1
|
de Pedro-Jové R, Corral J, Rocafort M, Puigvert M, Azam FL, Vandecaveye A, Macho AP, Balsalobre C, Coll NS, Orellano E, Valls M. Gene expression changes throughout the life cycle allow a bacterial plant pathogen to persist in diverse environmental habitats. PLoS Pathog 2023; 19:e1011888. [PMID: 38113281 PMCID: PMC10763947 DOI: 10.1371/journal.ppat.1011888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/03/2024] [Accepted: 12/07/2023] [Indexed: 12/21/2023] Open
Abstract
Bacterial pathogens exhibit a remarkable ability to persist and thrive in diverse ecological niches. Understanding the mechanisms enabling their transition between habitats is crucial to control dissemination and potential disease outbreaks. Here, we use Ralstonia solanacearum, the causing agent of the bacterial wilt disease, as a model to investigate pathogen adaptation to water and soil, two environments that act as bacterial reservoirs, and compare this information with gene expression in planta. Gene expression in water resembled that observed during late xylem colonization, with an intriguing induction of the type 3 secretion system (T3SS). Alkaline pH and nutrient scarcity-conditions also encountered during late infection stages-were identified as the triggers for this T3SS induction. In the soil environment, R. solanacearum upregulated stress-responses and genes for the use of alternate carbon sources, such as phenylacetate catabolism and the glyoxylate cycle, and downregulated virulence-associated genes. We proved through gain- and loss-of-function experiments that genes associated with the oxidative stress response, such as the regulator OxyR and the catalase KatG, are key for bacterial survival in soil, as their deletion cause a decrease in culturability associated with a premature induction of the viable but non culturable state (VBNC). This work identifies essential factors necessary for R. solanacearum to complete its life cycle and is the first comprehensive gene expression analysis in all environments occupied by a bacterial plant pathogen, providing valuable insights into its biology and adaptation to unexplored habitats.
Collapse
Affiliation(s)
- Roger de Pedro-Jové
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Jordi Corral
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Mercedes Rocafort
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Marina Puigvert
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Fàtima Latif Azam
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Agustina Vandecaveye
- Área Biología Molecular, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR-UNR-CONICET), Rosario, Santa Fe, Argentina
| | - Alberto P. Macho
- Shanghai Centre for Plant Stress Biology, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Carlos Balsalobre
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Núria S. Coll
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Elena Orellano
- Área Biología Molecular, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR-UNR-CONICET), Rosario, Santa Fe, Argentina
| | - Marc Valls
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| |
Collapse
|
2
|
Liu Q, Li C, Zhang X, Ding M, Liao X, Yan J, Hu M, Yang L, Wang X, Liao L, Li P, Zhou X. PhcX Is a LqsR-family response regulator that contributes to Ralstonia solanacearum virulence and regulates multiple virulence factors. mBio 2023; 14:e0202823. [PMID: 37787568 PMCID: PMC10653808 DOI: 10.1128/mbio.02028-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/15/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE The bacterial wilt caused by the soil-borne phytopathogen Ralstonia solanacearum is one of the most destructive crop diseases. To achieve a successful infection, R. solanacearum has evolved an intricate regulatory network to orchestrate the expression of an arsenal of virulence factors and fine-tune the allocation of energy. However, despite the wealth of knowledge gained in the past decades, many players and connections are still missing from the network. The importance of our study lies in the identification of PhcX, a novel conserved global regulator with critical roles in modulating the virulence and metabolism of R. solanacearum. PhcX affects many well-characterized regulators and exhibits contrasting modes of regulation from the central regulator PhcA on a variety of virulence-associated traits and genes. Our findings add a valuable piece to the puzzle of how the pathogen regulates its proliferation and infection, which is critical for understanding its pathogenesis and developing disease control strategies.
Collapse
Affiliation(s)
- Qingmei Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Chuhao Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Xiaohan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Mengfan Ding
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Xinyue Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Jinli Yan
- School of Agricultural Science, Xichang University, Xichang, China
| | - Ming Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Leilei Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Xiaoqing Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Lisheng Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Peng Li
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Provincial Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| |
Collapse
|
3
|
Plant-Pathogenic Ralstonia Phylotypes Evolved Divergent Respiratory Strategies and Behaviors To Thrive in Xylem. mBio 2023; 14:e0318822. [PMID: 36744950 PMCID: PMC9973335 DOI: 10.1128/mbio.03188-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacterial pathogens in the Ralstonia solanacearum species complex (RSSC) infect the water-transporting xylem vessels of plants, causing bacterial wilt disease. Strains in RSSC phylotypes I and III can reduce nitrate to dinitrogen via complete denitrification. The four-step denitrification pathway enables bacteria to use inorganic nitrogen species as terminal electron acceptors, supporting their growth in oxygen-limited environments such as biofilms or plant xylem. Reduction of nitrate, nitrite, and nitric oxide all contribute to the virulence of a model phylotype I strain. However, little is known about the physiological role of the last denitrification step, the reduction of nitrous oxide to dinitrogen by NosZ. We found that phylotypes I and III need NosZ for full virulence. However, strains in phylotypes II and IV are highly virulent despite lacking NosZ. The ability to respire by reducing nitrate to nitrous oxide does not greatly enhance the growth of phylotype II and IV strains. These partial denitrifying strains reach high cell densities during plant infection and cause typical wilt disease. However, unlike phylotype I and III strains, partial denitrifiers cannot grow well under anaerobic conditions or form thick biofilms in culture or in tomato xylem vessels. Furthermore, aerotaxis assays show that strains from different phylotypes have different oxygen and nitrate preferences. Together, these results indicate that the RSSC contains two subgroups that occupy the same habitat but have evolved divergent energy metabolism strategies to exploit distinct metabolic niches in the xylem. IMPORTANCE Plant-pathogenic Ralstonia spp. are a heterogeneous globally distributed group of bacteria that colonize plant xylem vessels. Ralstonia cells multiply rapidly in plants and obstruct water transport, causing fatal wilting and serious economic losses of many key food security crops. The virulence of these pathogens depends on their ability to grow to high cell densities in the low-oxygen xylem environment. Plant-pathogenic Ralstonia can use denitrifying respiration to generate ATP. The last denitrification step, nitrous oxide reduction by NosZ, contributes to energy production and virulence for only one of the three phytopathogenic Ralstonia species. These complete denitrifiers form thicker biofilms in culture and in tomato xylem, suggesting they are better adapted to hypoxic niches. Strains with partial denitrification physiology form less biofilm and are more often planktonic. They are nonetheless highly virulent. Thus, these closely related bacteria have adapted their core metabolic functions to exploit distinct microniches in the same habitat.
