1
|
Sana TG, Notopoulou A, Puygrenier L, Decossas M, Moreau S, Carlier A, Krasteva PV. Structures and roles of BcsD and partner scaffold proteins in proteobacterial cellulose secretion. Curr Biol 2024; 34:106-116.e6. [PMID: 38141614 DOI: 10.1016/j.cub.2023.11.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
Cellulose is the world's most abundant biopolymer, and similar to its role as a cell wall component in plants, it is a prevalent constituent of the extracellular matrix in bacterial biofilms. Although bacterial cellulose (BC) was first described in the 19th century, it was only recently revealed that it is produced by several distinct types of Bcs secretion systems that feature multiple accessory subunits in addition to a catalytic BcsAB synthase tandem. We recently showed that crystalline cellulose secretion in the Gluconacetobacter genus (α-Proteobacteria) is driven by a supramolecular BcsH-BcsD scaffold-the "cortical belt"-which stabilizes the synthase nanoarrays through an unexpected inside-out mechanism for secretion system assembly. Interestingly, while bcsH is specific for Gluconacetobacter, bcsD homologs are widespread in Proteobacteria. Here, we examine BcsD homologs and their gene neighborhoods from several plant-colonizing β- and γ-Proteobacteria proposed to secrete a variety of non-crystalline and/or chemically modified cellulosic polymers. We provide structural and mechanistic evidence that through different quaternary structure assemblies BcsD acts with proline-rich BcsH, BcsP, or BcsO partners across the proteobacterial clade to form synthase-interacting intracellular scaffolds that, in turn, determine the biofilm strength and architecture in species with strikingly different physiology and secreted biopolymers.
Collapse
Affiliation(s)
- Thibault G Sana
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac 33600, France; "Structural Biology of Biofilms" Group, European Institute of Chemistry and Biology (IECB), 2 Rue Robert Escarpit, Pessac 33600, France
| | - Areti Notopoulou
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac 33600, France; "Structural Biology of Biofilms" Group, European Institute of Chemistry and Biology (IECB), 2 Rue Robert Escarpit, Pessac 33600, France
| | - Lucie Puygrenier
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac 33600, France; "Structural Biology of Biofilms" Group, European Institute of Chemistry and Biology (IECB), 2 Rue Robert Escarpit, Pessac 33600, France
| | - Marion Decossas
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac 33600, France; "Structural Biology of Biofilms" Group, European Institute of Chemistry and Biology (IECB), 2 Rue Robert Escarpit, Pessac 33600, France
| | - Sandra Moreau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31326, France
| | - Aurélien Carlier
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31326, France; Laboratory of Microbiology, Ghent University, Ghent 9000, Belgium
| | - Petya V Krasteva
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac 33600, France; "Structural Biology of Biofilms" Group, European Institute of Chemistry and Biology (IECB), 2 Rue Robert Escarpit, Pessac 33600, France.
| |
Collapse
|
2
|
Coordinated bacterial and plant sulfur metabolism in Enterobacter sp. SA187-induced plant salt stress tolerance. Proc Natl Acad Sci U S A 2021; 118:2107417118. [PMID: 34772809 PMCID: PMC8609655 DOI: 10.1073/pnas.2107417118] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2021] [Indexed: 12/22/2022] Open
Abstract
Although plant growth–promoting bacteria (PGPB) enhance the performance of plants, only a few mechanisms have been identified so far. We show that the sulfur metabolisms in both PGPB Enterobacter sp. SA187 and Arabidopsis plants play a key role in plant salt stress tolerance. Salt stress induces a sulfur starvation response in plants that is attenuated by SA187. Arabidopsis sulfur metabolic mutants are hypersensitive to salt stress but can be rescued by SA187. Most plant sulfur metabolism occurs in chloroplasts and is linked to stress-induced accumulation of reactive oxygen species that is suppressed by SA187. This work reveals that plant salt stress tolerance requires the coordinated regulation of the sulfur metabolic pathways in both beneficial microbe and host plant. Enterobacter sp. SA187 is a root endophytic bacterium that maintains growth and yield of plants under abiotic stress conditions. In this work, we compared the metabolic wirings of Arabidopsis and SA187 in the free-living and endophytic interaction states. The interaction of SA187 with Arabidopsis induced massive changes in bacterial gene expression for chemotaxis, flagellar biosynthesis, quorum sensing, and biofilm formation. Besides modification of the bacterial carbon and energy metabolism, various nutrient and metabolite transporters and the entire sulfur pathway were up-regulated. Under salt stress, Arabidopsis resembled plants under sulfate starvation but not when colonized by SA187, which reprogramed the sulfur regulon of Arabidopsis. In accordance, salt hypersensitivity of multiple Arabidopsis sulfur metabolism mutants was partially or completely rescued by SA187 as much as by the addition of sulfate, L-cysteine, or L-methionine. Many components of the sulfur metabolism that are localized in the chloroplast were partially rescued by SA187. Finally, salt-induced accumulation of reactive oxygen species as well as the hypersensitivity of LSU mutants were suppressed by SA187. LSUs encode a central regulator linking sulfur metabolism to chloroplast superoxide dismutase activity. The coordinated regulation of the sulfur metabolic pathways in both the beneficial microorganism and the host plant is required for salt stress tolerance in Arabidopsis and might be a common mechanism utilized by different beneficial microbes to mitigate the harmful effects of different abiotic stresses on plants.
