Molecular Plant-Microbe Interactions®

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ISSN / EISSN : 0894-0282 / 0894-0282
Published by: Scientific Societies (10.1094)
Total articles ≅ 4,262
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Zhichao Zhang, , , Wenwu Ye, Suomeng Dong, , Yuanchao Wang
Molecular Plant-Microbe Interactions®;

Nucleosome-free open chromatin often harbor transcription factor (TF) binding sites that are associated with active cis-regulatory elements. However, analysis of open chromatin regions has rarely been applied to oomycete or fungal plant pathogens. In this study, we performed the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to identify open chromatin and cis-regulatory elements in Phytophthora sojae at the mycelial stage. We identified 10,389 peaks representing nucleosome-free regions (NFRs). The peaks were enriched in gene promoter regions and associated with 40% of P. sojae genes; transcription levels were higher for genes with multiple peaks than genes with a single peak and were higher for genes with a single peak than genes without peak. Chromatin accessibility was positively correlated with gene transcription level. Through motif discovery based on NFR peaks in core promoter regions, 25 candidates cis-regulatory motifs with evidence of TF-binding footprints were identified. These motifs exhibited various preferences for location in the promoter region and associations with the transcription level of their target genes, which included some putative pathogenicity-related genes. As the first study revealing the landscape of open chromatin and the correlation between chromatin accessibility and gene transcription level in oomycetes, the results provide a technical reference and data resources for future studies on the regulatory mechanisms of gene transcription.
Molecular Plant-Microbe Interactions®;

Curtobacterium flaccumfaciens complex species in the family Microbacteriaceae encompasses a group of plant pathogenic actinobacterial strains affecting annual crops and ornamental plants. The species includes five pathovars namely C. flaccumfaciens pv. betae, C. flaccumfaciens pv. flaccumfaciens, C. flaccumfaciens pv. ilicis, C. flaccumfaciens pv. oortii, and C. flaccumfaciens pv. poinsettiae. Despite the economic importance of C. flaccumfaciens, its members have rarely been investigated for their phylogenetic relationships, molecular characteristics and virulence repertories due in part to the lack of whole genome resources. Here we present the whole genome sequence of 17 C. flaccumfaciens strains representing members of four pathovars isolated from different plant species in a diverse geographical and temporal span. The genomic data presented in this study will pave the way of research on the comparative genomics, phylogenomics and taxonomy of C. flaccumfaciens, and extend our understanding of the virulence features of the species.
, , Jing Wu, , , Da-Song Chen, ,
Molecular Plant-Microbe Interactions®;

Gram-negative bacteria can produce outer membrane vesicles (OMVs), and most functional studies of OMVs have been focused on mammalian-bacterial interactions. However, research on the OMVs of rhizobia is still limited so far. In this work, we isolated and purified OMVs from Sinorhizobium fredii HH103 under free-living conditions that was set as control (C-OMVs) and symbiosis-mimicking conditions that was induced by genistein (G-OMVs). The soybean roots treated with G-OMVs displayed significant deformation of root hairs. G-OMVs significantly induced the expression of nodulation genes related to early symbiosis, while inhibited that of the defense genes of soybean. Proteomics analysis identified a total of 93 differential proteins between C-OMVs and G-OMVs, which are mainly associated with ribosome synthesis, flagellar assembly, two-component system, ABC transporters, oxidative phosphorylation, nitrogen metabolism, quorum sensing, glycerophospholipid metabolism and peptidoglycan biosynthesis. A total of 45 differential lipids were identified in lipidomics analysis. Correlation analysis of OMV proteome and lipidome data revealed that glycerophospholipid metabolism is the enriched KEGG metabolic pathway, and the expression of phosphatidylserine decarboxylase was significantly up-regulated in G-OMVs. The changes in three lipids related to symbiosis in the glycerophospholipid metabolism pathway were verified by ELISA. Our results indicate that glycerophospholipid metabolism contributes to rhizobia-soybean symbiosis via OMVs.
Molecular Plant-Microbe Interactions®, Volume 35, pp 28-38;