Collapse
|
4
|
Lin H, Ascher DB, Myung Y, Lamborg CH, Hallam SJ, Gionfriddo CM, Holt KE, Moreau JW. Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. THE ISME JOURNAL 2021; 15:1810-1825. [PMID: 33504941 DOI: 10.1101/2020.06.03.132969] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/17/2020] [Indexed: 05/21/2023]
Abstract
Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin that accumulates in terrestrial and marine food webs, with potential impacts on human health. This process requires the gene pair hgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet, British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicts that Marinimicrobia HgcAB proteins contain the highly conserved amino acid sites and folding structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognized.
Collapse
Affiliation(s)
- Heyu Lin
- School of Earth Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, PO Box 6492, Melbourne, VIC, 3004, Australia
| | - Yoochan Myung
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, PO Box 6492, Melbourne, VIC, 3004, Australia
| | - Carl H Lamborg
- Department of Ocean Sciences, University of California, Santa Cruz, CA, 95064, USA
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Caitlin M Gionfriddo
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN, 37831, USA
- Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Monash, VIC, 3800, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - John W Moreau
- School of Earth Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Currently at School of Geographical & Earth Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
| |
Collapse
|
5
|
Lin H, Ascher DB, Myung Y, Lamborg CH, Hallam SJ, Gionfriddo CM, Holt KE, Moreau JW. Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. THE ISME JOURNAL 2021; 15:1810-1825. [PMID: 33504941 PMCID: PMC8163782 DOI: 10.1038/s41396-020-00889-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/17/2020] [Indexed: 01/30/2023]
Abstract
Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin that accumulates in terrestrial and marine food webs, with potential impacts on human health. This process requires the gene pair hgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet, British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicts that Marinimicrobia HgcAB proteins contain the highly conserved amino acid sites and folding structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognized.
Collapse
Affiliation(s)
- Heyu Lin
- grid.1008.90000 0001 2179 088XSchool of Earth Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - David B. Ascher
- grid.1008.90000 0001 2179 088XStructural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1051.50000 0000 9760 5620Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, PO Box 6492, Melbourne, VIC 3004 Australia
| | - Yoochan Myung
- grid.1008.90000 0001 2179 088XStructural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1051.50000 0000 9760 5620Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, PO Box 6492, Melbourne, VIC 3004 Australia
| | - Carl H. Lamborg
- grid.205975.c0000 0001 0740 6917Department of Ocean Sciences, University of California, Santa Cruz, CA 95064 USA
| | - Steven J. Hallam
- grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z1 Canada ,grid.17091.3e0000 0001 2288 9830Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Caitlin M. Gionfriddo
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831 USA ,grid.419533.90000 0000 8612 0361Present Address: Smithsonian Environmental Research Center, Edgewater, MD 21037 USA
| | - Kathryn E. Holt
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Central Clinical School, Monash University, Monash, VIC 3800 Australia ,grid.8991.90000 0004 0425 469XDepartment of Infection Biology, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - John W. Moreau
- grid.1008.90000 0001 2179 088XSchool of Earth Sciences, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.8756.c0000 0001 2193 314XPresent Address: Currently at School of Geographical & Earth Sciences, University of Glasgow, Glasgow, G12 8QQ UK
| |
Collapse
|
6
|
Suresh P, Varathraju G, Shanmugaiah V, Almaary KS, Elbadawi YB, Mubarak A. Partial purification and characterization of 2, 4-diacetylphloroglucinol producing Pseudomonas fluorescens VSMKU3054 against bacterial wilt disease of tomato. Saudi J Biol Sci 2021; 28:2155-2167. [PMID: 33911932 PMCID: PMC8071909 DOI: 10.1016/j.sjbs.2021.02.073] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/17/2021] [Accepted: 02/22/2021] [Indexed: 11/27/2022] Open
Abstract
We find out the antimicrobial potential of partially purified 2,4-diacetylphloroglucinol (DAPG) against Ralstonia solanacearum and fungal plant pathogens isolated from tomato rhizobacterium Pseudomonas fluorescens VSMKU3054. The present study is mainly focused on the control of wilt disease of tomato by our isolate VSMKU3054 and DAPG. The cell free culture filtrate of P. fluorescens VSMKU3054 was significantly arrested the growth of R. solanacearum and fungal pathogens such as Rhizoctonia solani, Sclerotium rolfsii, Macrophomina phaseolina and Fusarium oxysporum compared to control. The existence of DAPG from the crude metabolites of P. fluorescens VSMKU3054 was confirmed on TLC with Rf value 0.34, which is coincide with that of authentic phloroglucinol. The partially purified DAPG exhibited much higher activity against R. solanacearum at 30 µg/ml than the fungal plant pathogens compared to control. The antimicrobial partially purified compound was identified as DAPG by UV, FT-IR and GC-MS analysis. The percentage of live cells of R. solanacearum when supplemented with DAPG at 30 µg/ml, significantly controlled the living nature of R. solanacearum up to 68% compared to tetracycline and universal control observed under high content screening analysis. The selected isolate P. fluorescens VSMKU3054 and DAPG significantly controlled wilt disease of tomato up to 59.5% and 42.12% on 3rd and 7th days compared to positive and negative control by detached leaf assay. Further, in silico analysis revealed that high interaction of DAPG encoding protease with lectin which is associated with R. solanacearum. Based on our findings, we confirmed that P. fluorescens VSMKU3054 and DAPG could be used a potential bio inoculants for the management of bacterial wilt disease of tomato.