Collapse
|
3
|
Liu L, Zhao X, Huang Y, Ke L, Wang R, Qi G. Protecting tobacco plants from O 3 injury by Bacillus velezensis with production of acetoin. PHYSIOLOGIA PLANTARUM 2020; 170:158-171. [PMID: 32386333 DOI: 10.1111/ppl.13120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPRs) confer benefits to crops by producing volatile organic compounds (VOCs) to trigger induced systemic tolerance (IST). Here we show that Bacillus velezensis GJ11, a kind of PGPRs, produce VOCs such as 2,3-butanediol and acetoin to trigger IST and cause stomatal closure against O3 injury in tobacco plants. Compared to 2,3-butanediol, acetoin was more effective on triggering IST against O3 injury. The bdh-knockout strain GJ11Δbdh with a blocked metabolic pathway from acetoin to 2,3-butanediol produced more acetoin triggering stronger IST against O3 injury than GJ11. Both acetoin and GJ11Δbdh effectively enhance the antioxidant enzymes activity (e.g. superoxide dismutase and catalases) that is favorable for scavenging the reactive oxygen species like H2 O2 in leaves after exposure to O3 . Consequently, less H2 O2 accumulation was observed, and reasonably less chlorophylls and proteins were damaged by H2 O2 in the tobacco leaves treated with acetoin or GJ11Δbdh. The field experiment also showed that both acetoin and GJ11Δbdh could protect tobacco plants from O3 injury after application by root-drench. This study provides new insights into the role of rhizobacterial B. velezensis and its volatile component of acetoin in triggering defense responses against stresses such as O3 in plants.
Collapse
Affiliation(s)
- Lidong Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yong Huang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Technology Center, Enshi State Tobacco Cooperation, Hubei Province Tobacco CO., Ltd., Enshi, China
| | - Luxin Ke
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Rui Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Technology Center, Enshi State Tobacco Cooperation, Hubei Province Tobacco CO., Ltd., Enshi, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
4
|
Mosquito S, Bertani I, Licastro D, Compant S, Myers MP, Hinarejos E, Levy A, Venturi V. In Planta Colonization and Role of T6SS in Two Rice Kosakonia Endophytes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:349-363. [PMID: 31609645 DOI: 10.1094/mpmi-09-19-0256-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Endophytes live inside plants and are often beneficial. Kosakonia is a novel bacterial genus that includes many diazotrophic plant-associated isolates. Plant-bacteria studies on two rice endophytic Kosakonia beneficial strains were performed, including comparative genomics, secretome profiling, in planta tests, and a field release trial. The strains are efficient rhizoplane and root endosphere colonizers and localized in the root cortex. Secretomics revealed 144 putative secreted proteins, including type VI secretory system (T6SS) proteins. A Kosakonia T6SS genomic knock-out mutant showed a significant decrease in rhizoplane and endosphere colonization ability. A field trial using rice seed inoculated with Kosakonia spp. showed no effect on plant growth promotion upon nitrogen stress and microbiome studies revealed that Kosakonia spp. were significantly more present in the inoculated rice. Comparative genomics indicated that several protein domains were enriched in plant-associated Kosakonia spp. This study highlights that Kosakonia is an important, recently classified genus involved in plant-bacteria interaction.