Duckweeds (Lemnaceae) are representative producers in fresh aquatic ecosystems and also yield sustainable biomass for animal feeds, human foods, and biofuels, and contribute toward effective wastewater treatment, thus enhancing duckweed productivity is a critical challenge. Plant growth-promoting bacteria (PGPB) can improve the productivity of terrestrial plants; however, duckweed–PGPB interactions remain unclear and no previous study has investigated the molecular mechanisms underlying duckweed–PGPB interaction. Herein, a PGPB, Ensifer sp. strain SP4, was newly isolated from giant duckweed (Spirodela polyrhiza (L.) Schleid.), and the interactions between S. polyrhiza and SP4 were investigated through physiological, biochemical, and metabolomic analyses. In S. polyrhiza and SP4 co-culture, SP4 increased the nitrogen (N), chlorophyll, and RuBisCO contents and the photosynthesis rate of S. polyrhiza by 2.5-, 2.5-, 2.7-, and 2.4-fold, respectively. Elevated photosynthesis increased the relative growth rate and biomass productivity of S. polyrhiza by 1.5- and 2.7-fold, respectively. SP4 significantly altered the metabolomic profile of S. polyrhiza, especially its amino acid profile. N stable isotope analysis revealed that organic N compounds were transferred from SP4 to S. polyrhiza. These N compounds, particularly glutamic acid, possibly triggered the increase in photosynthetic and growth activities. Accordingly, we propose a new model for the molecular mechanism underlying S. polyrhiza growth promotion by its associated bacteria Ensifer sp. SP4, which occurs through enhanced N compound metabolism and photosynthesis. Our findings show that Ensifer sp. SP4 is a promising PGPB for increasing biomass yield, wastewater purification activity, and CO2 capture of S. polyrhiza.
Aiko Tanaka, , , , Nobuo Yamaguchi, , , Osamu Nakayachi, , Nobukazu Tanaka, et al.
Molecular Plant-Microbe Interactions®, Volume 35, pp 73-84;

Agrobacterium tumefaciens is a bacterial pathogen that causes crown gall disease on a wide range of eudicot plants by genetic transformation. Besides T-DNA integrated by natural transformation in vegetative tissues of plants by pathogenic Agrobacterium, previous reports have indicated that T-DNA sequences originating from ancestral Agrobacterium sp. are present in the genomes of all cultivated sweet potato (Ipomoea batatas) analyzed. Expression of Agrobacterium-derived agrocinopine synthase (ACS) gene was detected in leaf and root tissues of sweet potato, suggesting that the plant can produce agrocinopine, a sugar-phosphodiester opine considered to be utilized by Agrobacterium in crown gall. To validate the product synthesized by I. batatas ACS (IbACS), we introduced IbACS into tobacco under a constitutive promoter. High voltage paper electrophoresis followed by alkaline silver nitrate staining detected the production of an agrocinopine-like substance in IbACS1-expressing tobacco, and further MS and NMR analyses of the product confirmed that IbACS can produce agrocinopine A from natural plant substrates. The partially purified compound was biologically active in an agrocinopine A bioassay. 16S rRNA amplicon sequencing and meta-transcriptome analysis revealed that the rhizosphere microbial community of tobacco was affected by the expression of IbACS. A new species of Leifsonia (actinobacteria) was isolated as an enriched bacterium in the rhizosphere of IbACS1-expressing tobacco. This Leifsonia sp. can catabolize agrocinopine A produced in tobacco, indicating that the production of agrocinopine A attracts rhizosphere bacteria which can utilize this sugar-phosphodiester. These results suggest a potential role of IbACS conserved among sweet potato cultivars in manipulating their microbial community.
Molecular Plant-Microbe Interactions®, Volume 35, pp 1-96;

Molecular Plant-Microbe Interactions Vol. 35 No. 1
Molecular Plant-Microbe Interactions®, Volume 35, pp 49-63;