Collapse
Affiliation(s)
- Perumal Suresh
- Department of Microbial Technology, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, Tamil Nadu, India
| | - Govintharaj Varathraju
- Department of Microbial Technology, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, Tamil Nadu, India
| | - Vellasamy Shanmugaiah
- Department of Microbial Technology, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, Tamil Nadu, India
| | - Khalid S Almaary
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - Yahya B Elbadawi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - Ayman Mubarak
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| |
Collapse
|
7
|
Sun M, Jing Y, Zhao X, Teng W, Qiu L, Zheng H, Li W, Han Y. Genome-wide association study of partial resistance to sclerotinia stem rot of cultivated soybean based on the detached leaf method. PLoS One 2020; 15:e0233366. [PMID: 32421759 PMCID: PMC7233537 DOI: 10.1371/journal.pone.0233366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
Sclerotinia stem rot (SSR) is a devastating fungal disease that causes severe yield losses of soybean worldwide. In the present study, a representative population of 185 soybean accessions was selected and utilized to identify the quantitative trait nucleotide (QTN) of partial resistance to soybean SSR via a genome-wide association study (GWAS). A total of 22,048 single-nucleotide polymorphisms (SNPs) with minor allele frequencies (MAF) > 5% and missing data < 3% were used to assess linkage disequilibrium (LD) levels. Association signals associated with SSR partial resistance were identified by two models, including compressed mixed linear model (CMLM) and multi-locus random-SNP-effect mixed linear model (mrMLM). Finally, seven QTNs with major effects (a known locus and six novel loci) via CMLM and nine novel QTNs with minor effects via mrMLM were detected in relation to partial resistance to SSR, respectively. One of all the novel loci (Gm05:14834789 on Chr.05), which was co-located by these two methods, might be a stable one that showed high significance in SSR partial resistance. Additionally, a total of 71 major and 85 minor candidate genes located in the 200-kb genomic region of each peak SNP detected by CMLM and mrMLM were found, respectively. By using a gene-based association, a total of six SNPs from three major effects genes and eight SNPs from four minor effects genes were identified. Of them, Glyma.18G012200 has been characterized as a significant element in controlling fungal disease in plants.
Collapse
Affiliation(s)
- Mingming Sun
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
- Heilongjiang Journal Press of Agricultural Science and Technology, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yan Jing
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongkun Zheng
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| |
Collapse
|
8
|
Elsayed TR, Jacquiod S, Nour EH, Sørensen SJ, Smalla K. Biocontrol of Bacterial Wilt Disease Through Complex Interaction Between Tomato Plant, Antagonists, the Indigenous Rhizosphere Microbiota, and Ralstonia solanacearum. Front Microbiol 2020; 10:2835. [PMID: 31998244 PMCID: PMC6967407 DOI: 10.3389/fmicb.2019.02835] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/22/2019] [Indexed: 11/25/2022] Open
Abstract
Ralstonia solanacearum (biovar2, race3) is the causal agent of bacterial wilt and this quarantine phytopathogen is responsible for massive losses in several commercially important crops. Biological control of this pathogen might become a suitable plant protection measure in areas where R. solanacearum is endemic. Two bacterial strains, Bacillus velezensis (B63) and Pseudomonas fluorescens (P142) with in vitro antagonistic activity toward R. solanacearum (B3B) were tested for rhizosphere competence, efficient biological control of wilt symptoms on greenhouse-grown tomato, and effects on the indigenous rhizosphere prokaryotic communities. The population densities of B3B and the antagonists were estimated in rhizosphere community DNA by selective plating, real-time quantitative PCR, and R. solanacearum-specific fliC PCR-Southern blot hybridization. Moreover, we investigated how the pathogen and/or the antagonists altered the composition of the tomato rhizosphere prokaryotic community by 16S rRNA gene amplicon sequencing. B. velezensis (B63) and P. fluorescens (P142)-inoculated plants showed drastically reduced wilt disease symptoms, accompanied by significantly lower abundance of the B3B population compared to the non-inoculated pathogen control. Pronounced shifts in prokaryotic community compositions were observed in response to the inoculation of B63 or P142 in the presence or absence of the pathogen B3B and numerous dynamic taxa were identified. Confocal laser scanning microscopy (CLSM) visualization of the gfp-tagged antagonist P142 revealed heterogeneous colonization patterns and P142 was detected in lateral roots, root hairs, epidermal cells, and within xylem vessels. Although competitive niche exclusion cannot be excluded, it is more likely that the inoculation of P142 or B63 and the corresponding microbiome shifts primed the plant defense against the pathogen B3B. Both inoculants are promising biological agents for efficient control of R. solanacearum under field conditions.