Collapse
Affiliation(s)
- Susan Mosquito
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Iris Bertani
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Danilo Licastro
- CBM S.c.r.l., Area Science Park-Basovizza, 34149 Trieste, Italy
| | - Stéphane Compant
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Vienna, Austria
| | - Michael P Myers
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | | | - Asaf Levy
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| |
Collapse
|
5
|
He W, Megharaj M, Wu CY, Subashchandrabose SR, Dai CC. Endophyte-assisted phytoremediation: mechanisms and current application strategies for soil mixed pollutants. Crit Rev Biotechnol 2019; 40:31-45. [PMID: 31656090 DOI: 10.1080/07388551.2019.1675582] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phytoremediation uses plants and associated microbes to remove pollutants from the environment and is considered a promising bioremediation method. Compared with well-described single contaminant treatments, the number of studies reporting phytoremediation of soil mixed pollutants has increased recently. Endophytes, including bacteria and fungi, exhibit beneficial traits for the promotion of plant growth, stress alleviation, and biodegradation. Moreover, endophytes either directly or indirectly assist host plants to survive high concentrations of organic and inorganic pollutants in the soil. Endophytic microorganisms can also regulate the plant metabolism in different ways, exhibiting a variety of physiological characteristics. This review summarizes the taxa and physiological properties of endophytic microorganisms that may participate in the detoxification of contaminant mixtures. Furthermore, potential biomolecules that may enhance endophyte mediated phytoremediation are discussed. The practical applications of pollutant-degrading endophytes and current strategies for applying this valuable bio-resource to soil phytoremediation are summarized.
Collapse
Affiliation(s)
- Wei He
- College of Life Sciences, Nanjing Normal University, Nanjing, China.,Global Centre for Environmental Remediation (GCER), The University of Newcastle (UoN), Callaghan, Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), The University of Newcastle (UoN), Callaghan, Australia
| | - Chun-Ya Wu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Suresh R Subashchandrabose
- Global Centre for Environmental Remediation (GCER), The University of Newcastle (UoN), Callaghan, Australia
| | - Chuan-Chao Dai
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| |
Collapse
|
6
|
Engineering Bacillus velezensis with high production of acetoin primes strong induced systemic resistance in Arabidopsis thaliana. Microbiol Res 2019; 227:126297. [DOI: 10.1016/j.micres.2019.126297] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/02/2019] [Accepted: 07/12/2019] [Indexed: 11/18/2022]
|
7
|
Lidor O, Dror O, Hamershlak D, Shoshana N, Belausov E, Zahavi T, Mozes-Daube N, Naor V, Zchori-Fein E, Iasur-Kruh L, Bahar O. Introduction of a putative biocontrol agent into a range of phytoplasma- and liberibacter-susceptible crop plants. PEST MANAGEMENT SCIENCE 2018; 74:811-819. [PMID: 29072824 DOI: 10.1002/ps.4775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/03/2017] [Accepted: 10/22/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Phytoplasma, the causative agent of Bois Noir disease of grapevines, are vectored by the planthopper Hyalesthes obsoletus (Hemiptera: Cixiidae). A Dyella-like bacterium (DLB) isolated from H. obsoletus inhibits the growth of Spiroplasma melliferum, a cultivable relative of phytoplasma. Additional evidence suggests that DLB can reduce the symptoms of yellows disease in grapevine plantlets. The aim of this study was to test whether DLB could colonize a range of phytoplasma- and liberibacter-sensitive crop plants, and thus assess its potential agricultural use. RESULTS Vitex agnus-castus, the preferred host plant of H. obsoletus was found to be a natural host of DLB, which was successfully introduced into a range of crop plants belonging to seven families. The most effective DLB application method was foliar spraying. Microscopy observation revealed that DLB aggregated on the leaf surface and around the stomata, suggesting that this is its route of entry. DLB was also present in the vascular tissues of plants, indicating that it moved systemically through the plant. CONCLUSIONS DLB is a potential biocontrol agent and its broad spectrum of host plants indicates the possibility of its future use against a range of diseases caused by phloem-limited bacteria. © 2017 Society of Chemical Industry.
