered in a wide range of non-soil, predominantly anaerobic habitats; and the metabolic capabilities, physiological preferences, and capacity of social behavior of such lineages remain unclear. Here, we analyzed genomes recovered from a metagenomic analysis of an anoxic freshwater spring in Oklahoma, USA that represent novel, yet-uncultured, orders and families in the Myxococcota. The genomes appear to lack the characteristic hallmarks for social behavior encountered in Myxococcota genomes, and displayed a significantly smaller genome size and a smaller number of genes encoding biosynthetic gene clusters, peptidases, signal transduction systems, and transcriptional regulators. Such perceived lack of social capacity was confirmed through detailed comparative genomic analysis of thirteen pathways associated with Myxococcota social behavior, as well as the implementation of machine learning approaches to predict social behavior based on genome composition. Metabolically, these novel Myxococcota are predicted to be strict anaerobes, utilizing fermentation, nitrate reduction, and dissimilarity sulfate reduction for energy acquisition. Our results highlight the broad patterns of metabolic diversity within the yet-uncultured Myxococcota and suggest that the evolution of predation and fruiting body formation in the Myxococcota has occurred in response to soil formation as a distinct habitat on earth.
Weiran Zhang, Weiwei Wang, Jinghong Wang, Guinan Shen, Yuan Yuan, Lei Yan, , Weidong Wang
Applied and Environmental Microbiology; https://doi.org/10.1128/aem.01355-21

Abstract:
Lignin is a complex natural organic polymer and is one of the primary components of lignocellulose. The efficient utilization of lignocellulose is limited because it is difficult to degrade lignin. In this study, we screened a lacz1 gene fragment encoding laccase from the macro transcriptome data of a microbial consortium WSC-6, which can efficiently degrade lignocellulose. The RT-qPCR results demonstrated that the expression level of the lacz1 gene during the peak period of lignocellulose degradation by WSC-6 increased by 30.63 times compared to the initial degradation period. Phylogenetic tree analysis demonstrated that the complete lacz1 gene is derived from Bacillus sp. and encoded laccase. The corresponding protein LacZ1 was expressed and purified by Ni-chelating affinity chromatography. The optimum temperature was 75°C, the optimum pH was 4.5, and the highest enzyme activity reached 16.39 U/mg. We found that Cu 2+ was an important cofactor needed for LacZ1 to have enzyme activity. The molecular weight distribution of lignin was determined by Gel Permeation Chromatography (GPC) and changes in the lignin structure were determined by 1H Nuclear Magnetic Resonance Spectra (1H NMR). The degradation products of lignin by LacZ1 were determined by Gas Chromatography and Mass Spectrometry (GC-MS), and three lignin degradation pathways (the gentian acid pathway, benzoic acid pathway, and protocatechuic acid pathway) were proposed. This study provides insight into the degradation of lignin and new insights into high-temperature bacterial laccase. IMPORTANCE Lignin is a natural aromatic polymer that is not easily degraded, hindering the efficient use of lignocellulose-rich biomass resources, such as straw. Biodegradation is a method of decomposing lignin that has recently received increasing attention. In this study, we screened a gene encoding laccase from the lignocellulose-degrading microbial consortium WSC-6, purified the corresponding protein LacZ1, characterized the enzymatic properties of laccase LacZ1, and speculated that the degradation pathway of LacZ1 degrades lignin. This study identified a new, high-temperature bacterial laccase that can degrade lignin, providing insight into lignin degradation by this laccase.
Aiai Xu, Jie Liu, Zhiying Guo, Changkun Wang, Kai Pan, Fangfang Zhang,
Applied and Environmental Microbiology; https://doi.org/10.1128/aem.01010-21

Abstract:
It is critical to identify the assembly processes and determinants of soil microbial communities to better predict soil microbial responses to environmental change in arid and semiarid areas. Here, soils from 16 grassland-only, 9 paired grassland and farmland, and 16 farmland-only sites were collected across the central Inner Mongolia Plateau covering a steep environmental gradient. Through analyzing the paired samples, we discovered that land uses had strong effects on soil microbial communities, but weak effects on their assembly processes. For all samples, although no environmental variables were significantly correlated with the net relatedness index (NRI), both the nearest taxon index (NTI) and the β-nearest taxon index (βNTI) were most related to mean annual precipitation (MAP). With the increase of MAP, soil microbial taxa at the tips of the phylogenetic tree were more clustered, and the contribution of determinism increased. Determinism (48.6%), especially variable selection (46.3%), and stochasticity (51.4%) were almost equal in farmland, while stochasticity (75.0%) was dominant in grassland. Additionally, Mantel tests and redundancy analyses (RDA) revealed that the main determinants of soil microbial community structure were MAP in grassland, but mean annual temperature (MAT) in farmland. MAP and MAT were also good predictors of the community composition (the top 200 dominant OTUs) in grassland and farmland, respectively. Collectively, in arid and semiarid areas, soil microbial communities were more sensitive to environmental change in farmland than in grassland, and unlike the major impact of MAP on grassland microbial communities, MAT was the primary driver of farmland microbial communities. Importance As one of the most diverse organisms, soil microbes play indispensable roles in many ecological processes in arid and semiarid areas with limited macrofaunal and plant diversity, yet the mechanisms underpinning soil microbial community are not fully understood. In this study, soil microbial communities were investigated along a 500 km transect covering a steep environmental gradient across farmland and grassland in the areas. The results showed that precipitation was the main factor mediating the assembly processes. Determinism was more influential in farmland, and variable selection of farmland was twice that of grassland. Temperature mainly drove farmland microbial communities, while precipitation mainly affected grassland microbial communities. These findings provide new information about the assembly processes and determinants of soil microbial communities in arid and semiarid areas, consequently improving the predictability of the community dynamics, which have implications for sustaining soil microbial diversity and ecosystem functioning, particularly under global climate change conditions.
Yang Yuan, Jun Liu, Tao-Tao Yang, Shao-Ming Gao, Bin Liao,
Applied and Environmental Microbiology; https://doi.org/10.1128/aem.01065-21