Collapse
Affiliation(s)
- Tarek R Elsayed
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany.,Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Samuel Jacquiod
- Marine Microbiological Section, Department of Biology, Faculty of Natural and Life Sciences, University of Copenhagen, Copenhagen, Denmark.,Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Eman H Nour
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Søren J Sørensen
- Marine Microbiological Section, Department of Biology, Faculty of Natural and Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| |
Collapse
|
9
|
Ferro P, Vaz-Moreira I, Manaia CM. Betaproteobacteria are predominant in drinking water: are there reasons for concern? Crit Rev Microbiol 2019; 45:649-667. [PMID: 31686572 DOI: 10.1080/1040841x.2019.1680602] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Betaproteobacteria include some of the most abundant and ubiquitous bacterial genera that can be found in drinking water, including mineral water. The combination of physiology and ecology traits place some Betaproteobacteria in the list of potential, yet sometimes neglected, opportunistic pathogens that can be transmitted by water or aqueous solutions. Indeed, some drinking water Betaproteobacteria with intrinsic and sometimes acquired antibiotic resistance, harbouring virulence factors and often found in biofilm structures, can persist after water disinfection and reach the consumer. This literature review summarises and discusses the current knowledge about the occurrence and implications of Betaproteobacteria in drinking water. Although the sparse knowledge on the ecology and physiology of Betaproteobacteria thriving in tap or bottled natural mineral/spring drinking water (DW) is an evidence of this review, it is demonstrated that DW holds a high diversity of Betaproteobacteria, whose presence may not be innocuous. Frequently belonging to genera also found in humans, DW Betaproteobacteria are ubiquitous in different habitats, have the potential to resist antibiotics either due to intrinsic or acquired mechanisms, and hold different virulence factors. The combination of these factors places DW Betaproteobacteria in the list of candidates of emerging opportunistic pathogens. Improved bacterial identification of clinical isolates associated with opportunistic infections and additional genomic and physiological studies may contribute to elucidate the potential impact of these bacteria.
Collapse
Affiliation(s)
- Pompeyo Ferro
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| |
Collapse
|
10
|
Refojo PN, Sena FV, Calisto F, Sousa FM, Pereira MM. The plethora of membrane respiratory chains in the phyla of life. Adv Microb Physiol 2019; 74:331-414. [PMID: 31126533 DOI: 10.1016/bs.ampbs.2019.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The diversity of microbial cells is reflected in differences in cell size and shape, motility, mechanisms of cell division, pathogenicity or adaptation to different environmental niches. All these variations are achieved by the distinct metabolic strategies adopted by the organisms. The respiratory chains are integral parts of those strategies especially because they perform the most or, at least, most efficient energy conservation in the cell. Respiratory chains are composed of several membrane proteins, which perform a stepwise oxidation of metabolites toward the reduction of terminal electron acceptors. Many of these membrane proteins use the energy released from the oxidoreduction reaction they catalyze to translocate charges across the membrane and thus contribute to the establishment of the membrane potential, i.e. they conserve energy. In this work we illustrate and discuss the composition of the respiratory chains of different taxonomic clades, based on bioinformatic analyses and on biochemical data available in the literature. We explore the diversity of the respiratory chains of Animals, Plants, Fungi and Protists kingdoms as well as of Prokaryotes, including Bacteria and Archaea. The prokaryotic phyla studied in this work are Gammaproteobacteria, Betaproteobacteria, Epsilonproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Chlamydiae, Verrucomicrobia, Acidobacteria, Planctomycetes, Cyanobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Aquificae, Thermotogae, Deferribacteres, Nitrospirae, Euryarchaeota, Crenarchaeota and Thaumarchaeota.
Collapse
Affiliation(s)
- Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipa Calisto
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal; University of Lisboa, Faculty of Sciences, BIOISI- Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| |
Collapse
|
11
|
Durand A, Bourbon ML, Steunou AS, Khalfaoui-Hassani B, Legrand C, Guitton A, Astier C, Ouchane S. Biogenesis of the bacterial cbb3 cytochrome c oxidase: Active subcomplexes support a sequential assembly model. J Biol Chem 2017; 293:808-818. [PMID: 29150446 DOI: 10.1074/jbc.m117.805184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/30/2017] [Indexed: 11/06/2022] Open
Abstract
The cbb3 oxidase has a high affinity for oxygen and is required for growth of bacteria, including pathogens, in oxygen-limited environments. However, the assembly of this oxidase is poorly understood. Most cbb3 are composed of four subunits: the catalytic CcoN subunit, the two cytochrome c subunits (CcoO and CcoP) involved in electron transfer, and the small CcoQ subunit with an unclear function. Here, we address the role of these four subunits in cbb3 biogenesis in the purple bacterium Rubrivivax gelatinosus Analyses of membrane proteins from different mutants revealed the presence of active CcoNQO and CcoNO subcomplexes and also showed that the CcoP subunit is not essential for their assembly. However, CcoP was required for the oxygen reduction activity in the absence of CcoQ. We also found that CcoQ is dispensable for forming an active CcoNOP subcomplex in membranes. CcoNOP exhibited oxygen reductase activity, indicating that the cofactors (hemes b and copper for CcoN and cytochromes c for CcoO and CcoP) were present within the subunits. Finally, we discovered the presence of a CcoNQ subcomplex and showed that CcoN is the required anchor for the assembly of the full CcoNQOP complex. On the basis of these findings, we propose a sequential assembly model in which the CcoQ subunit is required for the early maturation step: CcoQ first associates with CcoN before the CcoNQ-CcoO interaction. CcoP associates to CcoNQO subcomplex in the late maturation step, and once the CcoNQOP complex is fully formed, CcoQ is released for degradation by the FtsH protease. This model could be conserved in other bacteria, including the pathogenic bacteria lacking the assembly factor CcoH as in R. gelatinosus.
