151
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Savory EA, Weisberg AJ, Stevens DM, Creason AL, Fuller SL, Pearce EM, Chang JH. Phytopathogenic Rhodococcus Have Diverse Plasmids With Few Conserved Virulence Functions. Front Microbiol 2020; 11:1022. [PMID: 32523572 PMCID: PMC7261884 DOI: 10.3389/fmicb.2020.01022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/27/2020] [Indexed: 11/13/2022] Open
Abstract
Rhodococcus is a genus of Gram-positive bacteria with species that can cause growth deformations to a large number of plant species. This ability to cause disease is hypothesized to be dependent on a cluster of three gene loci on an almost 200 kb-sized linear plasmid. To reevaluate the roles of some of the genes in pathogenicity, we constructed and characterized deletion mutants of fasR and four fas genes. Findings confirmed that fasR, which encodes a putative transcriptional regulator, is necessary for pathogenesis. However, three of the fas genes, implicated in the metabolism of plant growth promoting cytokinins, are dispensable for the ability of the pathogen to cause disease. We also used long-read sequencing technology to generate high quality genome sequences for two phytopathogenic strains in which virulence genes are diverged in sequence and/or hypothesized to have recombined into the chromosome. Surprisingly, findings showed that the two strains carry extremely diverse virulence plasmids. Ortholog clustering identified only 12 genes present on all three virulence plasmids. Rhodococcus requires a small number of horizontally acquired traits to be pathogenic and the transmission of the corresponding genes, via recombination and conjugation, has the potential to rapidly diversify plasmids and bacterial populations.
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Affiliation(s)
- Elizabeth A Savory
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Danielle M Stevens
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Allison L Creason
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Skylar L Fuller
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Emma M Pearce
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.,Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
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152
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Khatabi B, Gharechahi J, Ghaffari MR, Liu D, Haynes PA, McKay MJ, Mirzaei M, Salekdeh GH. Plant-Microbe Symbiosis: What Has Proteomics Taught Us? Proteomics 2020; 19:e1800105. [PMID: 31218790 DOI: 10.1002/pmic.201800105] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/04/2019] [Indexed: 11/08/2022]
Abstract
Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics-based technologies has broadened our understanding of the molecular aspects of beneficial plant-microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis-specific and symbiosis-related proteins and post-translational modifications that play a critical role in mediating symbiotic plant-microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other "omics" data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis-based "omic" approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities is also discussed.
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Affiliation(s)
- Behnam Khatabi
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, MD, 21853, USA
| | - Javad Gharechahi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Dilin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China.,Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, P. R. China
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Matthew J McKay
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
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153
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Hough M, McClure A, Bolduc B, Dorrepaal E, Saleska S, Klepac-Ceraj V, Rich V. Biotic and Environmental Drivers of Plant Microbiomes Across a Permafrost Thaw Gradient. Front Microbiol 2020; 11:796. [PMID: 32499761 PMCID: PMC7243355 DOI: 10.3389/fmicb.2020.00796] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/03/2020] [Indexed: 02/01/2023] Open
Abstract
Plant-associated microbiomes are structured by environmental conditions and plant associates, both of which are being altered by climate change. The future structure of plant microbiomes will depend on the, largely unknown, relative importance of each. This uncertainty is particularly relevant for arctic peatlands, which are undergoing large shifts in plant communities and soil microbiomes as permafrost thaws, and are potentially appreciable sources of climate change feedbacks due to their soil carbon (C) storage. We characterized phyllosphere and rhizosphere microbiomes of six plant species, and bulk peat, across a permafrost thaw progression (from intact permafrost, to partially- and fully-thawed stages) via 16S rRNA gene amplicon sequencing. We tested the hypothesis that the relative influence of biotic versus environmental filtering (the role of plant species versus thaw-defined habitat) in structuring microbial communities would differ among phyllosphere, rhizosphere, and bulk peat. Using both abundance- and phylogenetic-based approaches, we found that phyllosphere microbial composition was more strongly explained by plant associate, with little influence of habitat, whereas in the rhizosphere, plant and habitat had similar influence. Network-based community analyses showed that keystone taxa exhibited similar patterns with stronger responses to drivers. However, plant associates appeared to have a larger influence on organisms belonging to families associated with methane-cycling than the bulk community. Putative methanogens were more strongly influenced by plant than habitat in the rhizosphere, and in the phyllosphere putative methanotrophs were more strongly influenced by plant than was the community at large. We conclude that biotic effects can be stronger than environmental filtering, but their relative importance varies among microbial groups. For most microbes in this system, biotic filtering was stronger aboveground than belowground. However, for putative methane-cyclers, plant associations have a stronger influence on community composition than environment despite major hydrological changes with thaw. This suggests that plant successional dynamics may be as important as hydrological changes in determining microbial relevance to C-cycling climate feedbacks. By partitioning the degree that plant versus environmental filtering drives microbiome composition and function we can improve our ability to predict the consequences of warming for C-cycling in other arctic areas undergoing similar permafrost thaw transitions.
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Affiliation(s)
- Moira Hough
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Amelia McClure
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Benjamin Bolduc
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, United States
| | - Ellen Dorrepaal
- Climate Impacts Research Centre, Umeå University, Umeå, Sweden
| | - Scott Saleska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Virginia Rich
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, United States
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154
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Ding LJ, Cui HL, Nie SA, Long XE, Duan GL, Zhu YG. Microbiomes inhabiting rice roots and rhizosphere. FEMS Microbiol Ecol 2020; 95:5420819. [PMID: 30916760 DOI: 10.1093/femsec/fiz040] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/26/2019] [Indexed: 11/12/2022] Open
Abstract
Land plants directly contact soil through their roots. An enormous diversity of microbes dwelling in root-associated zones, including endosphere (inside root), rhizoplane (root surface) and rhizosphere (soil surrounding the root surface), play essential roles in ecosystem functioning and plant health. Rice is a staple food that feeds over 50% of the global population. Its root is a unique niche, which is often characterized by an oxic region (e.g. the rhizosphere) surrounded by anoxic bulk soil. This oxic-anoxic interface has been recognized as a pronounced hotspot that supports dynamic biogeochemical cycles mediated by various functional microbial groups. Considering the significance of rice production upon global food security and the methane budget, novel insights into how the overall microbial community (i.e. the microbiome) of the rice root system influences ecosystem functioning is the key to improving crop health and sustainable productivity of paddy ecosystems, and alleviating methane emissions. This mini-review summarizes the current understanding of microbial diversity of rice root-associated compartments to some extent, especially the rhizosphere, and makes a comparison of rhizosphere microbial community structures between rice and other crops/plants. Moreover, this paper describes the interactions between root-related microbiomes and rice plants, and further discusses the key factors shaping the rice root-related microbiomes.
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Affiliation(s)
- Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hui-Ling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - San-An Nie
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Xi-En Long
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian Province, China
| | - Gui-Lan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian Province, China
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155
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Aydogan EL, Budich O, Hardt M, Choi YH, Jansen-Willems AB, Moser G, Müller C, Kämpfer P, Glaeser SP. Global warming shifts the composition of the abundant bacterial phyllosphere microbiota as indicated by a cultivation-dependent and -independent study of the grassland phyllosphere of a long-term warming field experiment. FEMS Microbiol Ecol 2020; 96:5835220. [DOI: 10.1093/femsec/fiaa087] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 05/08/2020] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
The leaf-colonizing bacterial microbiota was studied in a long-term warming experiment on a permanent grassland, which had been continuously exposed to increased surface temperature (+2°C) for more than six years. Two abundant plant species, Arrhenatherum elatius and Galium album, were studied. Surface warming reduced stomata opening and changed leaf metabolite profiles. Leaf surface colonization and the concentration of leaf-associated bacterial cells were not affected. However, bacterial 16S ribosomal RNA (rRNA) gene amplicon Illumina sequencing showed significant temperature effects on the plant species-specific phyllosphere microbiota. Warming partially affected the concentrations of cultured bacteria and had a significant effect on the composition of most abundant cultured plant species-specific bacteria. The abundance of Sphingomonas was significantly reduced. Sphingomonas isolates from warmed plots represented different phylotypes, had different physiological traits and were better adapted to higher temperatures. Among Methylobacterium isolates, a novel phylotype with a specific mxaFtype was cultured from plants of warmed plots while the most abundant phylotype cultured from control plots was strongly reduced. This study clearly showed a correlation of long-term surface warming with changes in the plant physiology and the development of a physiologically and genetically adapted phyllosphere microbiota.
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Affiliation(s)
- Ebru L Aydogan
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Olga Budich
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Martin Hardt
- Biomedical Research Center Seltersberg – Imaging Unit, Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Anne B Jansen-Willems
- Institute of Plant Ecology (IFZ), Justus Liebig University Giessen, D-39392 Giessen, Germany
| | - Gerald Moser
- Institute of Plant Ecology (IFZ), Justus Liebig University Giessen, D-39392 Giessen, Germany
| | - Christoph Müller
- Institute of Plant Ecology (IFZ), Justus Liebig University Giessen, D-39392 Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, D04V1W8 Dublin, Ireland
| | - Peter Kämpfer
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Stefanie P Glaeser
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
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156
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Bao L, Cai W, Cao J, Zhang X, Liu J, Chen H, Wei Y, Zhuang X, Zhuang G, Bai Z. Microbial community overlap between the phyllosphere and rhizosphere of three plants from Yongxing Island, South China Sea. Microbiologyopen 2020; 9:e1048. [PMID: 32315123 PMCID: PMC7349147 DOI: 10.1002/mbo3.1048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/24/2020] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
Phyllosphere and rhizosphere are unique and wide‐ranging habitats that harbor various microbial communities, which influence plant growth and health, and the productivity of the ecosystems. In this study, we characterized the shared microbiome of the phyllosphere and rhizosphere among three plants (Ipomoea pes‐caprae, Wedelia chinensis, and Cocos nucifera), to obtain an insight into the relationships between bacteria (including diazotrophic bacteria) and fungi, present on these host plants. Quantitative PCR showed that the abundances of the microbiome in the soil samples were significantly higher than those in the phyllosphere samples, though there was an extremely low abundance of fungi in bulk soil. High‐throughput sequencing showed that the alpha‐diversity of bacteria and fungi was higher in the rhizosphere than the phyllosphere samples associated with the same plant, while there was no obvious shift in the alpha‐diversity of diazotrophic communities between all the tested phyllosphere and soil samples. Results of the microbial composition showed that sample‐specific bacteria and fungi were found among the phyllosphere and rhizosphere of the different host plants. About 10%–27% of bacteria, including diazotrophs, and fungi overlapped between the phyllosphere and the rhizosphere of these host plants. No significant difference in microbial community structure was found among the tested rhizosphere samples, and soil properties had a higher influence on the soil microbial community structures than the host plant species.