Abstract:
Recent omics studies have provided invaluable insights into the metabolic potential, adaptation and evolution of novel archaeal lineages from a variety of extreme environments. We have utilized a genome-resolved metagenomic approach to recover eight medium- to high-quality metagenome-assembled genomes (MAGs) that likely represent a new order (“ Candidatus Sysuiplasmatales”) within Thermoplasmata from mine tailings and acid mine drainage (AMD) sediments sampled from two copper mines in South China. 16S rRNA gene based analyses revealed a narrow habitat range for these uncultured archaea limiting to AMD and hot spring-related environments. Metabolic reconstruction indicated a facultatively anaerobic heterotrophic lifestyle. This may allow the archaea to adapt to oxygen fluctuations and is thus in marked contrast to the majority of lineages in the domain Archaea which typically show obligately anaerobic metabolisms. Notably, “ Ca. Sysuiplasmatales” could conserve energy through degradation of fatty acids, amino acid metabolism and oxidation of reduced inorganic sulfur compounds (RISCs), suggesting that they may contribute to acid generation in the extreme mine environments. Unlike its closely related Methanomassiliicoccales and “ Ca. Gimiplasmatales”, “ Ca. Sysuiplasmatales” lack the capacity to perform methanogenesis and carbon fixation. Ancestral state reconstruction indicated that “ Ca. Sysuiplasmatales” and its closely related Methanomassiliicoccales, “ Ca. Gimiplasmatales”, and the SG8-5 and the RBG-16-68-12 orders originated from a facultatively anaerobic ancestor capable of carbon fixation via the bacterial-type H 4 F Wood–Ljungdahl pathway (WLP). Their metabolic divergence might be attributed to different evolutionary paths. Importance A wide array of archaea populate Earth’s extreme environments thereby they may play important roles in mediating biogeochemical processes such as iron and sulfur cycling. However, our knowledge of archaeal biology and evolution is still limited considering the uncultured majority of archaeal diversity. For instance, most order-level lineages except Thermoplasmatales, Aciduliprofundales and Methanomassiliicoccales within Thermoplasmata do not have cultured representatives. Here, we report the discovery and genomic characterization of a novel order, namely “ Ca . Sysuiplasmatales”, within Thermoplasmata in the extremely acidic mine environments. “ Ca . Sysuiplasmatales” are inferred to be facultatively anaerobic heterotrophs and likely contribute to acid generation through the oxidation of RISCs. The physiological divergence between “ Ca . Sysuiplasmatales” and its closely related Thermoplasmata lineages may be attributed to different evolutionary paths. These results expand our knowledge of archaea in the extreme mine ecosystem.
, , Peter Vandamme
Applied and Environmental Microbiology; https://doi.org/10.1128/aem.01169-21