Collapse
Affiliation(s)
- Anne Durand
- From the Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Marie-Line Bourbon
- From the Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Anne-Soisig Steunou
- From the Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Bahia Khalfaoui-Hassani
- From the Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Camille Legrand
- From the Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Audrey Guitton
- From the Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Chantal Astier
- From the Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Soufian Ouchane
- From the Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Énergie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| |
Collapse
|
12
|
Puigvert M, Guarischi-Sousa R, Zuluaga P, Coll NS, Macho AP, Setubal JC, Valls M. Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii. FRONTIERS IN PLANT SCIENCE 2017; 8:370. [PMID: 28373879 PMCID: PMC5357869 DOI: 10.3389/fpls.2017.00370] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/02/2017] [Indexed: 05/03/2023]
Abstract
Bacterial wilt of potatoes-also called brown rot-is a devastating disease caused by the vascular pathogen Ralstonia solanacearum that leads to significant yield loss. As in other plant-pathogen interactions, the first contacts established between the bacterium and the plant largely condition the disease outcome. Here, we studied the transcriptome of R. solanacearum UY031 early after infection in two accessions of the wild potato Solanum commersonii showing contrasting resistance to bacterial wilt. Total RNAs obtained from asymptomatic infected roots were deep sequenced and for 4,609 out of the 4,778 annotated genes in strain UY031 were recovered. Only 2 genes were differentially-expressed between the resistant and the susceptible plant accessions, suggesting that the bacterial component plays a minor role in the establishment of disease. On the contrary, 422 genes were differentially expressed (DE) in planta compared to growth on a synthetic rich medium. Only 73 of these genes had been previously identified as DE in a transcriptome of R. solanacearum extracted from infected tomato xylem vessels. Virulence determinants such as the Type Three Secretion System (T3SS) and its effector proteins, motility structures, and reactive oxygen species (ROS) detoxifying enzymes were induced during infection of S. commersonii. On the contrary, metabolic activities were mostly repressed during early root colonization, with the notable exception of nitrogen metabolism, sulfate reduction and phosphate uptake. Several of the R. solanacearum genes identified as significantly up-regulated during infection had not been previously described as virulence factors. This is the first report describing the R. solanacearum transcriptome directly obtained from infected tissue and also the first to analyze bacterial gene expression in the roots, where plant infection takes place. We also demonstrate that the bacterial transcriptome in planta can be studied when pathogen numbers are low by sequencing transcripts from infected tissue avoiding prokaryotic RNA enrichment.
Collapse
Affiliation(s)
- Marina Puigvert
- Department of Genetics, University of BarcelonaBarcelona, Spain
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
| | | | - Paola Zuluaga
- Department of Genetics, University of BarcelonaBarcelona, Spain
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
| | - Núria S. Coll
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
| | - Alberto P. Macho
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences (CAS)Shanghai, China
| | - João C. Setubal
- Department of Biochemistry, University of São PauloSão Paulo, Brazil
| | - Marc Valls
- Department of Genetics, University of BarcelonaBarcelona, Spain
- Centre for Research in Agricultural Genomics CSIC-IRTA, Autonomous University of BarcelonaBellaterra, Spain
| |
Collapse
|
13
|
Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota. mSystems 2017; 2:mSystems00171-16. [PMID: 28168224 PMCID: PMC5285517 DOI: 10.1128/msystems.00171-16] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 01/04/2017] [Indexed: 01/01/2023] Open
Abstract
Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease. Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem. IMPORTANCE Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease.
Collapse
|
14
|
Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)). Stand Genomic Sci 2016; 11:38. [PMID: 27274784 PMCID: PMC4891895 DOI: 10.1186/s40793-016-0162-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 05/24/2016] [Indexed: 02/01/2023] Open
Abstract
Thioalkalimicrobium cyclicum Sorokin et al. 2002 is a member of the family Piscirickettsiaceae in the order Thiotrichales. The γ-proteobacterium belongs to the colourless sulfur-oxidizing bacteria isolated from saline soda lakes with stable alkaline pH, such as Lake Mono (California) and Soap Lake (Washington State). Strain ALM 1T is characterized by its adaptation to life in the oxic/anoxic interface towards the less saline aerobic waters (mixolimnion) of the stable stratified alkaline salt lakes. Strain ALM 1T is the first representative of the genus Thioalkalimicrobium whose genome sequence has been deciphered and the fourth genome sequence of a type strain of the Piscirickettsiaceae to be published. The 1,932,455 bp long chromosome with its 1,684 protein-coding and 50 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008.