Collapse
Affiliation(s)
- Ofir Lidor
- Department of Entomology, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, Israel
| | - Orit Dror
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Dor Hamershlak
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Nofar Shoshana
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Eduard Belausov
- Microscopy Unit, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | | | - Netta Mozes-Daube
- Department of Entomology, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, Israel
| | - Vered Naor
- Shamir Research Institute, Katzrin, Israel
- Ohallo College, Katzrin, Israel
| | - Einat Zchori-Fein
- Department of Entomology, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, Israel
| | - Lilach Iasur-Kruh
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel, Israel
| | - Ofir Bahar
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| |
Collapse
|
8
|
Huang L, Xu W, Su Y, Zhao L, Yan Q. Regulatory role of the RstB-RstA system in adhesion, biofilm production, motility, and hemolysis. Microbiologyopen 2018; 7:e00599. [PMID: 29573209 PMCID: PMC6182747 DOI: 10.1002/mbo3.599] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/15/2018] [Accepted: 01/15/2018] [Indexed: 01/19/2023] Open
Abstract
For infection, initial invasion of the host is of great importance, with adhesion playing a critical role. We previously demonstrated rstA and rstB are remarkably downregulated in Vibrio alginolyticus cultured under heavy metal and acidic stresses, with impaired adhesion, suggesting that rstA and rstB might be involved in adhesion regulation. The present study showed that rstA and rstB silencing resulted in impaired adhesion, biofilm production, motility, hemolysis, and virulence. Meanwhile, changes of temperature, starvation, and pH remarkably affected rstA and rstB expression. These findings indicated that (1) rstA and rstB are critical regulators of adhesion in V. alginolyticus; (2) rstA and rstB have remarkable effects on biofilm production, motility, hemolysis, and virulence in V. alginolyticus; (3) rstA and rstB modulate adhesion in response to environmental changes of temperature, pH, and starvation.
Collapse
Affiliation(s)
- Lixing Huang
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde, Fujian, China.,Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China
| | - Wei Xu
- Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Yongquan Su
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde, Fujian, China.,College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Lingmin Zhao
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China
| | - Qingpi Yan
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde, Fujian, China.,Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China
| |
Collapse
|
9
|
Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome. mSystems 2018; 3:mSystems00070-17. [PMID: 29404422 PMCID: PMC5781258 DOI: 10.1128/msystems.00070-17] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/20/2017] [Indexed: 12/24/2022] Open
Abstract
The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth. Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops and biofeedstocks. In some cases, the microbial community associated with plants has been shown to alleviate plant stress and increase plant growth under suboptimal growing conditions. A systematic understanding of how the microbial community changes under these conditions is required to understand the contribution of the microbiome to water utilization, nutrient uptake, and ultimately yield. Using a microbiome inoculation strategy, we studied how the belowground microbiome of Populus deltoides changes in response to diverse environmental conditions, including water limitation, light limitation (shading), and metal toxicity. While plant responses to treatments in terms of growth, photosynthesis, gene expression and metabolite profiles were varied, we identified a core set of bacterial genera that change in abundance in response to host stress. The results of this study indicate substantial structure in the plant microbiome community and identify potential drivers of the phytobiome response to stress. IMPORTANCE The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth.