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Affiliation(s)
- Lijun Bao
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Wenyang Cai
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jianxi Cao
- Tangshan Ecology and Environment Bureau Fengrun Branch, Tangshan, China
| | - Xiaofen Zhang
- Institute of Naval Engineering Design, Naval Research Academy, Beijing, China
| | - Jinhong Liu
- Institute of Naval Engineering Design, Naval Research Academy, Beijing, China
| | - Hao Chen
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yuansong Wei
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Guoqiang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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157
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Yan M, Zeng X, Wang J, Meharg AA, Meharg C, Tang X, Zhang L, Bai L, Zhang J, Su S. Dissolved organic matter differentially influences arsenic methylation and volatilization in paddy soils. JOURNAL OF HAZARDOUS MATERIALS 2020; 388:121795. [PMID: 31818673 DOI: 10.1016/j.jhazmat.2019.121795] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/15/2019] [Accepted: 11/29/2019] [Indexed: 06/10/2023]
Abstract
The effect of dissolved organic matter (DOM), derived from composted pig manure or rice straw, on arsenic methylation and subsequent biovolatilization in paddy soils was investigated. Arsine production following pig manure DOM application was 2.7- and 9.6-fold higher than that of soils treated with rice straw DOM and the control, respectively. Trimethylarsine was the dominant arsine at 54 %, followed by dimethylarsine at 22 %, arsine at 21 %, and monomethylarsine at 3 %. The copy numbers of the total and As-methylating bacteria were significantly enhanced in paddy soils treated with DOM. Pig manure DOM altered soil bacterial profile by increasing the OTU number of As methylation-inducing bacteria, such as Proteobacteria, Bacteroidetes, Geobacter, Sphingomonas, Streptomyces, and Rhodopseudomonas, thereby promoting As volatilization and methylation in paddy soils. The higher relative content of alkyl-C, N-alkyl C, and carboxyl-C in pig manure DOM was responsible for the increase in total and arsM-carrying bacteria in paddy soils, leading to enhanced As methylation. These observations will promote a better understanding of the role of DOM in mediating As methylation and volatilization, along with how organic fertilization affects straighthead disorder of rice, a condition caused by methylated arsenic species.
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Affiliation(s)
- Mengmeng Yan
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing, 100081, PR China; School of Geography & Environmental Science, Guizhou Normal University, Guiyang, 550001, Guizhou Province, PR China
| | - Xibai Zeng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing, 100081, PR China
| | - Ji Wang
- School of Geography & Environmental Science, Guizhou Normal University, Guiyang, 550001, Guizhou Province, PR China
| | - Andy A Meharg
- Institute for Global Food Security, Queen's University Belfast, Biological Sciences, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Caroline Meharg
- Institute for Global Food Security, Queen's University Belfast, Biological Sciences, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Xianjing Tang
- Institute of Soil and Water Resources and Environmental Science, Zhejiang University, Hangzhou, 310058, PR China
| | - Lili Zhang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, PR China
| | - Lingyu Bai
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing, 100081, PR China
| | - Junzheng Zhang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, Harbin, 150080, PR China
| | - Shiming Su
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing, 100081, PR China.
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158
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Zverev AO, Pershina EV, Shapkin VM, Kichko AK, Mitrofanova OP, Kobylyanskii VD, Yuzikhin OS, Belimov AA, Andronov EE. Molecular Analysis of the Rhizosphere Microbial Communities from Gramineous Plants Grown on Contrasting Soils. Microbiology (Reading) 2020. [DOI: 10.1134/s002626172001018x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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159
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Abstract
Geobacter and Pseudomonas spp. cohabit many of the same environments, where Geobacter spp. often dominate. Both bacteria are capable of extracellular electron transfer (EET) and play important roles in biogeochemical cycling. Although they recently in 2017 were demonstrated to undergo direct interspecies electron transfer (DIET) with one another, the genetic evolution of this syntrophic interaction has not been examined. Here, we use whole-genome sequencing of the cocultures before and after adaptive evolution to determine whether genetic selection is occurring. We also probe their interaction on a temporal level and determine whether their interaction dynamics change over the course of adaptive evolution. This study brings to light the multifaceted nature of interactions between just two microorganisms within a controlled environment and will aid in improving metabolic models of microbial communities comprising these two bacteria. Interactions between microorganisms in mixed communities are highly complex, being either syntrophic, neutral, predatory, or competitive. Evolutionary changes can occur in the interaction dynamics between community members as they adapt to coexistence. Here, we report that the syntrophic interaction between Geobacter sulfurreducens and Pseudomonas aeruginosa coculture change in their dynamics over evolutionary time. Specifically, Geobacter sp. dominance increases with adaptation within the cocultures, as determined through quantitative PCR and fluorescence in situ hybridization. This suggests a transition from syntrophy to competition and demonstrates the rapid adaptive capacity of Geobacter spp. to dominate in cocultures with P. aeruginosa. Early in coculture establishment, two single-nucleotide variants in the G. sulfurreducensfabI and tetR genes emerged that were strongly selected for throughout coculture evolution with P. aeruginosa phenazine wild-type and phenazine-deficient mutants. Sequential window acquisition of all theoretical spectra-mass spectrometry (SWATH-MS) proteomics revealed that the tetR variant cooccurred with the upregulation of an adenylate cyclase transporter, CyaE, and a resistance-nodulation-division (RND) efflux pump notably known for antibiotic efflux. To determine whether antibiotic production was driving the increased expression of the multidrug efflux pump, we tested Pseudomonas-derived phenazine-1-carboxylic acid (PHZ-1-CA) for its potential to inhibit Geobacter growth and drive selection of the tetR and fabI genetic variants. Despite its inhibitory properties, PHZ-1-CA did not drive variant selection, indicating that other antibiotics may drive overexpression of the efflux pump and CyaE or that a novel role exists for these proteins in the context of this interaction.
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160
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Agrahari RK, Singh P, Koyama H, Panda SK. Plant-microbe Interactions for Sustainable Agriculture in the Post-genomic Era. Curr Genomics 2020; 21:168-178. [PMID: 33071611 PMCID: PMC7521031 DOI: 10.2174/1389202921999200505082116] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/21/2020] [Accepted: 03/30/2020] [Indexed: 11/22/2022] Open
Abstract
Plant-microbe interactions are both symbiotic and antagonistic, and the knowledge of both these interactions is equally important for the progress of agricultural practice and produce. This review gives an insight into the recent advances that have been made in the plant-microbe interaction study in the post-genomic era and the application of those for enhancing agricultural production. Adoption of next-generation sequencing (NGS) and marker assisted selection of resistant genes in plants, equipped with cloning and recombination techniques, has progressed the techniques for the development of resistant plant varieties by leaps and bounds. Genome-wide association studies (GWAS) of both plants and microbes have made the selection of desirable traits in plants and manipulation of the genomes of both plants and microbes effortless and less time-consuming. Stress tolerance in plants has been shown to be accentuated by association of certain microorganisms with the plant, the study and application of the same have helped develop stress-resistant varieties of crops. Beneficial microbes associated with plants are being extensively used for the development of microbial consortia that can be applied directly to the plants or the soil. Next-generation sequencing approaches have made it possible to identify the function of microbes associated in the plant microbiome that are both culturable and non-culturable, thus opening up new doors and possibilities for the use of these huge resources of microbes that can have a potential impact on agriculture.
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Affiliation(s)
| | | | | | - Sanjib Kumar Panda
- Address correspondence to this author at the Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH 8, Bandarsindri, Ajmer 305817, Rajasthan, India; Tel: 9435370608; E-mail:
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161
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Zervas A, Zeng Y, Madsen AM, Hansen LH. Genomics of Aerobic Photoheterotrophs in Wheat Phyllosphere Reveals Divergent Evolutionary Patterns of Photosynthetic Genes in Methylobacterium spp. Genome Biol Evol 2020; 11:2895-2908. [PMID: 31626703 PMCID: PMC6798729 DOI: 10.1093/gbe/evz204] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2019] [Indexed: 01/02/2023] Open
Abstract
Phyllosphere is a habitat to a variety of viruses, bacteria, fungi, and other microorganisms, which play a fundamental role in maintaining the health of plants and mediating the interaction between plants and ambient environments. A recent addition to this catalogue of microbial diversity was the aerobic anoxygenic phototrophs (AAPs), a group of widespread bacteria that absorb light through bacteriochlorophyll α (BChl a) to produce energy without fixing carbon or producing molecular oxygen. However, culture representatives of AAPs from phyllosphere and their genome information are lacking, limiting our capability to assess their potential ecological roles in this unique niche. In this study, we investigated the presence of AAPs in the phyllosphere of a winter wheat (Triticum aestivum L.) in Denmark by employing bacterial colony based infrared imaging and MALDI-TOF mass spectrometry (MS) techniques. A total of ∼4,480 colonies were screened for the presence of cellular BChl a, resulting in 129 AAP isolates that were further clustered into 21 groups based on MALDI-TOF MS profiling, representatives of which were sequenced using the Illumina NextSeq and Oxford Nanopore MinION platforms. Seventeen draft and four complete genomes of AAPs were assembled belonging in Methylobacterium, Rhizobium, Roseomonas, and a novel Alsobacter. We observed a diverging pattern in the evolutionary rates of photosynthesis genes among the highly homogenous AAP strains of Methylobacterium (Alphaproteobacteria), highlighting an ongoing genomic innovation at the gene cluster level.
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Affiliation(s)
- Athanasios Zervas
- Section of Environmental Microbiology and Biotechnology, Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Yonghui Zeng
- Section of Environmental Microbiology and Biotechnology, Department of Environmental Science, Aarhus University, Roskilde, Denmark.,Aarhus Institute of Advanced Studies, Aarhus University, Denmark
| | - Anne Mette Madsen
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Lars H Hansen
- Section of Environmental Microbiology and Biotechnology, Department of Environmental Science, Aarhus University, Roskilde, Denmark.,Environmental Microbial Genomics Group, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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Miebach M, Schlechter RO, Clemens J, Jameson PE, Remus-Emsermann MN. Litterbox-A gnotobiotic Zeolite-Clay System to Investigate Arabidopsis-Microbe Interactions. Microorganisms 2020; 8:E464. [PMID: 32218313 PMCID: PMC7232341 DOI: 10.3390/microorganisms8040464] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/19/2020] [Accepted: 03/23/2020] [Indexed: 11/21/2022] Open
Abstract
Plants are colonised by millions of microorganisms representing thousands of species withvarying effects on plant growth and health. The microbial communities found on plants arecompositionally consistent and their overall positive effect on the plant is well known. However,the effects of individual microbiota members on plant hosts and vice versa, as well as the underlyingmechanisms, remain largely unknown. Here, we describe "Litterbox", a highly controlled system toinvestigate plant-microbe interactions. Plants were grown gnotobiotically, otherwise sterile, onzeolite-clay, a soil replacement that retains enough moisture to avoid subsequent watering.Litterbox-grown plants resemble greenhouse-grown plants more closely than agar-grown plantsand exhibit lower leaf epiphyte densities (106 cfu/g), reflecting natural conditions. Apolydimethylsiloxane (PDMS) sheet was used to cover the zeolite, significantly lowering thebacterial load in the zeolite and rhizosphere. This reduced the likelihood of potential systemicresponses in leaves induced by microbial rhizosphere colonisation. We present results of exampleexperiments studying the transcriptional responses of leaves to defined microbiota members andthe spatial distribution of bacteria on leaves. We anticipate that this versatile and affordable plantgrowth system will promote microbiota research and help in elucidating plant-microbe interactionsand their underlying mechanisms.