Collapse
|
15
|
Ailloud F, Lowe TM, Robène I, Cruveiller S, Allen C, Prior P. In planta comparative transcriptomics of host-adapted strains of Ralstonia solanacearum. PeerJ 2016; 4:e1549. [PMID: 26788428 PMCID: PMC4715432 DOI: 10.7717/peerj.1549] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/09/2015] [Indexed: 01/01/2023] Open
Abstract
Background. Ralstonia solanacearum is an economically important plant pathogen with an unusually large host range. The Moko (banana) and NPB (not pathogenic to banana) strain groups are closely related but are adapted to distinct hosts. Previous comparative genomics studies uncovered very few differences that could account for the host range difference between these pathotypes. To better understand the basis of this host specificity, we used RNAseq to profile the transcriptomes of an R. solanacearum Moko strain and an NPB strain under in vitro and in planta conditions. Results. RNAs were sequenced from bacteria grown in rich and minimal media, and from bacteria extracted from mid-stage infected tomato, banana and melon plants. We computed differential expression between each pair of conditions to identify constitutive and host-specific gene expression differences between Moko and NPB. We found that type III secreted effectors were globally up-regulated upon plant cell contact in the NPB strain compared with the Moko strain. Genes encoding siderophore biosynthesis and nitrogen assimilation genes were highly up-regulated in the NPB strain during melon pathogenesis, while denitrification genes were up-regulated in the Moko strain during banana pathogenesis. The relatively lower expression of oxidases and the denitrification pathway during banana pathogenesis suggests that R. solanacearum experiences higher oxygen levels in banana pseudostems than in tomato or melon xylem. Conclusions. This study provides the first report of differential gene expression associated with host range variation. Despite minimal genomic divergence, the pathogenesis of Moko and NPB strains is characterized by striking differences in expression of virulence- and metabolism-related genes.
Collapse
Affiliation(s)
- Florent Ailloud
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération International en Recherche Agronomique pour le Développement, Saint-Pierre, France; Laboratoire de la Santé des Végétaux, Agence Nationale Sécurité Sanitaire Alimentaire Nationale, Saint-Pierre, France
| | - Tiffany M Lowe
- Department of Plant Pathology, University of Wisconsin-Madison , Madison, WI , United States
| | - Isabelle Robène
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération International en Recherche Agronomique pour le Développement , Saint-Pierre , France
| | - Stéphane Cruveiller
- Laboratoire d'Analyses Bioinformatiques pour la Genomique et le Metabolisme, Commissariat à l'Energie Atomique et aux Energies Alternatives, Evry, France; UMR CNRS 8030 - Génomique Métabolique, Centre National de la Recherche Scientifique, Evry, France
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison , Madison, WI , United States
| | - Philippe Prior
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération International en Recherche Agronomique pour le Développement, Saint-Pierre, France; Département de Santé des Plantes et Environnement, Institut National de la Recherche Agronomique, Sophia Antipolis, France
| |
Collapse
|
16
|
Ralstonia solanacearum uses inorganic nitrogen metabolism for virulence, ATP production, and detoxification in the oxygen-limited host xylem environment. mBio 2015; 6:e02471. [PMID: 25784703 PMCID: PMC4453514 DOI: 10.1128/mbio.02471-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Genomic data predict that, in addition to oxygen, the bacterial plant pathogen Ralstonia solanacearum can use nitrate (NO3−), nitrite (NO2−), nitric oxide (NO), and nitrous oxide (N2O) as terminal electron acceptors (TEAs). Genes encoding inorganic nitrogen reduction were highly expressed during tomato bacterial wilt disease, when the pathogen grows in xylem vessels. Direct measurements found that tomato xylem fluid was low in oxygen, especially in plants infected by R. solanacearum. Xylem fluid contained ~25 mM NO3−, corresponding to R. solanacearum’s optimal NO3− concentration for anaerobic growth in vitro. We tested the hypothesis that R. solanacearum uses inorganic nitrogen species to respire and grow during pathogenesis by making deletion mutants that each lacked a step in nitrate respiration (ΔnarG), denitrification (ΔaniA, ΔnorB, and ΔnosZ), or NO detoxification (ΔhmpX). The ΔnarG, ΔaniA, and ΔnorB mutants grew poorly on NO3− compared to the wild type, and they had reduced adenylate energy charge levels under anaerobiosis. While NarG-dependent NO3− respiration directly enhanced growth, AniA-dependent NO2− reduction did not. NO2− and NO inhibited growth in culture, and their removal depended on denitrification and NO detoxification. Thus, NO3− acts as a TEA, but the resulting NO2− and NO likely do not. None of the mutants grew as well as the wild type in planta, and strains lacking AniA (NO2− reductase) or HmpX (NO detoxification) had reduced virulence on tomato. Thus, R. solanacearum exploits host NO3− to respire, grow, and cause disease. Degradation of NO2− and NO is also important for successful infection and depends on denitrification and NO detoxification systems. The plant-pathogenic bacterium Ralstonia solanacearum causes bacterial wilt, one of the world’s most destructive crop diseases. This pathogen’s explosive growth in plant vascular xylem is poorly understood. We used biochemical and genetic approaches to show that R. solanacearum rapidly depletes oxygen in host xylem but can then respire using host nitrate as a terminal electron acceptor. The microbe uses its denitrification pathway to detoxify the reactive nitrogen species nitrite (a product of nitrate respiration) and nitric oxide (a plant defense signal). Detoxification may play synergistic roles in bacterial wilt virulence by converting the host’s chemical weapon into an energy source. Mutant bacterial strains lacking elements of the denitrification pathway could not grow as well as the wild type in tomato plants, and some mutants were also reduced in virulence. Our results show how a pathogen’s metabolic activity can alter the host environment in ways that increase pathogen success.