Collapse
|
10
|
Yi Y, de Jong A, Frenzel E, Kuipers OP. Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates. Front Microbiol 2017; 8:1487. [PMID: 28824604 PMCID: PMC5543090 DOI: 10.3389/fmicb.2017.01487] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/24/2017] [Indexed: 12/11/2022] Open
Abstract
Plant root secreted compounds alter the gene expression of associated microorganisms by acting as signal molecules that either stimulate or repel the interaction with beneficial or harmful species, respectively. However, it is still unclear whether two distinct groups of beneficial bacteria, non-plant-associated (soil) strains and plant-associated (endophytic) strains, respond uniformly or variably to the exposure with root exudates. Therefore, Bacillus mycoides, a potential biocontrol agent and plant growth-promoting bacterium, was isolated from the endosphere of potatoes and from soil of the same geographical region. Confocal fluorescence microscopy of plants inoculated with GFP-tagged B. mycoides strains showed that the endosphere isolate EC18 had a stronger plant colonization ability and competed more successfully for the colonization sites than the soil isolate SB8. To dissect these phenotypic differences, the genomes of the two strains were sequenced and the transcriptome response to potato root exudates was compared. The global transcriptome profiles evidenced that the endophytic isolate responded more pronounced than the soil-derived isolate and a higher number of significant differentially expressed genes were detected. Both isolates responded with the alteration of expression of an overlapping set of genes, which had previously been reported to be involved in plant–microbe interactions; including organic substance metabolism, oxidative reduction, and transmembrane transport. Notably, several genes were specifically upregulated in the endosphere isolate EC18, while being oppositely downregulated in the soil isolate SB8. These genes mainly encoded membrane proteins, transcriptional regulators or were involved in amino acid metabolism and biosynthesis. By contrast, several genes upregulated in the soil isolate SB8 and downregulated in the endosphere isolate EC18 were related to sugar transport, which might coincide with the different nutrient availability in the two environments. Altogether, the presented transcriptome profiles provide highly improved insights into the life strategies of plant-associated endophytes and soil isolates of B. mycoides.
Collapse
Affiliation(s)
- Yanglei Yi
- Molecular Genetics Department, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands
| | - Anne de Jong
- Molecular Genetics Department, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands
| | - Elrike Frenzel
- Molecular Genetics Department, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands
| | - Oscar P Kuipers
- Molecular Genetics Department, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands
| |
Collapse
|
11
|
Khan AR, Park GS, Asaf S, Hong SJ, Jung BK, Shin JH. Complete genome analysis of Serratia marcescens RSC-14: A plant growth-promoting bacterium that alleviates cadmium stress in host plants. PLoS One 2017; 12:e0171534. [PMID: 28187139 PMCID: PMC5302809 DOI: 10.1371/journal.pone.0171534] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 01/22/2017] [Indexed: 11/28/2022] Open
Abstract
Serratia marcescens RSC-14 is a Gram-negative bacterium that was previously isolated from the surface-sterilized roots of the Cd-hyperaccumulator Solanum nigrum. The strain stimulates plant growth and alleviates Cd stress in host plants. To investigate the genetic basis for these traits, the complete genome of RSC-14 was obtained by single-molecule real-time sequencing. The genome of S. marcescens RSC-14 comprised a 5.12-Mbp-long circular chromosome containing 4,593 predicted protein-coding genes, 22 rRNA genes, 88 tRNA genes, and 41 pseudogenes. It contained genes with potential functions in plant growth promotion, including genes involved in indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis, and phosphate solubilization. Moreover, annotation using NCBI and Rapid Annotation using Subsystem Technology identified several genes that encode antioxidant enzymes as well as genes involved in antioxidant production, supporting the observed resistance towards heavy metals, such as Cd. The presence of IAA pathway-related genes and oxidative stress-responsive enzyme genes may explain the plant growth-promoting potential and Cd tolerance, respectively. This is the first report of a complete genome sequence of Cd-tolerant S. marcescens and its plant growth promotion pathway. The whole-genome analysis of this strain clarified the genetic basis underlying its phenotypic and biochemical characteristics, underpinning the beneficial interactions between RSC-14 and plants.