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Affiliation(s)
- Moritz Miebach
- School of Biological Sciences, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8053, New Zealand; (M.M.); (R.O.S.); (J.C.); (P.E.J.)
| | - Rudolf O. Schlechter
- School of Biological Sciences, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8053, New Zealand; (M.M.); (R.O.S.); (J.C.); (P.E.J.)
- Biomolecular Interaction Centre, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8053, New Zealand
| | - John Clemens
- School of Biological Sciences, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8053, New Zealand; (M.M.); (R.O.S.); (J.C.); (P.E.J.)
| | - Paula E. Jameson
- School of Biological Sciences, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8053, New Zealand; (M.M.); (R.O.S.); (J.C.); (P.E.J.)
| | - Mitja N.P. Remus-Emsermann
- School of Biological Sciences, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8053, New Zealand; (M.M.); (R.O.S.); (J.C.); (P.E.J.)
- Biomolecular Interaction Centre, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8053, New Zealand
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163
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Macey MC, Pratscher J, Crombie AT, Murrell JC. Impact of plants on the diversity and activity of methylotrophs in soil. MICROBIOME 2020; 8:31. [PMID: 32156318 PMCID: PMC7065363 DOI: 10.1186/s40168-020-00801-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/10/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Methanol is the second most abundant volatile organic compound in the atmosphere, with the majority produced as a metabolic by-product during plant growth. There is a large disparity between the estimated amount of methanol produced by plants and the amount which escapes to the atmosphere. This may be due to utilisation of methanol by plant-associated methanol-consuming bacteria (methylotrophs). The use of molecular probes has previously been effective in characterising the diversity of methylotrophs within the environment. Here, we developed and applied molecular probes in combination with stable isotope probing to identify the diversity, abundance and activity of methylotrophs in bulk and in plant-associated soils. RESULTS Application of probes for methanol dehydrogenase genes (mxaF, xoxF, mdh2) in bulk and plant-associated soils revealed high levels of diversity of methylotrophic bacteria within the bulk soil, including Hyphomicrobium, Methylobacterium and members of the Comamonadaceae. The community of methylotrophic bacteria captured by this sequencing approach changed following plant growth. This shift in methylotrophic diversity was corroborated by identification of the active methylotrophs present in the soils by DNA stable isotope probing using 13C-labelled methanol. Sequencing of the 16S rRNA genes and construction of metagenomes from the 13C-labelled DNA revealed members of the Methylophilaceae as highly abundant and active in all soils examined. There was greater diversity of active members of the Methylophilaceae and Comamonadaceae and of the genus Methylobacterium in plant-associated soils compared to the bulk soil. Incubating growing pea plants in a 13CO2 atmosphere revealed that several genera of methylotrophs, as well as heterotrophic genera within the Actinomycetales, assimilated plant exudates in the pea rhizosphere. CONCLUSION In this study, we show that plant growth has a major impact on both the diversity and the activity of methanol-utilising methylotrophs in the soil environment, and thus, the study contributes significantly to efforts to balance the terrestrial methanol and carbon cycle. Video abstract.
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Affiliation(s)
- Michael C. Macey
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, Buckinghamshire MK7 6AA UK
| | - Jennifer Pratscher
- The Lyell Centre, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Research Avenue South, Edinburgh, EH14 4AP UK
| | - Andrew T. Crombie
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
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164
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Yadav AN, Singh J, Rastegari AA, Yadav N. Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications. ACTA ACUST UNITED AC 2020. [PMCID: PMC7123684 DOI: 10.1007/978-3-030-38453-1_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.
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Affiliation(s)
- Ajar Nath Yadav
- Department of Biotechnology, Eternal University, Baru Sahib, Himachal Pradesh India
| | - Joginder Singh
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab India
| | | | - Neelam Yadav
- Gopi Nath PG College, Veer Bahadur Singh Purvanchal University, Ghazipur, Uttar Pradesh India
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165
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Phenotypic diversity of Methylobacterium associated with rice landraces in North-East India. PLoS One 2020; 15:e0228550. [PMID: 32092057 PMCID: PMC7039438 DOI: 10.1371/journal.pone.0228550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/19/2020] [Indexed: 11/19/2022] Open
Abstract
The ecology and distribution of many bacteria is strongly associated with specific eukaryotic hosts. However, the impact of such host association on bacterial ecology and evolution is not well understood. Bacteria from the genus Methylobacterium consume plant-derived methanol, and are some of the most abundant and widespread plant-associated bacteria. In addition, many of these species impact plant fitness. To determine the ecology and distribution of Methylobacterium in nature, we sampled bacteria from 36 distinct rice landraces, traditionally grown in geographically isolated locations in North-East (NE) India. These landraces have been selected for diverse phenotypic traits by local communities, and we expected that the divergent selection on hosts may have also generated divergence in associated Methylobacterium strains. We determined the ability of 91 distinct rice-associated Methylobacterium isolates to use a panel of carbon sources, finding substantial variability in carbon use profiles. Consistent with our expectation, across spatial scales this phenotypic variation was largely explained by host landrace identity rather than geographical factors or bacterial taxonomy. However, variation in carbon utilisation was not correlated with sugar exudates on leaf surfaces, suggesting that bacterial carbon use profiles do not directly determine bacterial colonization across landraces. Finally, experiments showed that at least some rice landraces gain an early growth advantage from their specific phyllosphere-colonizing Methylobacterium strains. Together, our results suggest that landrace-specific host-microbial relationships may contribute to spatial structure in rice-associated Methylobacterium in a natural ecosystem. In turn, association with specific bacteria may provide new ways to preserve and understand diversity in one of the most important food crops of the world.
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166
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Khan AL, Asaf S, M. Abed RM, Ning Chai Y, N. Al-Rawahi A, Mohanta TK, Al-Rawahi A, Schachtman DP, Al-Harrasi A. Rhizosphere Microbiome of Arid Land Medicinal Plants and Extra Cellular Enzymes Contribute to Their Abundance. Microorganisms 2020; 8:microorganisms8020213. [PMID: 32033333 PMCID: PMC7074696 DOI: 10.3390/microorganisms8020213] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 02/07/2023] Open
Abstract
Revealing the unexplored rhizosphere microbiome of plants in arid environments can help in understanding their interactions between microbial communities and plants during harsh growth conditions. Here, we report the first investigation of rhizospheric fungal and bacterial communities of Adenium obesum, Aloe dhufarensis and Cleome austroarabica using next-generation sequencing approaches. A. obesum and A. dhufarensis grows in dry tropical and C. austroarabica in arid conditions of Arabian Peninsula. The results indicated the presence of 121 fungal and 3662 bacterial operational taxonomic units (OTUs) whilst microbial diversity was significantly high in the rhizosphere of A. obesum and A. dhufarensis and low in C. austroarabica. Among fungal phyla, Ascomycota and Basidiomycota were abundantly associated within rhizospheres of all three plants. However, Mucoromycota was only present in the rhizospheres of A. obesum and A. dhufarensis, suggesting a variation in fungal niche on the basis of host and soil types. In case of bacterial communities, Actinobacteria, Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, and Verrucomicrobia were predominant microbial phyla. These results demonstrated varying abundances of microbial structure across different hosts and locations in arid environments. Rhizosphere’s extracellular enzymes analysis revealed varying quantities, where, glucosidase, cellulase, esterase, and 1-aminocyclopropane-1-carboxylate deaminase were significantly higher in the rhizosphere of A. dhufarensis, while phosphatase and indole-acetic acid were highest in the rhizosphere of A. obesum. In conclusion, current findings usher for the first time the core microbial communities in the rhizospheric regions of three arid plants that vary greatly with location, host and soil conditions, and suggest the presence of extracellular enzymes could help in maintaining plant growth during the harsh environmental conditions.
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Affiliation(s)
- Abdul Latif Khan
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
- Correspondence: (A.L.K.); (A.A.-H.)
| | - Sajjad Asaf
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
| | - Raeid M. M. Abed
- Sultan Qaboos University, College of Science, Biology Department, Muscat 123, Sultanate of Oman;
| | - Yen Ning Chai
- Department of Agronomy and Horticulture and Centre for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (Y.N.C.); (D.P.S.)
| | - Ahmed N. Al-Rawahi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
| | - Tapan Kumar Mohanta
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
| | - Daniel P. Schachtman
- Department of Agronomy and Horticulture and Centre for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (Y.N.C.); (D.P.S.)
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
- Correspondence: (A.L.K.); (A.A.-H.)
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167
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Yu AO, Leveau JHJ, Marco ML. Abundance, diversity and plant-specific adaptations of plant-associated lactic acid bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:16-29. [PMID: 31573142 DOI: 10.1111/1758-2229.12794] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
Lactic acid bacteria (LAB) are essential for many fruit, vegetable and grain food and beverage fermentations. However, the numbers, diversity and plant-specific adaptions of LAB found on plant tissues prior to the start of those fermentations are not well understood. When measured, these bacteria have been recovered from the aerial surfaces of plants in a range from <10 CFU g-1 to over 108.5 CFU g-1 of plant tissue and in lower quantities from the soil and rhizosphere. Plant-associated LAB include well-known generalist taxa such as Lactobacillus plantarum and Leuconostoc mesenteroides, which are essential for numerous food and beverage fermentations. Other plant-associated LAB encompass specialist taxa such as Lactobacillus florum and Fructobacillus, many of which were discovered relatively recently and their significance on plants and in foods is not yet recognized. LAB recovered from plants possess the capacity to consume plant sugars, detoxify phenolic compounds and tolerate the numerous biotic and abiotic stresses common to plant surfaces. Although most generalist and some specialist LAB grow rapidly in food and beverages fermentations and can cause spoilage of fresh and fermented fruits and vegetables, the importance of living plants as habitats for these bacteria and LAB contributions to plant microbiomes remain to be shown.