Collapse
|
17
|
Lowe TM, Ailloud F, Allen C. Hydroxycinnamic Acid Degradation, a Broadly Conserved Trait, Protects Ralstonia solanacearum from Chemical Plant Defenses and Contributes to Root Colonization and Virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:286-97. [PMID: 25423265 PMCID: PMC4329107 DOI: 10.1094/mpmi-09-14-0292-fi] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Plants produce hydroxycinnamic acid (HCA) defense compounds to combat pathogens, such as the bacterium Ralstonia solanacearum. We showed that an HCA degradation pathway is genetically and functionally conserved across diverse R. solanacearum strains. Further, a feruloyl-CoA synthetase (Δfcs) mutant that cannot degrade HCA was less virulent on tomato plants. To understand the role of HCA degradation in bacterial wilt disease, we tested the following hypotheses: HCA degradation helps the pathogen i) grow, as a carbon source; ii) spread, by reducing HCA-derived physical barriers; and iii) survive plant antimicrobial compounds. Although HCA degradation enabled R. solanacearum growth on HCA in vitro, HCA degradation was dispensable for growth in xylem sap and root exudate, suggesting that HCA are not significant carbon sources in planta. Acetyl-bromide quantification of lignin demonstrated that R. solanacearum infections did not affect the gross quantity or distribution of stem lignin. However, the Δfcs mutant was significantly more susceptible to inhibition by two HCA, namely, caffeate and p-coumarate. Finally, plant colonization assays suggested that HCA degradation facilitates early stages of infection and root colonization. Together, these results indicated that ability to degrade HCA contributes to bacterial wilt virulence by facilitating root entry and by protecting the pathogen from HCA toxicity.
Collapse
Affiliation(s)
- Tiffany M. Lowe
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Florent Ailloud
- Peuplements Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT), INRA-CIRAD, Saint Pierre, La Réunion, France
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
- Corresponding Author: Caitilyn Allen; ; 608-262-9578
| |
Collapse
|
18
|
Characterization of an ntrX mutant of Neisseria gonorrhoeae reveals a response regulator that controls expression of respiratory enzymes in oxidase-positive proteobacteria. J Bacteriol 2013; 195:2632-41. [PMID: 23564168 DOI: 10.1128/jb.02062-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
NtrYX is a sensor-histidine kinase/response regulator two-component system that has had limited characterization in a small number of Alphaproteobacteria. Phylogenetic analysis of the response regulator NtrX showed that this two-component system is extensively distributed across the bacterial domain, and it is present in a variety of Betaproteobacteria, including the human pathogen Neisseria gonorrhoeae. Microarray analysis revealed that the expression of several components of the respiratory chain was reduced in an N. gonorrhoeae ntrX mutant compared to that in the isogenic wild-type (WT) strain 1291. These included the cytochrome c oxidase subunit (ccoP), nitrite reductase (aniA), and nitric oxide reductase (norB). Enzyme activity assays showed decreased cytochrome oxidase and nitrite reductase activities in the ntrX mutant, consistent with microarray data. N. gonorrhoeae ntrX mutants had reduced capacity to survive inside primary cervical cells compared to the wild type, and although they retained the ability to form a biofilm, they exhibited reduced survival within the biofilm compared to wild-type cells, as indicated by LIVE/DEAD staining. Analyses of an ntrX mutant in a representative alphaproteobacterium, Rhodobacter capsulatus, showed that cytochrome oxidase activity was also reduced compared to that in the wild-type strain SB1003. Taken together, these data provide evidence that the NtrYX two-component system may be a key regulator in the expression of respiratory enzymes and, in particular, cytochrome c oxidase, across a wide range of proteobacteria, including a variety of bacterial pathogens.
Collapse
|
19
|
Genin S, Denny TP. Pathogenomics of the Ralstonia solanacearum species complex. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:67-89. [PMID: 22559068 DOI: 10.1146/annurev-phyto-081211-173000] [Citation(s) in RCA: 332] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Ralstonia solanacearum is a major phytopathogen that attacks many crops and other plants over a broad geographical range. The extensive genetic diversity of strains responsible for the various bacterial wilt diseases has in recent years led to the concept of an R. solanacearum species complex. Genome sequencing of more than 10 strains representative of the main phylogenetic groups has broadened our knowledge of the evolution and speciation of this pathogen and led to the identification of novel virulence-associated functions. Comparative genomic analyses are now opening the way for refined functional studies. The many molecular determinants involved in pathogenicity and host-range specificity are described, and we also summarize current understanding of their roles in pathogenesis and how their expression is tightly controlled by an intricate virulence regulatory network.
Collapse
Affiliation(s)
- Stéphane Genin
- INRA, Laboratoire des Interactions Plantes-Microorganismes, UMR441, F-31326 Castanet-Tolosan, France.