Collapse
Affiliation(s)
- Abdur Rahim Khan
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - Gun-Seok Park
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sajjad Asaf
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sung-Jun Hong
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Byung Kwon Jung
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Ho Shin
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|
12
|
Estendorfer J, Stempfhuber B, Haury P, Vestergaard G, Rillig MC, Joshi J, Schröder P, Schloter M. The Influence of Land Use Intensity on the Plant-Associated Microbiome of Dactylis glomerata L. FRONTIERS IN PLANT SCIENCE 2017; 8:930. [PMID: 28680426 PMCID: PMC5478725 DOI: 10.3389/fpls.2017.00930] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/18/2017] [Indexed: 05/07/2023]
Abstract
In this study, we investigated the impact of different land use intensities (LUI) on the root-associated microbiome of Dactylis glomerata (orchardgrass). For this purpose, eight sampling sites with different land use intensity levels but comparable soil properties were selected in the southwest of Germany. Experimental plots covered land use levels from natural grassland up to intensively managed meadows. We used 16S rRNA gene based barcoding to assess the plant-associated community structure in the endosphere, rhizosphere and bulk soil of D. glomerata. Samples were taken at the reproductive stage of the plant in early summer. Our data indicated that roots harbor a distinct bacterial community, which clearly differed from the microbiome of the rhizosphere and bulk soil. Our results revealed Pseudomonadaceae, Enterobacteriaceae and Comamonadaceae as the most abundant endophytes independently of land use intensity. Rhizosphere and bulk soil were dominated also by Proteobacteria, but the most abundant families differed from those obtained from root samples. In the soil, the effect of land use intensity was more pronounced compared to root endophytes leading to a clearly distinct pattern of bacterial communities under different LUI from rhizosphere and bulk soil vs. endophytes. Overall, a change of community structure on the plant-soil interface was observed, as the number of shared OTUs between all three compartments investigated increased with decreasing land use intensity. Thus, our findings suggest a stronger interaction of the plant with its surrounding soil under low land use intensity. Furthermore, the amount and quality of available nitrogen was identified as a major driver for shifts in the microbiome structure in all compartments.
Collapse
Affiliation(s)
- Jennifer Estendorfer
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum MünchenNeuherberg, Germany
| | - Barbara Stempfhuber
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum MünchenNeuherberg, Germany
| | - Paula Haury
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum MünchenNeuherberg, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum MünchenNeuherberg, Germany
| | | | - Jasmin Joshi
- Biodiversity Research/Systematic Botany, Institute for Biochemistry und Biology, University of PotsdamPotsdam, Germany
| | - Peter Schröder
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum MünchenNeuherberg, Germany
- *Correspondence: Peter Schröder,
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum MünchenNeuherberg, Germany
- Chair of Soil Science, Technical University of MunichFreising, Germany
| |
Collapse
|
13
|
Armanhi JSL, de Souza RSC, Damasceno NDB, de Araújo LM, Imperial J, Arruda P. A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome. FRONTIERS IN PLANT SCIENCE 2017; 8:2191. [PMID: 29354144 PMCID: PMC5759035 DOI: 10.3389/fpls.2017.02191] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/12/2017] [Indexed: 05/08/2023]
Abstract
The soil-plant ecosystem harbors an immense microbial diversity that challenges investigative approaches to study traits underlying plant-microbe association. Studies solely based on culture-dependent techniques have overlooked most microbial diversity. Here we describe the concomitant use of culture-dependent and -independent techniques to target plant-beneficial microbial groups from the sugarcane microbiome. The community-based culture collection (CBC) approach was used to access microbes from roots and stalks. The CBC recovered 399 unique bacteria representing 15.9% of the rhizosphere core microbiome and 61.6-65.3% of the endophytic core microbiomes of stalks. By cross-referencing the CBC (culture-dependent) with the sugarcane microbiome profile (culture-independent), we designed a synthetic community comprised of naturally occurring highly abundant bacterial groups from roots and stalks, most of which has been poorly explored so far. We then used maize as a model to probe the abundance-based synthetic inoculant. We show that when inoculated in maize plants, members of the synthetic community efficiently colonize plant organs, displace the natural microbiota and dominate at 53.9% of the rhizosphere microbial abundance. As a result, inoculated plants increased biomass by 3.4-fold as compared to uninoculated plants. The results demonstrate that abundance-based synthetic inoculants can be successfully applied to recover beneficial plant microbes from plant microbiota.