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Affiliation(s)
- Annabelle O Yu
- Department of Food Science & Technology, University of California Davis, Davis, CA, USA
| | - Johan H J Leveau
- Department of Plant Pathology, University of California Davis, Davis, CA, USA
| | - Maria L Marco
- Department of Food Science & Technology, University of California Davis, Davis, CA, USA
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168
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O'Banion BS, O'Neal L, Alexandre G, Lebeis SL. Bridging the Gap Between Single-Strain and Community-Level Plant-Microbe Chemical Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:124-134. [PMID: 31687914 DOI: 10.1094/mpmi-04-19-0115-cr] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Although the influence of microbiomes on the health of plant hosts is evident, specific mechanisms shaping the structure and dynamics of microbial communities in the phyllosphere and rhizosphere are only beginning to become clear. Traditionally, plant-microbe interactions have been studied using cultured microbial isolates and plant hosts but the rising use of 'omics tools provides novel snapshots of the total complex community in situ. Here, we discuss the recent advances in tools and techniques used to monitor plant-microbe interactions and the chemical signals that influence these relationships in above- and belowground tissues. Particularly, we highlight advances in integrated microscopy that allow observation of the chemical exchange between individual plant and microbial cells, as well as high-throughput, culture-independent approaches to investigate the total genetic and metabolic contribution of the community. The chemicals discussed have been identified as relevant signals across experimental spectrums. However, mechanistic insight into the specific interactions mediated by many of these chemicals requires further testing. Experimental designs that attempt to bridge the gap in biotic complexity between single strains and whole communities will advance our understanding of the chemical signals governing plant-microbe associations in the rhizosphere and phyllosphere.
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Affiliation(s)
- Bridget S O'Banion
- Department of Microbiology, University of Tennessee, Knoxville, TN, U.S.A
| | - Lindsey O'Neal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee
| | - Gladys Alexandre
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee
| | - Sarah L Lebeis
- Department of Microbiology, University of Tennessee, Knoxville, TN, U.S.A
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169
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Revealing the Variation and Stability of Bacterial Communities in Tomato Rhizosphere Microbiota. Microorganisms 2020; 8:microorganisms8020170. [PMID: 31991727 PMCID: PMC7074737 DOI: 10.3390/microorganisms8020170] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/18/2020] [Accepted: 01/22/2020] [Indexed: 12/14/2022] Open
Abstract
Microorganisms that colonize the plant rhizosphere can contribute to plant health, growth and productivity. Although the importance of the rhizosphere microbiome is known, we know little about the underlying mechanisms that drive microbiome assembly and composition. In this study, the variation, assembly and composition of rhizobacterial communities in 11 tomato cultivars, combined with one cultivar in seven different sources of soil and growing substrate, were systematically investigated. The tomato rhizosphere microbiota was dominated by bacteria from the phyla Proteobacteria, Bacteroidetes, and Acidobacteria, mainly comprising Rhizobiales, Xanthomonadales, Burkholderiales, Nitrosomonadales, Myxococcales, Sphingobacteriales, Cytophagales and Acidobacteria subgroups. The bacterial community in the rhizosphere microbiota of the samples in the cultivar experiment mostly overlapped with that of tomato cultivar MG, which was grown in five natural field soils, DM, JX, HQ, QS and XC. The results supported the hypothesis that tomato harbors largely conserved communities and compositions of rhizosphere microbiota that remains consistent in different cultivars of tomato and even in tomato cultivar grown in five natural field soils. However, significant differences in OTU richness (p < 0.0001) and bacterial diversity (p = 0.0014 < 0.01) were observed among the 7 different sources of soil and growing substrate. Two artificial commercial nutrient soils, HF and CF, resulted in a distinct tomato rhizosphere microbiota in terms of assembly and core community compared with that observed in natural field soils. PERMANOVA of beta diversity based on the combined data from the cultivar and soil experiments demonstrated that soil (growing substrate) and plant genotype (cultivar) had significant impacts on the rhizosphere microbial communities of tomato plants (soil, F = 22.29, R2 = 0.7399, p < 0.001; cultivar, F = 2.04, R2 = 0.3223, p = 0.008). Of these two factors, soil explained a larger proportion of the compositional variance in the tomato rhizosphere microbiota. The results demonstrated that the assembly process of rhizosphere bacterial communities was collectively influenced by soil, including the available bacterial sources and biochemical properties of the rhizosphere soils, and plant genotype.
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170
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Flores-Núñez VM, Fonseca-García C, Desgarennes D, Eloe-Fadrosh E, Woyke T, Partida-Martínez LP. Functional Signatures of the Epiphytic Prokaryotic Microbiome of Agaves and Cacti. Front Microbiol 2020; 10:3044. [PMID: 32010100 PMCID: PMC6978686 DOI: 10.3389/fmicb.2019.03044] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/17/2019] [Indexed: 01/07/2023] Open
Abstract
Microbial symbionts account for survival, development, fitness and evolution of eukaryotic hosts. These microorganisms together with their host form a biological unit known as holobiont. Recent studies have revealed that the holobiont of agaves and cacti comprises a diverse and structured microbiome, which might be important for its adaptation to drylands. Here, we investigated the functional signatures of the prokaryotic communities of the soil and the episphere, that includes the rhizosphere and phyllosphere, associated with the cultivated Agave tequilana and the native and sympatric Agave salmiana, Opuntia robusta and Myrtillocactus geometrizans by mining shotgun metagenomic data. Consistent with previous phylogenetic profiling, we found that Proteobacteria, Actinobacteria and Firmicutes were the main represented phyla in the episphere of agaves and cacti, and that clustering of metagenomes correlated with the plant compartment. In native plants, genes related to aerobic anoxygenic phototrophy and photosynthesis were enriched in the phyllosphere and soil, while genes coding for biofilm formation and quorum sensing were enriched in both epiphytic communities. In the episphere of cultivated A. tequilana fewer genes were identified, but they belonged to similar pathways than those found in native plants. A. tequilana showed a depletion in several genes belonging to carbon metabolism, secondary metabolite biosynthesis and xenobiotic degradation suggesting that its lower microbial diversity might be linked to functional losses. However, this species also showed an enrichment in biofilm and quorum sensing in the epiphytic compartments, and evidence for nitrogen fixation in the rhizosphere. Aerobic anoxygenic phototrophic markers were represented by Rhizobiales (Methylobacterium) and Rhodospirillales (Belnapia) in the phyllosphere, while photosystem genes were widespread in Bacillales and Cyanobacteria. Nitrogen fixation and biofilm formation genes were mostly related to Proteobacteria. These analyses support the idea of niche differentiation in the rhizosphere and phyllosphere of agaves and cacti and shed light on the potential mechanisms by which epiphytic microbial communities survive and colonize plants of arid and semiarid ecosystems. This study establishes a guideline for testing the relevance of the identified functional traits on the microbial community and the plant fitness.
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Affiliation(s)
- Víctor M Flores-Núñez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | - Citlali Fonseca-García
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico.,Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Damaris Desgarennes
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico.,Red de Biodiversidad y Sistemática, Instituto de Ecología, Xalapa, Mexico
| | - Emiley Eloe-Fadrosh
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Tanja Woyke
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Laila P Partida-Martínez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
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171
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Lai K, Thai Nguyen N, Miwa H, Yasuda M, Huu Nguyen H, Okazaki S. Diversity of Methylobacterium spp. in the Rice of the Vietnamese Mekong Delta. Microbes Environ 2020; 35:ME19111. [PMID: 31969531 PMCID: PMC7104282 DOI: 10.1264/jsme2.me19111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/27/2019] [Indexed: 11/12/2022] Open
Abstract
The Vietnamese Mekong delta is one of the largest rice-producing areas globally. Methylobacterium spp. are persistent colonizers of the rice plant and exert beneficial effects on plant growth and health. Sixty-one Methylobacterium strains belonging to seven species were predominantly isolated from the phyllosphere of rice cultivated in six Mekong delta provinces. Inoculation tests revealed that some strains exhibited plant growth-promoting activity. Moreover, three strains possessed the novel characteristics of inducing leaf bleaching and killing rice seedlings. These results revealed the complex diversity of Methylobacterium in Mekong delta rice and that healthy and productive rice cultivation requires a proper balance of Methylobacterium.
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Affiliation(s)
- Khoa Lai
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Saiwaicho 3–5–8, Fuchu, Tokyo 183–8509, Japan
- National Agro-Forestry-Fisheries Quality Assurance Department branch 4, 271—To Ngoc Van St, Linh Dong ward, Thu Duc district, Ho Chi Minh City, Vietnam
| | - Ngoc Thai Nguyen
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwaicho 3–5–8, Fuchu, Tokyo 183–8509, Japan
| | - Hiroki Miwa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwaicho 3–5–8, Fuchu, Tokyo 183–8509, Japan
| | - Michiko Yasuda
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwaicho 3–5–8, Fuchu, Tokyo 183–8509, Japan
| | - Hiep Huu Nguyen
- Department of Microbial Biotechnology, Biotechnology Research and Development Institute, Cantho University, II—St 3/2, Ninh Kieu ward, Cantho City, Vietnam
| | - Shin Okazaki
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Saiwaicho 3–5–8, Fuchu, Tokyo 183–8509, Japan
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwaicho 3–5–8, Fuchu, Tokyo 183–8509, Japan
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172
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Bacterial communities in the rhizosphere, phyllosphere and endosphere of tomato plants. PLoS One 2019; 14:e0223847. [PMID: 31703074 PMCID: PMC6839845 DOI: 10.1371/journal.pone.0223847] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/30/2019] [Indexed: 11/19/2022] Open
Abstract
Plants harbor diverse bacterial communities, which play crucial roles in plant health and growth, in their rhizosphere, phyllosphere and endosphere. Tomato is an important model for studying plant-microbe interactions, but comparison of its associated bacterial community is still lacking. In this study, using Illumina sequencing of 16S rRNA amplicons, we characterized and compared the bacterial size and community from rootzone soil as well as the rhizosphere, phyllosphere and endosphere of roots, stems, leaves, fruits and seeds of tomato plants that were grown in greenhouse conditions. Habitat (soil, phyllospheric, and endophytic) structured the community. The bacterial communities from the soil-type samples (rootzone soil and rhizosphere) showed the highest richness and diversity. The lowest bacterial diversity occurred in the phyllospheric samples, while the lowest richness occurred in the endosphere. Among the endophytic samples, both bacterial diversity and richness varied in different tissues, with the highest values in roots. The most abundant phyla in the tomato-associated community was Proteobacteria, with the exception of the seeds and jelly, where both Proteobacteria and Firmicutes were dominant. At the genus level, the sequences of Pseudomonas and Acinetobacter were prevalent in the rhizosphere, and in the phyllosphere, more than 97% of the sequences were assigned to Acinetobacter. For the endophytes, Acinetobacter, Enterobacter, and Pseudomonas were the abundant genera in the roots, stems and leaves. In the fruits, the bacterial endophytes varied in different compartments, with Enterobacter being enriched in the pericarp and seeds, Acinetobacter in the placenta, and Weissella in the jelly. The present data provide a comprehensive description of the tomato-associated bacterial community and will be useful for better understanding plant-microbe interactions and selecting suitable bacterial taxa for tomato production.