| | | |
Collapse
|
20
|
Remenant B, de Cambiaire JC, Cellier G, Jacobs JM, Mangenot S, Barbe V, Lajus A, Vallenet D, Medigue C, Fegan M, Allen C, Prior P. Ralstonia syzygii, the Blood Disease Bacterium and some Asian R. solanacearum strains form a single genomic species despite divergent lifestyles. PLoS One 2011; 6:e24356. [PMID: 21931687 PMCID: PMC3169583 DOI: 10.1371/journal.pone.0024356] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 08/06/2011] [Indexed: 12/19/2022] Open
Abstract
The Ralstonia solanacearum species complex includes R. solanacearum, R. syzygii, and the Blood Disease Bacterium (BDB). All colonize plant xylem vessels and cause wilt diseases, but with significant biological differences. R. solanacearum is a soilborne bacterium that infects the roots of a broad range of plants. R. syzygii causes Sumatra disease of clove trees and is actively transmitted by cercopoid insects. BDB is also pathogenic to a single host, banana, and is transmitted by pollinating insects. Sequencing and DNA-DNA hybridization studies indicated that despite their phenotypic differences, these three plant pathogens are actually very closely related, falling into the Phylotype IV subgroup of the R. solanacearum species complex. To better understand the relationships among these bacteria, we sequenced and annotated the genomes of R. syzygii strain R24 and BDB strain R229. These genomes were compared to strain PSI07, a closely related Phylotype IV tomato isolate of R. solanacearum, and to five additional R. solanacearum genomes. Whole-genome comparisons confirmed previous phylogenetic results: the three phylotype IV strains share more and larger syntenic regions with each other than with other R. solanacearum strains. Furthermore, the genetic distances between strains, assessed by an in-silico equivalent of DNA-DNA hybridization, unambiguously showed that phylotype IV strains of BDB, R. syzygii and R. solanacearum form one genomic species. Based on these comprehensive data we propose a revision of the taxonomy of the R. solanacearum species complex. The BDB and R. syzygii genomes encoded no obvious unique metabolic capacities and contained no evidence of horizontal gene transfer from bacteria occupying similar niches. Genes specific to R. syzygii and BDB were almost all of unknown function or extrachromosomal origin. Thus, the pathogenic life-styles of these organisms are more probably due to ecological adaptation and genomic convergence during vertical evolution than to the acquisition of DNA by horizontal transfer.
Collapse
Affiliation(s)
- Benoît Remenant
- Peuplements Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT), INRA-CIRAD, Saint Pierre, La Réunion, France
| | - Jean-Charles de Cambiaire
- Peuplements Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT), CIRAD, Saint Pierre, La Réunion, France
| | - Gilles Cellier
- Peuplements Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT), CIRAD, Saint Pierre, La Réunion, France
- Unité Ravageurs et Agents Pathogènes Tropicaux, Agence Nationale de Sécurité Sanitaire, Laboratoire de la Santé des Végétaux, Saint Pierre, La Réunion, France
| | - Jonathan M. Jacobs
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sophie Mangenot
- Institut de Génomique, Genoscope, Commissariat à l'Energie Atomique (CEA) Direction des Sciences du Vivant, Evry, France
| | - Valérie Barbe
- Institut de Génomique, Genoscope, Commissariat à l'Energie Atomique (CEA) Direction des Sciences du Vivant, Evry, France
| | - Aurélie Lajus
- Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, CNRS-UMR 8030, Evry, France
- Institut de Génomique, Genoscope, Commissariat à l'Energie Atomique (CEA) Direction des Sciences du Vivant, Evry, France
| | - David Vallenet
- Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, CNRS-UMR 8030, Evry, France
- Institut de Génomique, Genoscope, Commissariat à l'Energie Atomique (CEA) Direction des Sciences du Vivant, Evry, France
| | - Claudine Medigue
- Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, CNRS-UMR 8030, Evry, France
- Institut de Génomique, Genoscope, Commissariat à l'Energie Atomique (CEA) Direction des Sciences du Vivant, Evry, France
| | - Mark Fegan
- Department of Primary Industries, Biosciences Research Division, Attwood, Victoria, Australia
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Philippe Prior
- Peuplements Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT), INRA-CIRAD, Saint Pierre, La Réunion, France
- * E-mail:
| |
Collapse
|
21
|
Colburn-Clifford JM, Scherf JM, Allen C. Ralstonia solanacearum Dps contributes to oxidative stress tolerance and to colonization of and virulence on tomato plants. Appl Environ Microbiol 2010; 76:7392-9. [PMID: 20870795 PMCID: PMC2976212 DOI: 10.1128/aem.01742-10] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 09/14/2010] [Indexed: 02/06/2023] Open
Abstract
Ralstonia solanacearum, an economically important soilborne plant pathogen, infects host roots to cause bacterial wilt disease. However, little is known about this pathogen's behavior in the rhizosphere and early in pathogenesis. In response to root exudates from tomato, R. solanacearum strain UW551 upregulated a gene resembling Dps, a nonspecific DNA binding protein from starved cells that is critical for stress survival in other bacteria. An R. solanacearum dps mutant had increased hydrogen peroxide sensitivity and mutation rate under starvation. Furthermore, dps expression was positively regulated by the oxidative stress response regulator OxyR. These functional results are consistent with a Dps annotation. The dps mutant caused slightly delayed bacterial wilt disease in tomato after a naturalistic soil soak inoculation. However, the dps mutant had a more pronounced reduction in virulence when bacteria were inoculated directly into host stems, suggesting that Dps helps R. solanacearum adapt to conditions inside plants. Passage through a tomato plant conferred transient increased hydrogen peroxide tolerance on both wild-type and dps mutant strains, demonstrating that R. solanacearum acquires Dps-independent oxidative stress tolerance during adaptation to the host environment. The dps mutant strain was also reduced in adhesion to tomato roots and tomato stem colonization. These results indicate that Dps is important when cells are starved or in stationary phase and that Dps contributes quantitatively to host plant colonization and bacterial wilt virulence. They further suggest that R. solanacearum must overcome oxidative stress during the bacterial wilt disease cycle.
Collapse
Affiliation(s)
| | - Jacob M. Scherf
- University of Wisconsin—Madison Department of Plant Pathology, 1630 Linden Drive, Madison, Wisconsin 53706
| | - Caitilyn Allen
- University of Wisconsin—Madison Department of Plant Pathology, 1630 Linden Drive, Madison, Wisconsin 53706
| |
Collapse
|