Cyanodermella asteris is a fungal endophyte from Aster tataricus, a perennial plant from the Northern part of Asia. Here, we demonstrated an interaction of C. asteris with Arabidospis thaliana, Chinese cabbage, rapeseed, tomato, maize or sunflower resulting in different phenotypes such as shorter main roots, massive lateral root growth, higher leaf and root biomass, and increased anthocyanin levels. In a variety of co-cultivation assays, it was shown that these altered phenotypes are caused by fungal CO2, volatile organic compounds, and soluble compounds, notably astins. Astins A, C and G induced plant growth when they were individually included in the medium. In return, A. thaliana stimulates the fungal astin C production during co-cultivation. Taken together, our results indicate a bilateral interaction between the fungus and the plant. A stress response in plants is induced by fungal metabolites while plant stress hormones induced astin C production of the fungus. Interestingly, our results not only show unidirectional influence of the fungus on the plant, but vice versa. The plant is able to influence growth and secondary metabolite production in the endophyte, even when both organisms do not live in close contact, suggesting the involvement of volatile compounds.
Mengru Dou, , , Xiaojian Yuan, , , , Tingting Chen, Yuejin Wang,
Molecular Plant-Microbe Interactions®, Volume 35, pp 90-93;

Grape ripe rot is an important disease that has seriously damaged the yield and quality of grape worldwide. The disease is caused by Colletotrichum viniferum, a hemibiotrophic fungus that belongs to the Glomerellaceae family of Sordariomycetes class. Here, this work presents the genome of C. viniferum stain CvYL2a from grape based on Illumina HiSeq 2500 and PacBio RS II. The high-quality genome consists of 70 contigs with a 73.41 Mb genome size and encodes 14,668 protein-coding genes. These genes were annotated using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, EuKaryotic Orthologous Groups, Non-redundant Protein, and Swiss-Prot database. In addition, we identified a series of genes involved in pathogenicity including 909 carbohydrate-active enzymes, 67 secondary metabolite gene clusters, and 307 Cytochrome P450 enzymes. This genome sequence provides a valuable reference for the research on grape-C. viniferum interactions, the pathogenesis of C. viniferum, and comparative genome analyses. Keywords: Colletotrichum viniferum, grape, genome, pathogenesis
Molecular Plant-Microbe Interactions®, Volume 35, pp 94-95;

The complete genome sequence of Xanthomonas arboricola pv. corylina A7 was obtained by a hybrid approach combining Pacbio and Illumina HiSeq sequencing data. A single circular chromosome of 5.1 mb with 65.47% G+C content was obtained. We identified 4344 coding sequences and some genes involved in copper resistance. To our knowledge, the data presented herein is the first report of high-quality whole genome of X. arboricola pv. corylina, isolated from infected hazelnut trees in southern Chile.
Rong Huang, Haichao Feng, , , , , Qi-Rong Shen,
Molecular Plant-Microbe Interactions®, Volume 35, pp 64-72;

Probiotic Bacillus colonizing plant root surfaces has been reported to improve its beneficial effect. Chemotaxis, adhesion, aggregation and biofilm formation are the four steps of root colonization by plant-growth-promoting rhizobacteria (PGPRs). Compared to the other three well studied processes, adhesion of PGPRs is less known. In this study, using mutant strains deleted for potential adhesin genes in a PGPR strain Bacillus velezensis SQR9, adherence to both cucumber root surface and abiotic surface by those strains was evaluated. Results showed that deletion mutations ΔlytB, ΔV529_10500, ΔfliD, ΔyhaN and ΔsacB reduced the adhesion to root surface, while among them, only ΔfliD had significant defects in adhesion to abiotic surfaces (glass and polystyrene). In addition, B. velevzensis SQR9 mutants defective in adhesion to root surfaces showed a deficiency in rhizosphere colonization. Among the encoded proteins, FliD and YhaN played vital roles in root adhesion. This research systematically explored the potential adhesins in a well-studied PGPR strain, and also indicated that adhesion progress was required for roots colonization, which will help to enhance the rhizosphere colonization and beneficial function of PGPRs in agricultural production.
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