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Finkel OM, Salas-González I, Castrillo G, Spaepen S, Law TF, Teixeira PJPL, Jones CD, Dangl JL. The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response. PLoS Biol 2019; 17:e3000534. [PMID: 31721759 PMCID: PMC6876890 DOI: 10.1371/journal.pbio.3000534] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/25/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
Abstract
Phosphate starvation response (PSR) in nonmycorrhizal plants comprises transcriptional reprogramming resulting in severe physiological changes to the roots and shoots and repression of plant immunity. Thus, plant-colonizing microorganisms-the plant microbiota-are exposed to direct influence by the soil's phosphorus (P) content itself as well as to the indirect effects of soil P on the microbial niches shaped by the plant. The individual contribution of these factors to plant microbiota assembly remains unknown. To disentangle these direct and indirect effects, we planted PSR-deficient Arabidopsis mutants in a long-term managed soil P gradient and compared the composition of their shoot and root microbiota to wild-type plants across different P concentrations. PSR-deficiency had a larger effect on the composition of both bacterial and fungal plant-associated microbiota than soil P concentrations in both roots and shoots. To dissect plant-microbe interactions under variable P conditions, we conducted a microbiota reconstitution experiment. Using a 185-member bacterial synthetic community (SynCom) across a wide P concentration gradient in an agar matrix, we demonstrated a shift in the effect of bacteria on the plant from a neutral or positive interaction to a negative one, as measured by rosette size. This phenotypic shift was accompanied by changes in microbiota composition: the genus Burkholderia was specifically enriched in plant tissue under P starvation. Through a community drop-out experiment, we demonstrated that in the absence of Burkholderia from the SynCom, plant shoots accumulated higher ortophosphate (Pi) levels than shoots colonized with the full SynCom but only under Pi starvation conditions. Therefore, Pi-stressed plants are susceptible to colonization by latent opportunistic competitors found within their microbiome, thus exacerbating the plant's Pi starvation.
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Affiliation(s)
- Omri M. Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gabriel Castrillo
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Stijn Spaepen
- Department Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Theresa F. Law
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Paulo José Pereira Lima Teixeira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Corbin D. Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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174
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Cordero J, de Freitas JR, Germida JJ. Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada. Can J Microbiol 2019; 66:71-85. [PMID: 31658427 DOI: 10.1139/cjm-2019-0330] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rhizosphere and root associated bacteria are key components of plant microbiomes and influence crop production. In sustainable agriculture, it is important to investigate bacteria diversity in various plant species and how edaphic factors influence the bacterial microbiome. In this study, we used high-throughput sequencing to assess bacterial communities associated with the rhizosphere and root interior of canola, wheat, field pea, and lentil grown at four locations in Saskatchewan, Canada. Rhizosphere bacteria communities exhibited distinct profiles among crops and sampling locations. However, each crop was associated with distinct root endophytic bacterial communities, suggesting that crop species may influence the selection of root bacterial microbiome. Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla in the root interior, whereas Gemmatimonadetes, Firmicutes, and Acidobacteria were prevalent in the rhizosphere soil. Pseudomonas and Stenotrophomonas were predominant in the rhizosphere and root interior, whereas Acinetobacter, Arthrobacter, Rhizobium, Streptomyces, Variovorax, and Xanthomonas were dominant in the root interior of all crops. The relative abundance of specific bacterial groups in the rhizosphere correlated with soil pH and silt and organic matter contents; however, there was no correlation between root endophytes and analyzed soil properties. These results suggest that the root microbiome may be modulated by plant factors rather than soil characteristics.
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Affiliation(s)
- Jorge Cordero
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada.,Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - J Renato de Freitas
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada.,Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - James J Germida
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
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175
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Lucaciu R, Pelikan C, Gerner SM, Zioutis C, Köstlbacher S, Marx H, Herbold CW, Schmidt H, Rattei T. A Bioinformatics Guide to Plant Microbiome Analysis. FRONTIERS IN PLANT SCIENCE 2019; 10:1313. [PMID: 31708944 PMCID: PMC6819368 DOI: 10.3389/fpls.2019.01313] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/20/2019] [Indexed: 05/18/2023]
Abstract
Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.
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Affiliation(s)
| | | | | | | | | | | | | | - Hannes Schmidt
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
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176
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Erythritol as a single carbon source improves cultural isolation of Burkholderia pseudomallei from rice paddy soils. PLoS Negl Trop Dis 2019; 13:e0007821. [PMID: 31634353 PMCID: PMC6822774 DOI: 10.1371/journal.pntd.0007821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/31/2019] [Accepted: 10/01/2019] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Isolation of the soil bacterium Burkholderia pseudomallei from tropical environments is important to generate a global risk map for man and animals to acquire the infectious disease melioidosis. There is increasing evidence, that the currently recommended soil culture protocol using threonine-basal salt solution with colistin (TBSS-C50) for enrichment of B. pseudomallei and Ashdown agar for subsequent subculture lacks sensitivity. We therefore investigated, if the otherwise rarely encountered erythritol catabolism of B. pseudomallei might be exploited to improve isolation of this bacterium from soil. METHODOLOGY/PRINCIPAL FINDINGS Based on TBSS-C50, we designed a new colistin-containing medium with erythritol as the single carbon source (EM). This medium was validated in various culture protocols by analyzing 80 soil samples from 16 different rice fields in Vietnam. B. pseudomallei enrichment was determined in all culture supernatants by a specific quantitative PCR (qPCR) targeting the type three secretion system 1. 51 out of 80 (63.8%) soil samples gave a positive qPCR signal in at least one of the culture conditions. We observed a significantly higher enrichment shown by lower median cycle threshold values for B. pseudomallei in a two-step culture with TBSS-C50 for 48 h followed by EM for 96h compared to single cultures in TBSS-C50 for either 48h or 144h (p<0.0001, respectively). Accordingly, B. pseudomallei could be isolated on Ashdown agar in 58.8% (30/51) of samples after subcultures from our novel two-step enrichment culture compared to only 9.8% (5/51) after standard enrichment with TBSS-C50 for 48h (p<0.0001) or 25.5% (13/51; p<0.01) after TBSS-C50 for 144h. CONCLUSIONS/SIGNIFICANCE In the present study, we show that specific exploitation of B. pseudomallei metabolic capabilities in enrichment protocols leads to a significantly improved isolation rate of this pathogen from soil compared to established standard procedures. Our new culture method might help to facilitate the creation of environmental risk maps for melioidosis in the future.
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177
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Shyntum DY, Nkomo NP, Shingange NL, Gricia AR, Bellieny-Rabelo D, Moleleki LN. The Impact of Type VI Secretion System, Bacteriocins and Antibiotics on Bacterial Competition of Pectobacterium carotovorum subsp. brasiliense and the Regulation of Carbapenem Biosynthesis by Iron and the Ferric-Uptake Regulator. Front Microbiol 2019; 10:2379. [PMID: 31681235 PMCID: PMC6813493 DOI: 10.3389/fmicb.2019.02379] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/30/2019] [Indexed: 12/17/2022] Open
Abstract
The complexity of plant microbial communities provides a rich model for investigating biochemical and regulatory strategies involved in interbacterial competition. Within these niches, the soft rot Enterobacteriaceae (SRE) represents an emerging group of plant-pathogens causing soft rot/blackleg diseases resulting in economic losses worldwide in a variety of crops. A preliminary screening using next-generation sequencing of 16S rRNA comparatively analyzing healthy and diseased potato tubers, identified several taxa from Proteobacteria to Firmicutes as potential potato endophytes/plant pathogens. Subsequent to this, a range of molecular and computational techniques were used to determine the contribution of antimicrobial factors such as bacteriocins, carbapenem and type VI secretion system (T6SS), found in an aggressive SRE (Pectobacterium carotovorum subsp. brasiliense strain PBR1692 - Pcb1692) against these endophytes/plant pathogens. The results showed growth inhibition of several Proteobacteria by Pcb1692 depends either on carbapenem or pyocin production. Whereas for targeted Firmicutes, only the Pcb1692 pyocin seems to play a role in growth inhibition. Furthermore, production of carbapenem by Pcb1692 was observably dependent on the presence of environmental iron and oxygen. Additionally, upon deletion of fur, slyA and expI regulators, carbapenem production ceased, implying a complex regulatory mechanism involving these three genes. Finally, the results demonstrated that although T6SS confers no relevant advantage during in vitro competition, a significant attenuation in competition by the mutant strain lacking a functional T6SS was observed in planta. IMPORTANCE Soft rot Enterobacteriaceae (SRE) represents important phytopathogens causing soft rot/blackleg diseases in a variety of crops leading to huge economic losses worldwide. These pathogens have been isolated alongside other bacteria from different environments such as potato tubers, stems, roots and from the soil. In these environments, SREs coexist with other bacteria where they have to compete for scarce nutrients and other resources. In this report, we show that Pectobacterium carotovorum subsp. brasiliense strain PBR1692 - Pcb1692, which represents one of the SREs, inhibits growth of several different bacteria by producing different antimicrobial compounds. These antimicrobial compounds can be secreted inside or outside the plant host, allowing Pcb1692 to effectively colonize different types of ecological niches. By analyzing the genome sequences of several SREs, we show that other SREs likely deploy similar antimicrobials to target other bacteria.
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Affiliation(s)
- Divine Yufetar Shyntum
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Ntombikayise Precious Nkomo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Ntwanano Luann Shingange
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Alessandro Rino Gricia
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Daniel Bellieny-Rabelo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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178
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Janakiev T, Dimkić I, Bojić S, Fira D, Stanković S, Berić T. Bacterial communities of plum phyllosphere and characterization of indigenous antagonistic Bacillus thuringiensis R3/3 isolate. J Appl Microbiol 2019; 128:528-543. [PMID: 31606926 DOI: 10.1111/jam.14488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 12/01/2022]
Abstract
AIMS The characterization of bacterial communities diversity on four local plum cultivars in two phenological stages using culture-dependent and culture-independent methods and screening among culturable plum community for indigenous bacteria active against phytopathogens. METHODS AND RESULTS The bacterial communities associated with leaves and fruits of four local Serbian plum cultivars (Požegača, Ranka, Čačanska Lepotica and Čačanska Rodna) were investigated in two phenological stages during early (May) and late (July) fruit maturation. Metagenomic approach revealed Methylobacterium, Sphingomonas and Hymenobacter as dominant genera. The most frequently isolated representatives with cultivable approach were pseudomonads with Pseudomonas syringae and Pseudomonas graminis, the most likely resident species of plum community. Antagonistic Bacillus thuringiensis R3/3 isolate from plum phyllosphere had ability to produce exoenzymes, reduce the growth of phytopathogenic bacteria in co-culture environment and show quorum quenching activity. CONCLUSIONS Plum cultivar and growth season contribute to the structure of the bacterial community associated with plum. Plum phyllosphere is good source of antagonists effective against phytopathogens. SIGNIFICANCE AND IMPACT OF STUDY Knowledge of bacterial communities on plum will have an impact on studies related to phyllosphere ecology and biocontrol. The indigenous antagonistic isolate, B. thuringiensis R3/3, from plum could be further investigated for its potential use in biological control of plum diseases.