Abstract:
Burkholderia cepacia complex strain R-12632 produces ditropolonyl sulfide, an unusual sulfur-containing tropone, via a yet unknown biosynthetic pathway. Ditropolonyl sulfide purified from a culture of strain R-12632 inhibits the growth of various Gram-positive and Gram-negative multidrug resistant bacteria, with minimum inhibitory concentration (MIC) values as low as 16 μg/ml. In the present study we used a transposon mutagenesis approach combined with metabolite analyses to identify the genetic basis for antibacterial activity of strain R-12632 against Gram-negative bacterial pathogens. Fifteen of the 8304 transposon mutants investigated completely lost antibacterial activity against Klebsiella pneumoniae LMG 2095. In these loss-of-activity mutants, nine genes were interrupted. Four of those genes were involved in assimilatory sulfate reduction, two in phenylacetic acid (PAA) catabolism and one in glutathione metabolism. Via semipreparative fractionation and metabolite identification, it was confirmed that inactivation of the PAA degradation pathway or glutathione metabolism led to loss of ditropolonyl sulfide production. Based on earlier studies on the biosynthesis of tropolone compounds, the requirement for a functional PAA catabolic pathway for antibacterial activity in strain R-12632 indicated that this pathway likely provides the tropolone backbone for ditropolonyl sulfide. Loss of activity observed in mutants defective in assimilatory sulfate reduction and glutathione biosynthesis suggested that cysteine and glutathione are potential sources of the sulfur atom linking the two tropolone moieties. The demonstrated antibacterial activity of the unusual antibacterial compound ditropolonyl sulfide warrants further studies into its biosynthesis and biological role. Importance Burkholderia bacteria are historically known for their biocontrol properties and have been proposed as a promising and underexplored source of bioactive specialized metabolites. Burkholderia cepacia complex strain R-12632 inhibits various Gram-positive and Gram-negative resistant pathogens and produces numerous specialized metabolites, among which ditropolonyl sulfide. This unusual antimicrobial has been poorly studied and its biosynthetic pathway remained unknown. In the present study, we performed transposon mutagenesis of strain R-12632 and performed genome and metabolite analyses of loss-of-activity mutants to study the genetic basis for antibacterial activity. Our results indicate that the phenylacetic acid catabolism, assimilatory sulfate reduction and glutathione metabolism are necessary for ditropolonyl sulfide production. These findings contribute to understanding the biosynthesis and biological role of this unusual antimicrobial.
Sadat M. R. Khattab,
Applied and Environmental Microbiology; https://doi.org/10.1128/aem.00268-21

Abstract:
Glycerol is an eco-friendly solvent that enhances plant biomass decomposition via glycerolysis in many pretreatment methods. Nonetheless, inefficient conversion of glycerol to ethanol by natural Saccharomyces cerevisiae limits its use in these processes. Here, we have developed an efficient glycerol-converting yeast strain by genetically modifying the oxidation of cytosolic nicotinamide adenine dinucleotide (NADH) by an O 2 -dependent dynamic shuttle and abolishing both glycerol phosphorylation and biosynthesis in S. cerevisiae D452-2 strain, as well as vigorous expression of whole genes in the DHA-pathway ( Candid utilis glycerol facilitator, Ogataea polymorpha glycerol dehydrogenase, endogenous dihydroxyacetone kinase, and triosephosphate isomerase). The engineered strain showed conversion efficiencies (CE) up to 0.49 g ethanol/g glycerol (98% of theoretical CE), with production rate >1 g/L −1 h −1 when glycerol was supplemented in a single fed-batch fermentation in a rich medium. Furthermore, the engineered strain converted a mixture of glycerol and glucose into bioethanol (>86 g/L) with 92.8% CE. To the best of our knowledge, this is the highest reported titer of bioethanol produced from glycerol and glucose. Notably, we developed a glycerol-utilizing transformant from parent strain, which cannot utilize glycerol as a sole carbon source. The developed strain converted glycerol to ethanol with a productivity of 0.44 g/L −1 h −1 on minimal medium under semi-aerobic conditions. Our findings will promote the utilization of glycerol in eco-friendly biorefineries and integrate bioethanol and plant-oil industries. IMPORTANCE With the development of efficient lignocellulosic biorefineries, glycerol has attracted attention as an eco-friendly biomass-derived solvent that can enhance the dissociation of lignin and cell wall polysaccharides during the pretreatment process. Co-conversion of glycerol with the sugars released from biomass after glycerolysis increases the resources for ethanol production and lowers the burden of component separation. However, low conversion efficiency from glycerol and sugars limits the industrial application of this process. Therefore, the generation of an efficient glycerol-fermenting yeast will promote the applicability of integrated biorefineries. Hence, metabolic flux control in yeast grown on glycerol will lead to the generation of cell factories that produce chemicals, which will boost biodiesel and bioethanol industries. Additionally, the use of glycerol-fermenting yeast will reduce global warming and generation of agricultural waste, leading to the establishment of a sustainable society.
Zhengyu Wu, Maojin Tian, Rongjing Zhang,
Applied and Environmental Microbiology; https://doi.org/10.1128/aem.01674-21

Abstract:
We developed a robust bead assay for studying flagellar motor behavior of Pseudomonas aeruginosa . Using this assay, we studied the dynamics of the two stator systems in the flagellar motor. We found that the two sets of stators function differently, with MotAB stators providing higher total torque, and MotCD stators ensuring more stable motor speed. The motors in wild-type cells adjust the stator compositions according to the environment, resulting in an optimal performance in environmental exploration compared to mutants with one set of stators. The bead assay we developed here can be further used to study P. aeruginosa chemotaxis at the level of single cell using the motor behavior as the chemotaxis output. Importance Cells of Pseudomonas aeruginosa possess a single polar flagellum, driven by a rotatory motor powered by two sets of torque-generating units (stators). We developed a robust bead assay for studying the behavior of the flagellar motor in P. aeruginosa , by attaching a microsphere to shortened flagellar filament and using it as an indicator of motor rotation. Using this assay, we revealed the dynamics of the two stator systems in the flagellar motor, and found that the motors in wild-type cells adjust the stator compositions according to the environment, resulting in an optimal performance in environmental exploration compared to mutants with one set of stators.
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