Collapse
Affiliation(s)
- Jaderson Silveira Leite Armanhi
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Rafael Soares Correa de Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Natália de Brito Damasceno
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Laura M. de Araújo
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
- Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Paulo Arruda
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
- *Correspondence: Paulo Arruda
| |
Collapse
|
14
|
Lee SJ, Thapa LP, Lee JH, Choi HS, Kim SB, Park C, Kim SW. Stimulation of 2,3-butanediol production by upregulation of alsR gene transcription level with acetate addition in Enterobacter aerogenes ATCC 29007. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
15
|
Luo G, Huang L, Su Y, Qin Y, Xu X, Zhao L, Yan Q. flrA, flrB and flrC regulate adhesion by controlling the expression of critical virulence genes in Vibrio alginolyticus. Emerg Microbes Infect 2016; 5:e85. [PMID: 27485498 PMCID: PMC5034100 DOI: 10.1038/emi.2016.82] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 12/24/2022]
Abstract
Adhesion is an important virulence trait of Vibrio alginolyticus. Bacterial adhesion is influenced by environmental conditions; however, the molecular mechanism underlying this effect remains unknown. The expression levels of flrA, flrB and flrC were significantly downregulated in adhesion-deficient V. alginolyticus strains cultured under Cu2+, Pb2+, Hg2+ and low-pH stresses. Silencing these genes led to deficiencies in adhesion, motility, flagellar assembly, biofilm formation and exopolysaccharide (EPS) production. The expression levels of fliA, flgH, fliS, fliD, cheR, cheV and V12G01_22158 (Gene ID) were significantly downregulated in all of the RNAi groups, whereas the expression levels of toxT, ctxB, acfA, hlyA and tlh were upregulated in flrA- and flrC-silenced groups. These genes play a key role in the virulence mechanisms of most pathogenic Vibrio species. Furthermore, the expression of flrA, flrB and flrC was significantly influenced by temperature, salinity, starvation and pH. These results indicate that (1) flrA, flrB and flrC are important for V. alginolyticus adhesion; (2) flrA, flrB and flrC significantly influence bacterial adhesion, motility, biofilm formation and EPS production by controlling expression of key genes involved in those phenotypes; and (3) flrA, flrB and flrC regulate adhesion in the natural environment with different temperatures, pH levels, salinities and starvation time.
Collapse
Affiliation(s)
- Gang Luo
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian 361021, China
| | - Lixing Huang
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian 361021, China
| | - Yongquan Su
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361102, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde, Fujian 352000, China
| | - Yingxue Qin
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian 361021, China
| | - Xiaojin Xu
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian 361021, China
| | - Lingmin Zhao
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian 361021, China
| | - Qingpi Yan
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian 361021, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde, Fujian 352000, China
| |
Collapse
|
16
|
Timm CM, Campbell AG, Utturkar SM, Jun SR, Parales RE, Tan WA, Robeson MS, Lu TYS, Jawdy S, Brown SD, Ussery DW, Schadt CW, Tuskan GA, Doktycz MJ, Weston DJ, Pelletier DA. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment. Front Microbiol 2015; 6:1118. [PMID: 26528266 PMCID: PMC4604316 DOI: 10.3389/fmicb.2015.01118] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/28/2015] [Indexed: 12/13/2022] Open
Abstract
The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates.
Collapse
Affiliation(s)
- Collin M Timm
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Alisha G Campbell
- Department of Natural Sciences, Northwest Missouri State University Maryville, MO, USA
| | - Sagar M Utturkar
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Se-Ran Jun
- Joint Institute for Computational Sciences, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Rebecca E Parales
- Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA
| | - Watumesa A Tan
- Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA
| | - Michael S Robeson
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Fish, Wildlife and Conservation Biology, Colorado State University Fort Collins, CO, USA
| | - Tse-Yuan S Lu
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - David W Ussery
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Department of Microbiology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| |
Collapse
|
17
|
Firrincieli A, Otillar R, Salamov A, Schmutz J, Khan Z, Redman RS, Fleck ND, Lindquist E, Grigoriev IV, Doty SL. Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1. Front Microbiol 2015; 6:978. [PMID: 26441909 PMCID: PMC4585186 DOI: 10.3389/fmicb.2015.00978] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 09/03/2015] [Indexed: 12/22/2022] Open
Affiliation(s)
- Andrea Firrincieli
- Department for Innovation Biological, Agro-Food and Forest System, University of Tuscia Tuscia, Italy
| | - Robert Otillar
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Asaf Salamov
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA ; HudsonAlpha Institute for Biotechnology Huntsville, AL, USA
| | - Zareen Khan
- School of Environmental and Forest Sciences, University of Washington Seattle, WA, USA
| | | | - Neil D Fleck
- School of Environmental and Forest Sciences, University of Washington Seattle, WA, USA
| | - Erika Lindquist
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Sharon L Doty
- School of Environmental and Forest Sciences, University of Washington Seattle, WA, USA
| |
Collapse
|