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Affiliation(s)
- T Janakiev
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - I Dimkić
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - S Bojić
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - D Fira
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - S Stanković
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - T Berić
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
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179
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Yoneyama T, Terakado-Tonooka J, Bao Z, Minamisawa K. Molecular Analyses of the Distribution and Function of Diazotrophic Rhizobia and Methanotrophs in the Tissues and Rhizosphere of Non-Leguminous Plants. PLANTS 2019; 8:plants8100408. [PMID: 31614562 PMCID: PMC6843303 DOI: 10.3390/plants8100408] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/26/2019] [Accepted: 10/10/2019] [Indexed: 01/16/2023]
Abstract
Biological nitrogen fixation (BNF) by plants and its bacterial associations represent an important natural system for capturing atmospheric dinitrogen (N2) and processing it into a reactive form of nitrogen through enzymatic reduction. The study of BNF in non-leguminous plants has been difficult compared to nodule-localized BNF in leguminous plants because of the diverse sites of N2 fixation in non-leguminous plants. Identification of the involved N2-fixing bacteria has also been difficult because the major nitrogen fixers were often lost during isolation attempts. The past 20 years of molecular analyses has led to the identification of N2 fixation sites and active nitrogen fixers in tissues and the rhizosphere of non-leguminous plants. Here, we examined BNF hotspots in six reported non-leguminous plants. Novel rhizobia and methanotrophs were found to be abundantly present in the free-living state at sites where carbon and energy sources were predominantly available. In the carbon-rich apoplasts of plant tissues, rhizobia such as Bradyrhizobium spp. microaerobically fix N2. In paddy rice fields, methane molecules generated under anoxia are oxidized by xylem aerenchyma-transported oxygen with the simultaneous fixation of N2 by methane-oxidizing methanotrophs. We discuss the effective functions of the rhizobia and methanotrophs in non-legumes for the acquisition of fixed nitrogen in addition to research perspectives.
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Affiliation(s)
- Tadakatsu Yoneyama
- Department of Applied Biological Chemistry, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
- National Agriculture and Food Research Organization, Kannondai 3-1-1, Tsukuba, Ibaraki 305-8666, Japan.
| | - Junko Terakado-Tonooka
- National Agriculture and Food Research Organization, Kannondai 3-1-1, Tsukuba, Ibaraki 305-8666, Japan.
| | - Zhihua Bao
- School of Ecology and Environment, Inner Mongolia University, 235 West University Blvd., Hohhot 010021, Inner Mongolia, China.
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
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180
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Allen ME, Piefer AJ, Cole SN, Werner JJ, Benziger PT, Grieneisen L, Britton SJ. Characterization of Microbial Communities Populating the Inflorescences of Humulus lupulus L. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2019. [DOI: 10.1080/03610470.2019.1667739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Mary E. Allen
- Biology Department, Hartwick College, Oneonta, NY, U.S.A.
| | | | - Sean N. Cole
- Biologics Department, Q2 Solutions, Ithaca, NY, U.S.A.
| | - Jeffrey J. Werner
- Chemistry Department, State University of New York at Cortland, Cortland, NY, U.S.A.
| | - Peter T. Benziger
- Department of Microbiology and Immunology, Stony Brook University, Stony Book, NY, U.S.A.
| | - Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, U.S.A.
| | - Scott J. Britton
- Research & Development, Brewery Duvel Moortgat, Puurs-Sint-Amands, Belgium
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181
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Schlechter RO, Miebach M, Remus-Emsermann MN. Driving factors of epiphytic bacterial communities: A review. J Adv Res 2019; 19:57-65. [PMID: 31341670 PMCID: PMC6630024 DOI: 10.1016/j.jare.2019.03.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/29/2022] Open
Abstract
Bacteria establish complex, compositionally consistent communities on healthy leaves. Ecological processes such as dispersal, diversification, ecological drift, and selection as well as leaf surface physicochemistry and topology impact community assembly. Since the leaf surface is an oligotrophic environment, species interactions such as competition and cooperation may be major contributors to shape community structure. Furthermore, the plant immune system impacts on microbial community composition, as plant cells respond to bacterial molecules and shape their responses according to the mixture of molecules present. Such tunability of the plant immune network likely enables the plant host to differentiate between pathogenic and non-pathogenic colonisers, avoiding costly immune responses to non-pathogenic colonisers. Plant immune responses are either systemically distributed or locally confined, which in turn affects the colonisation pattern of the associated microbiota. However, how each of these factors impacts the bacterial community is unclear. To better understand this impact, bacterial communities need to be studied at a micrometre resolution, which is the scale that is relevant to the members of the community. Here, current insights into the driving factors influencing the assembly of leaf surface-colonising bacterial communities are discussed, with a special focus on plant host immunity as an emerging factor contributing to bacterial leaf colonisation.
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Affiliation(s)
- Rudolf O. Schlechter
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Moritz Miebach
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mitja N.P. Remus-Emsermann
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
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182
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Thapa SP, Davis EW, Lyu Q, Weisberg AJ, Stevens DM, Clarke CR, Coaker G, Chang JH. The Evolution, Ecology, and Mechanisms of Infection by Gram-Positive, Plant-Associated Bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:341-365. [PMID: 31283433 DOI: 10.1146/annurev-phyto-082718-100124] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Gram-positive bacteria are prominent members of plant-associated microbial communities. Although many are hypothesized to be beneficial, some are causative agents of economically important diseases of crop plants. Because the features of Gram-positive bacteria are fundamentally different relative to those of Gram-negative bacteria, the evolution and ecology as well as the mechanisms used to colonize and infect plants also differ. Here, we discuss recent advances in our understanding of Gram-positive, plant-associated bacteria and provide a framework for future research directions on these important plant symbionts.
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Affiliation(s)
- Shree P Thapa
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Edward W Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
| | - Qingyang Lyu
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
| | - Danielle M Stevens
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Integrative Genetics and Genomics, University of California, Davis, California 95616, USA
| | - Christopher R Clarke
- Genetic Improvement for Fruits and Vegetables Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, Maryland 20705, USA
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
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183
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Sun W, Sun X, Li B, Häggblom MM, Han F, Xiao E, Zhang M, Wang Q, Li F. Bacterial response to antimony and arsenic contamination in rice paddies during different flooding conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 675:273-285. [PMID: 31030134 DOI: 10.1016/j.scitotenv.2019.04.146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 03/31/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
Rice is more vulnerable to arsenic (As) and antimony (Sb) contamination than other cereals due to the special cultivation methods, during which irrigation conditions are adjusted depending upon the growth stages. The changes in irrigation conditions may alter the oxidation states of Sb and As, which influences their mobility and bioavailability and hence uptake by rice. In this study, bacterial responses to As and Sb contamination in rice fields were investigated during two different stages of rice growth: the vegetative stage (flooded conditions), and the ripening stage (drained conditions). The substantial changes in the irrigation conditions caused a variation in geochemical parameters including the As- and Sb-extractable fractions. As and Sb were more mobile and bioaccessible during the flooded than under drained conditions. The microbial communities varied during two irrigation conditions, suggesting that the geochemical conditions may have different effects on the innate paddy microbiota. Therefore, various statistical tools including co-occurrence network and random forest (RF) were performed to reveal the environment-microbe interactions in two different irrigation conditions. One of the notable findings is that Sb- and As-related parameters exerted more influences during the flooded than under drained conditions. Furthermore, a detailed RF analysis indicated that the individual bacterial taxa may also respond differently to contaminant fractions during the two irrigation conditions. Notably, RF indicated that individual taxa such as Clostridiaceae and Geobacter may be responsible for biotransformation of As and Sb (e.g., As and Sb reduction). The results provided knowledge for As and Sb transformation during contrasting irrigation conditions and the potential mitigation strategy for contaminant removal.
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Affiliation(s)
- Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China.
| | - Xiaoxu Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Feng Han
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Enzong Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Miaomiao Zhang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Qi Wang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
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184
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Establishment Limitation Constrains the Abundance of Lactic Acid Bacteria in the Napa Cabbage Phyllosphere. Appl Environ Microbiol 2019; 85:AEM.00269-19. [PMID: 31003989 DOI: 10.1128/aem.00269-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/14/2019] [Indexed: 12/15/2022] Open
Abstract
Patterns of phyllosphere diversity have become increasingly clear with high-throughput sequencing surveys, but the processes that control phyllosphere diversity are still emerging. Through a combination of lab and field experiments using Napa cabbage and lactic acid bacteria (LAB), we examined how dispersal and establishment processes shape the ecological distributions of phyllosphere bacteria. We first determined the abundance and diversity of LAB on Napa cabbage grown at three sites using both culture-based approaches and 16S rRNA gene amplicon sequencing. Across all sites, LAB made up less than 0.9% of the total bacterial community abundance. To assess whether LAB were low in abundance in the Napa cabbage phyllosphere due to a limited abundance in local species pools (source limitation), we quantified LAB in leaf and soil samples across 51 vegetable farms and gardens throughout the northeastern United States. Across all sites, LAB comprised less than 3.2% of the soil bacterial communities and less than 1.6% of phyllosphere bacterial communities. To assess whether LAB are unable to grow in the phyllosphere even if they dispersed at high rates (establishment limitation), we used a gnotobiotic Napa cabbage system in the lab with experimental communities mimicking various dispersal rates of LAB. Even at high dispersal rates, LAB became rare or completely undetectable in experimental communities, suggesting that they are also establishment limited. Collectively, our data demonstrate that the low abundance of LAB in phyllosphere communities may be explained by establishment limitation.IMPORTANCE The quality and safety of vegetable fermentations are dependent on the activities of LAB naturally present in the phyllosphere. Despite their critical role in determining the success of fermentation, the processes that determine the abundance and diversity of LAB in vegetables used for fermentation are poorly characterized. Our work demonstrates that the limited ability of LAB to grow in the cabbage phyllosphere environment may constrain their abundance on cabbage leaves. These results suggest that commercial fermentation of Napa cabbage proceeds despite low and variable abundances of LAB across different growing regions. Propagule limitation may also explain ecological distributions of other rare members of phyllosphere microbes.
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185
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Mukhtar S, Ishaq A, Hassan S, Mehnaz S, Mirza MS, Malik KA. Comparison of Microbial Communities Associated with Halophyte (Salsola stocksii) and Non-Halophyte (Triticum aestivum) Using Culture-Independent Approaches. Pol J Microbiol 2019; 66:353-364. [PMID: 29319512 DOI: 10.5604/01.3001.0010.4866] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Halophyte microbiome contributes significantly to plant performance and can provide information regarding complex ecological processes involved in osmoregulation of these plants. The objective of this study is to investigate the microbiomes associated with belowground (rhizosphere), internal (endosphere) and aboveground (phyllosphere) tissues of halophyte (Salsola stocksii) through metagenomics approach. Plant samples were collected from Khewra Salt Mines. The metagenomic DNA from soil, root and shoot samples was isolated with the help of FastDNA spin kit. Through PCR, the 16S rRNA gene from four different Salsola plants and wheat plants was amplified and cloned in InsTAclone PCR cloning kit. Metagenomic analyses from rhizosphere, endosphere and phyllosphere of Salsola showed that approximately 29% bacteria were uncultured and unclassified. Proteobacteria and Actinobacteria were the most abundant phyla in Salsola and wheat. However, Firmicutes, Acidobacteria, Bacteriodetes, Planctomycetes, Cyanobacteria, Thermotogae, Verrucomicrobia, Choroflexi and Euryarchaeota were predominant groups from halophyte whereas Actinobacteria, Proteobacteria, Firmicutes, Cyanobacteria, Acidobacteria, Bacteriodetes, Planctomycetes and Verrucomicrobia were predominant phyla of wheat samples. Diversity and differences of microbial flora of Salsola and wheat suggested that functional interactions between plants and microorganisms contribute to salt stress tolerance.
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Affiliation(s)
- Salma Mukhtar
- Department of Biological Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Ayesha Ishaq
- Department of Biological Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Sara Hassan
- Department of Biological Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Samina Mehnaz
- Department of Biological Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Muhammad S Mirza
- Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Kauser A Malik
- Department of Biological Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
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186
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Gupta S, Pandey S. Unravelling the biochemistry and genetics of ACC deaminase-An enzyme alleviating the biotic and abiotic stress in plants. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.plgene.2019.100175] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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187
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Abdulmajeed AM, Qaderi MM. Differential effects of environmental stressors on physiological processes and methane emissions in pea (Pisum sativum) plants at various growth stages. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:715-723. [PMID: 31055132 DOI: 10.1016/j.plaphy.2019.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
Many studies have investigated the effects of one or two environmental factors on methane (CH4) emissions from plants at a single growth stage, but the impact that multiple co-occurring stress factors may have on emissions at different growth stages has rarely been studied. The objective of this study was to examine the effects of temperature, ultraviolet-B (UVB) radiation, and watering regime on CH4 emissions and some relevant physiological characteristics of pea (Pisum sativum L. cv. 237 J Sundance) plants at three growth stages. We grew plants under two temperature regimes (22/18 °C and 28/24 °C; 16 h light/8 h dark), two UVB levels [0 and 5 kJ m-2 d-1] and two watering regimes (well-watered, watering plants to field capacity, and water-stressed, watering plants at wilting point). Measurements were then taken after 10, 20, and 30 days of growth under experimental conditions, following seven days of initial growth under 22/18 °C. Higher temperatures, UVB5, and water stress adversely affected photosynthesis and chlorophyll fluorescence, but increased CH4 emissions, which decreased with increased plant age. Also, interaction of higher temperatures and UVB5 reversed the pattern of CH4 emissions at growth stages, compared to that of other treatments. We conclude that CH4 emission decreases with plant age, and it is affected by stress factors through changes in physiological activities of plants.
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Affiliation(s)
- Awatif M Abdulmajeed
- Department of Biology, Life Science Centre, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Mirwais M Qaderi
- Department of Biology, Life Science Centre, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada; Department of Biology, Mount Saint Vincent University, 166 Bedford Highway, Halifax, Nova Scotia, B3M 2J6, Canada.
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188
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Chen QL, Cui HL, Su JQ, Penuelas J, Zhu YG. Antibiotic Resistomes in Plant Microbiomes. TRENDS IN PLANT SCIENCE 2019; 24:530-541. [PMID: 30890301 DOI: 10.1016/j.tplants.2019.02.010] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 05/10/2023]
Abstract
Microorganisms associated with plants may alter the traits of the human microbiome important for human health, but this alteration has largely been overlooked. The plant microbiome is an interface between plants and the environment, and provides many ecosystem functions such as improving nutrient uptake and protecting against biotic and abiotic stress. The plant microbiome also represents a major pathway by which humans are exposed to microbes and genes consumed with food, such as pathogenic bacteria, antibiotic-resistant bacteria, and antibiotic-resistance genes. In this review we highlight the main findings on the composition and function of the plant microbiome, and underline the potential of plant microbiomes in the dissemination of antibiotic resistance via food consumption or direct contact.
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Affiliation(s)
- Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hui-Ling Cui
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Josep Penuelas
- Consejo Superior de Investigaciones Científicas (CSIC), Global Ecology Unit, Centre for Ecological Research and Forestry Applications (CREAF)-CSIC-Universitat Autonoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Catalonia, Spain; CREAF, Cerdanyola del Vallès, 08193 Barcelona, Catalonia, Spain
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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189
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Light and Microbial Lifestyle: The Impact of Light Quality on Plant–Microbe Interactions in Horticultural Production Systems—A Review. HORTICULTURAE 2019. [DOI: 10.3390/horticulturae5020041] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Horticultural greenhouse production in circumpolar regions (>60° N latitude), but also at lower latitudes, is dependent on artificial assimilation lighting to improve plant performance and the profitability of ornamental crops, and to secure production of greenhouse vegetables and berries all year round. In order to reduce energy consumption and energy costs, alternative technologies for lighting have been introduced, including light-emitting diodes (LED). This technology is also well-established within urban farming, especially plant factories. Different light technologies influence biotic and abiotic conditions in the plant environment. This review focuses on the impact of light quality on plant–microbe interactions, especially non-phototrophic organisms. Bacterial and fungal pathogens, biocontrol agents, and the phyllobiome are considered. Relevant molecular mechanisms regulating light-quality-related processes in bacteria are described and knowledge gaps are discussed with reference to ecological theories.
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190
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Doni F, Mispan MS, Suhaimi NSM, Ishak N, Uphoff N. Roles of microbes in supporting sustainable rice production using the system of rice intensification. Appl Microbiol Biotechnol 2019; 103:5131-5142. [PMID: 31101941 DOI: 10.1007/s00253-019-09879-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 10/26/2022]
Abstract
The system of rice intensification (SRI) is an agroecological approach to rice cultivation that seeks to create optimal conditions for healthy plant growth by minimizing inter-plant competition, transplanting widely spaced young single seedlings, and optimizing favorable soil conditions with organic amendments, increased soil aeration by weeding, and controlled water management. These practices improve rice plant growth with yields up to three times more than with conventional cultivation methods, and increase crop resilience under biotic and abiotic stresses. This review discusses the roles of beneficial microbes in improving rice plant growth, yield, and resilience when SRI practices are used, and how these modifications in plant, soil, water, and nutrient management affect the populations and diversity of soil microorganisms. Mechanisms whereby symbiotic microbes support rice plants' growth and performance are also discussed.
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Affiliation(s)
- Febri Doni
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Muhamad Shakirin Mispan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | | | - Nazri Ishak
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Norman Uphoff
- SRI International Network and Resources Center, Cornell University, Ithaca, NY, 14853, USA
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191
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Abstract
Microorganisms colonizing plant surfaces and internal tissues provide a number of life-support functions for their host. Despite increasing recognition of the vast functional capabilities of the plant microbiome, our understanding of the ecology and evolution of the taxonomically hyperdiverse microbial communities is limited. Here, we review current knowledge of plant genotypic and phenotypic traits as well as allogenic and autogenic factors that shape microbiome composition and functions. We give specific emphasis to the impact of plant domestication on microbiome assembly and how insights into microbiomes of wild plant relatives and native habitats can contribute to reinstate or enrich for microorganisms with beneficial effects on plant growth, development, and health. Finally, we introduce new concepts and perspectives in plant microbiome research, in particular how community ecology theory can provide a mechanistic framework to unravel the interplay of distinct ecological processes-i.e., selection, dispersal, drift, diversification-that structure the plant microbiome.
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Affiliation(s)
- Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands;
| | - Francisco Dini-Andreote
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands;
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands; .,Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands; .,Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
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192
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Hurtado-McCormick V, Kahlke T, Petrou K, Jeffries T, Ralph PJ, Seymour JR. Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome. Front Microbiol 2019; 10:1011. [PMID: 31139163 PMCID: PMC6527750 DOI: 10.3389/fmicb.2019.01011] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/23/2019] [Indexed: 11/29/2022] Open
Abstract
Seagrasses are globally distributed marine plants that represent an extremely valuable component of coastal ecosystems. Like terrestrial plants, seagrass productivity and health are likely to be strongly governed by the structure and function of the seagrass microbiome, which will be distributed across a number of discrete microenvironments within the plant, including the phyllosphere, the endosphere and the rhizosphere, all different in physical and chemical conditions. Here we examined patterns in the composition of the microbiome of the seagrass Zostera muelleri, within six plant-associated microenvironments sampled across four different coastal locations in New South Wales, Australia. Amplicon sequencing approaches were used to characterize the diversity and composition of bacterial, microalgal, and fungal microbiomes and ultimately identify "core microbiome" members that were conserved across sampling microenvironments. Discrete populations of bacteria, microalgae and fungi were observed within specific seagrass microenvironments, including the leaves and roots and rhizomes, with "core" taxa found to persist within these microenvironments across geographically disparate sampling sites. Bacterial, microalgal and fungal community profiles were most strongly governed by intrinsic features of the different seagrass microenvironments, whereby microscale differences in community composition were greater than the differences observed between sampling regions. However, our results showed differing strengths of microbial preferences at the plant scale, since this microenvironmental variability was more pronounced for bacteria than it was for microalgae and fungi, suggesting more specific interactions between the bacterial consortia and the seagrass host, and potentially implying a highly specialized coupling between seagrass and bacterial metabolism and ecology. Due to their persistence within a given seagrass microenvironment, across geographically discrete sampling locations, we propose that the identified "core" microbiome members likely play key roles in seagrass physiology as well as the ecology and biogeochemistry of seagrass habitats.
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Affiliation(s)
| | - Tim Kahlke
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Katherina Petrou
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Thomas Jeffries
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - Peter J. Ralph
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Justin Robert Seymour
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
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193
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Fogler K, Guron GKP, Wind LL, Keenum IM, Hession WC, Krometis LA, Strawn LK, Pruden A, Ponder MA. Microbiota and Antibiotic Resistome of Lettuce Leaves and Radishes Grown in Soils Receiving Manure-Based Amendments Derived From Antibiotic-Treated Cows. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00022] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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194
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Cui HL, Duan GL, Zhang H, Cheng W, Zhu YG. Microbiota in non-flooded and flooded rice culms. FEMS Microbiol Ecol 2019; 95:5393367. [PMID: 30889240 DOI: 10.1093/femsec/fiz036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/18/2019] [Indexed: 01/21/2023] Open
Abstract
Rice plants are the habitat for large and diverse populations of microbes, which play important roles on rice health and productivity. However, the response of microbiome on rice culm to water flooding is poorly understood. In this study, the bacterial community on non-flooded (RSA) and flooded (RSB) rice culms was investigated through 16S rRNA gene sequencing. The results showed that RSA and RSB had significantly distinct bacterial communities. In RSA, Gammaproteobacteria and Pantoea were the most abundant class (57%), genus (37.06%), respectively, while in RSB, the most abundant phylum and genus was Firmicutes (54%) and Bacillus (52.63%), respectively. Compared with RSA, the abundance of 27 genera significantly increased and 21 genera significantly decreased in RSB, and some remarkably changed species, such as Aeromonas, Bacillus were identified, which are sensitive to non-flooded or flooded conditions. In addition, rare operational taxonomic units (OTUs) was much more than abundant OTUs in all samples, and RSB had significantly higher bacterial richness than RSA due to having more rare taxa. Our study would advance the insights into the microbiome of rice culms and its response to flooding, which would help to identify potential beneficial bacteria for improving crop health and sustainable productivity in agroecosystems.
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Affiliation(s)
- Hui-Ling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, Haidian District, Beijing 100085, People's Republic of China.,University of Chinese Academy of Sciences, 19A Yuquan Rd, Beijing 100049, People's Republic of China
| | - Gui-Lan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, Haidian District, Beijing 100085, People's Republic of China
| | - Hongmei Zhang
- Jiaxing Academy of Agricultural Sciences, Shuangqiao Town, Xiuzhou District, Jiaxing 314016, People's Republic of China
| | - Wangda Cheng
- Jiaxing Academy of Agricultural Sciences, Shuangqiao Town, Xiuzhou District, Jiaxing 314016, People's Republic of China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, Haidian District, Beijing 100085, People's Republic of China.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences,1799 Jimei Rd, Xiamen 361021, Fujian Province, People's Republic of China
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195
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Chistoserdova L. New pieces to the lanthanide puzzle. Mol Microbiol 2019; 111:1127-1131. [DOI: 10.1111/mmi.14210] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2019] [Indexed: 01/05/2023]
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196
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Wang X, Cai M, Zhou Y. Biological influence of cry1Ab gene insertion on the endophytic bacteria community in transgenic rice. Turk J Biol 2019; 42:231-239. [PMID: 30814885 DOI: 10.3906/biy-1708-32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The commercial release of genetically modified (GMO) rice for insect control in China is a subject of debate. Although a series of studies have focused on the safety evaluation of the agroecosystem, the endophytes of transgenic rice are rarely considered. Here, the influence of endophyte populations and communities was investigated and compared for transgenic and nontransgenic rice. Population-level investigation suggested that cry1Ab gene insertion influenced to a varying degree the rice endophytes at the seedling stage, but a significant difference was only observed in leaves of Bt22 (Zhejiang22 transgenic rice) between the GMO and wild-type rice. Community-level analysis using the 16S rRNA gene showed that strains of the phyla Proteobacteria and Firmicutes were the predominant groups occurring in the three transgenic rice plants and their corresponding parents. By contrast, the endophytic communities of Minghui63 and Xiushui11 showed a weaker response to cry1Ab gene insertion than did Zhejiang22, and the community results were consistent with the population-level investigation. The populations and communities of rice endophytes were affected by the cry1Ab gene to a different extent in different rice varieties and plant tissues. The results of this study broaden our understanding of unexpected transgenic influences on nontarget organisms.
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Affiliation(s)
- Xu Wang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science Technology, Anhui Agricultural University , Heifei , P.R. China
| | - Mengyu Cai
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science Technology, Anhui Agricultural University , Heifei , P.R. China
| | - Yu Zhou
- State Key Laboratory Breeding Base for Zhejiang Sustainable Plant Pest Control, Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Zhejiang Province Key Laboratory for Food Safety, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences , Hangzhou , P.R. China.,State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science Technology, Anhui Agricultural University , Heifei , P.R. China
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197
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Suárez-Moreno ZR, Vinchira-Villarraga DM, Vergara-Morales DI, Castellanos L, Ramos FA, Guarnaccia C, Degrassi G, Venturi V, Moreno-Sarmiento N. Plant-Growth Promotion and Biocontrol Properties of Three Streptomyces spp. Isolates to Control Bacterial Rice Pathogens. Front Microbiol 2019; 10:290. [PMID: 30858835 PMCID: PMC6398372 DOI: 10.3389/fmicb.2019.00290] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 02/04/2019] [Indexed: 11/23/2022] Open
Abstract
Bacterial Panicle Blight caused by Burkholderia glumae is a major disease of rice, which has dramatically affected rice production around the world in the last years. In this study we describe the assessment of three Streptomyces isolates as biocontrol agents for B. glumae. Additionally, the presence of other plant-growth promoting abilities and their possible beneficial effects upon their inoculation on rice plants was evaluated as an ecological analysis for their future inoculation in rice crops. Two isolates (A20 and 5.1) inhibited growth of virulent B. glumae strains, as well as a wide range of bacterial and fungal species, while a third strain (7.1) showed only antifungal activity. In vitro tests demonstrated the ability of these strains to produce siderophores, Indoleacetic acid (IAA), extracellular enzymes and solubilizing phosphate. Greenhouse experiments with two rice cultivars indicated that Streptomyces A20 is able to colonize rice plants and promote plant growth in both cultivars. Furthermore, an egfp tagged mutant was generated and colonization experiments were performed, indicating that Streptomyces A20 –GFP was strongly associated with root hairs, which may be related to the plant growth promotion observed in the gnotobiotic experiments. In order to characterize the antimicrobial compounds produced by strain A20 bacteria, mass spectrometry analyses were performed. This technique indicated that A20 produced several antimicrobial compounds with sizes below 3 kDa and three of these molecules were identified as Streptotricins D, E and F. These findings indicate the potential of Streptomyces A20 as a biocontrol inoculant to protect rice plants against bacterial diseases.
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Affiliation(s)
| | | | | | | | - Freddy A Ramos
- Departamento de Química. Universidad Nacional de Colombia, Bogotá, Colombia
| | - Corrado Guarnaccia
- Biotechnology Development Unit, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Giuliano Degrassi
- Bacteriology and Plant Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Vittorio Venturi
- Bacteriology and Plant Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
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198
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Ochsner AM, Hemmerle L, Vonderach T, Nüssli R, Bortfeld-Miller M, Hattendorf B, Vorholt JA. Use of rare-earth elements in the phyllosphere colonizer Methylobacterium extorquens PA1. Mol Microbiol 2019; 111:1152-1166. [PMID: 30653750 PMCID: PMC6850437 DOI: 10.1111/mmi.14208] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2019] [Indexed: 01/03/2023]
Abstract
Until recently, rare‐earth elements (REEs) had been thought to be biologically inactive. This view changed with the discovery of the methanol dehydrogenase XoxF that strictly relies on REEs for its activity. Some methylotrophs only contain xoxF, while others, including the model phyllosphere colonizer Methylobacterium extorquens PA1, harbor this gene in addition to mxaFI encoding a Ca2+‐dependent enzyme. Here we found that REEs induce the expression of xoxF in M. extorquens PA1, while repressing mxaFI, suggesting that XoxF is the preferred methanol dehydrogenase in the presence of sufficient amounts of REE. Using reporter assays and a suppressor screen, we found that lanthanum (La3+) is sensed both in a XoxF‐dependent and independent manner. Furthermore, we investigated the role of REEs during Arabidopsisthaliana colonization. Element analysis of the phyllosphere revealed the presence of several REEs at concentrations up to 10 μg per g dry weight. Complementary proteome analyses of M. extorquens PA1 identified XoxF as a top induced protein in planta and a core set of La3+‐regulated proteins under defined artificial media conditions. Among these was a REE‐binding protein that is encoded next to a gene for a TonB‐dependent transporter. The latter was essential for REE‐dependent growth on methanol indicating chelator‐assisted uptake of REEs.
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Affiliation(s)
- Andrea M Ochsner
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Lucas Hemmerle
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Thomas Vonderach
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Ralph Nüssli
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Miriam Bortfeld-Miller
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Bodo Hattendorf
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
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Toju H, Okayasu K, Notaguchi M. Leaf-associated microbiomes of grafted tomato plants. Sci Rep 2019; 9:1787. [PMID: 30741982 PMCID: PMC6370777 DOI: 10.1038/s41598-018-38344-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/14/2018] [Indexed: 01/19/2023] Open
Abstract
Bacteria and fungi form complex communities (microbiomes) in above- and below-ground organs of plants, contributing to hosts' growth and survival in various ways. Recent studies have suggested that host plant genotypes control, at least partly, plant-associated microbiome compositions. However, we still have limited knowledge of how microbiome structures are determined in/on grafted crop plants, whose above-ground (scion) and below-ground (rootstock) genotypes are different with each other. By using eight varieties of grafted tomato plants, we examined how rootstock genotypes could determine the assembly of leaf endophytic microbes in field conditions. An Illumina sequencing analysis showed that both bacterial and fungal community structures did not significantly differ among tomato plants with different rootstock genotypes: rather, sampling positions in the farmland contributed to microbiome variation in a major way. Nonetheless, a further analysis targeting respective microbial taxa suggested that some bacteria and fungi could be preferentially associated with particular rootstock treatments. Specifically, a bacterium in the genus Deinococcus was found disproportionately from ungrafted tomato individuals. In addition, yeasts in the genus Hannaella occurred frequently on the tomato individuals whose rootstock genotype was "Ganbarune". Overall, this study suggests to what extent leaf microbiome structures can be affected/unaffected by rootstock genotypes in grafted crop plants.
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Affiliation(s)
- Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan.
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan.
| | - Koji Okayasu
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Michitaka Notaguchi
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
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Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils. Sci Rep 2019; 9:1042. [PMID: 30705356 PMCID: PMC6355873 DOI: 10.1038/s41598-018-37776-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 12/12/2018] [Indexed: 12/23/2022] Open
Abstract
The rhizosphere is considered the primary place for soil microbiome differentiation and plays a key role in plant survival, especially for those subjected to environmental stress. Using high-throughput sequencing of the 16S rRNA gene, we analyzed and compared soil bacterial communities associated to four of the most abundant high altitude native plant species of the Chilean Andean grasslands. We examined three soil compartments: the rhizosphere (bacteria firmly attached to the roots), the rhizosphere-surrounding soil (bacteria loosely attached to the roots) and the bulk soil (plant-free soil). The rhizosphere microbiome was in all cases the least diverse, exposing that the bulk soil was a more complex environment. Taxonomic analysis revealed an abrupt change between the rhizosphere and the rest of the non-rhizospheric soils. Thus, while rhizobacterial communities were enriched in Proteobacteria (mainly Alphaproteobacteria), Actinobacteria (mostly Blastocatellia) dominated in bulk soils. Finally, we detected certain taxonomic rhizosphere signatures, which could be attributed to a particular genotype. Overall, our results indicate that the thin layer of soil surrounding the roots constitute a distinctive soil environment. This study contributes to expand the knowledge about soil bacterial communities in the Chilean highlands and takes the first step to understand the processes that might lead to the rhizosphere differentiation in that area.
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