1
|
Xiao Y, Zhang S, Li H, Teng K, Wu S, Liu Y, Yu F, He Z, Li L, Li L, Meng D, Yin H, Wang Y. Metagenomic insights into the response of soil microbial communities to pathogenic Ralstonia solanacearum. FRONTIERS IN PLANT SCIENCE 2024; 15:1325141. [PMID: 38434434 PMCID: PMC10904623 DOI: 10.3389/fpls.2024.1325141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/17/2024] [Indexed: 03/05/2024]
Abstract
Understanding the response of soil microbial communities to pathogenic Ralstonia solanacearum is crucial for preventing bacterial wilt outbreaks. In this study, we investigated the soil physicochemical and microbial community to assess their impact on the pathogenic R.solanacearum through metagenomics. Our results revealed that certain archaeal taxa were the main contributors influencing the health of plants. Additionally, the presence of the pathogen showed a strong negative correlation with soil phosphorus levels, while soil phosphorus was significantly correlated with bacterial and archaeal communities. We found that the network of microbial interactions in healthy plant rhizosphere soils was more complex compared to diseased soils. The diseased soil network had more linkages, particularly related to the pathogen occurrence. Within the network, the family Comamonadaceae, specifically Ramlibacter_tataouinensis, was enriched in healthy samples and showed a significantly negative correlation with the pathogen. In terms of archaea, Halorubrum, Halorussus_halophilus (family: Halobacteriaceae), and Natronomonas_pharaonis (family: Haloarculaceae) were enriched in healthy plant rhizosphere soils and showed negative correlations with R.solanacearum. These findings suggested that the presence of these archaea may potentially reduce the occurrence of bacterial wilt disease. On the other hand, Halostagnicola_larseniia and Haloterrigena_sp._BND6 (family: Natrialbaceae) had higher relative abundance in diseased plants and exhibited significantly positive correlations with R.solanacearum, indicating their potential contribution to the pathogen's occurrence. Moreover, we explored the possibility of functional gene sharing among the correlating bacterial pairs within the Molecular Ecological Network. Our analysis revealed 468 entries of horizontal gene transfer (HGT) events, emphasizing the significance of HGT in shaping the adaptive traits of plant-associated bacteria, particularly in relation to host colonization and pathogenicity. Overall, this work revealed key factors, patterns and response mechanisms underlying the rhizosphere soil microbial populations. The findings offer valuable guidance for effectively controlling soil-borne bacterial diseases and developing sustainable agriculture practices.
Collapse
Affiliation(s)
- Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Sai Zhang
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Hongguang Li
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Kai Teng
- Xiangxi Tobacco Co Hunan Prov, Changsha, China
| | - Shaolong Wu
- Hunan Tobacco Research Institute, Changsha, China
| | - Yongbin Liu
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Fahui Yu
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Zhihong He
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Lijuan Li
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yujie Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| |
Collapse
|
2
|
Aroney STN, Pini F, Kessler C, Poole PS, Sánchez-Cañizares C. The motility and chemosensory systems of Rhizobium leguminosarum, their role in symbiosis, and link to PTS Ntr regulation. Environ Microbiol 2024; 26:e16570. [PMID: 38216524 DOI: 10.1111/1462-2920.16570] [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: 09/18/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Motility and chemotaxis are crucial processes for soil bacteria and plant-microbe interactions. This applies to the symbiotic bacterium Rhizobium leguminosarum, where motility is driven by flagella rotation controlled by two chemotaxis systems, Che1 and Che2. The Che1 cluster is particularly important in free-living motility prior to the establishment of the symbiosis, with a che1 mutant delayed in nodulation and reduced in nodulation competitiveness. The Che2 system alters bacteroid development and nodule maturation. In this work, we also identified 27 putative chemoreceptors encoded in the R. leguminosarum bv. viciae 3841 genome and characterized its motility in different growth conditions. We describe a metabolism-based taxis system in rhizobia that acts at high concentrations of dicarboxylates to halt motility independent of chemotaxis. Finally, we show how PTSNtr influences cell motility, with PTSNtr mutants exhibiting reduced swimming in different media. Motility is restored by the active forms of the PTSNtr output regulatory proteins, unphosphorylated ManX and phosphorylated PtsN. Overall, this work shows how rhizobia typify soil bacteria by having a high number of chemoreceptors and highlights the importance of the motility and chemotaxis mechanisms in a free-living cell in the rhizosphere, and at different stages of the symbiosis.
Collapse
Affiliation(s)
| | | | - Celia Kessler
- Department of Biology, University of Oxford, Oxford, UK
| | | | | |
Collapse
|
3
|
Greenwich JL, Heckel BC, Alakavuklar MA, Fuqua C. The ChvG-ChvI Regulatory Network: A Conserved Global Regulatory Circuit Among the Alphaproteobacteria with Pervasive Impacts on Host Interactions and Diverse Cellular Processes. Annu Rev Microbiol 2023; 77:131-148. [PMID: 37040790 DOI: 10.1146/annurev-micro-120822-102714] [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] [Indexed: 04/13/2023]
Abstract
The ChvG-ChvI two-component system is conserved among multiple Alphaproteobacteria. ChvG is a canonical two-component system sensor kinase with a single large periplasmic loop. Active ChvG directs phosphotransfer to its cognate response regulator ChvI, which controls transcription of target genes. In many alphaproteobacteria, ChvG is regulated by a third component, a periplasmic protein called ExoR, that maintains ChvG in an inactive state through direct interaction. Acidic pH stimulates proteolysis of ExoR, unfettering ChvG-ChvI to control its regulatory targets. Activated ChvI among different alphaproteobacteria controls a broad range of cellular processes, including symbiosis and virulence, exopolysaccharide production, biofilm formation, motility, type VI secretion, cellular metabolism, envelope composition, and growth. Low pH is a virulence signal in Agrobacterium tumefaciens, but in other systems, conditions that cause envelope stress may also generally activate ChvG-ChvI. There is mounting evidence that these regulators influence diverse aspects of bacterial physiology, including but not limited to host interactions.
Collapse
Affiliation(s)
| | - Brynn C Heckel
- Department of Biology, Indiana University, Bloomington, Indiana, USA; ,
- Current affiliation: California State University, Dominguez Hills, California, USA;
| | - Melene A Alakavuklar
- Department of Biology, Indiana University, Bloomington, Indiana, USA; ,
- Current affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA;
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, Indiana, USA; ,
| |
Collapse
|
6
|
Calvopina-Chavez DG, Howarth RE, Memmott AK, Pech Gonzalez OH, Hafen CB, Jensen KT, Benedict AB, Altman JD, Burnside BS, Childs JS, Dallon SW, DeMarco AC, Flindt KC, Grover SA, Heninger E, Iverson CS, Johnson AK, Lopez JB, Meinzer MA, Moulder BA, Moulton RI, Russell HS, Scott TM, Shiobara Y, Taylor MD, Tippets KE, Vainerere KM, Von Wallwitz IC, Wagley M, Wiley MS, Young NJ, Griffitts JS. A large-scale genetic screen identifies genes essential for motility in Agrobacterium fabrum. PLoS One 2023; 18:e0279936. [PMID: 36598925 PMCID: PMC9812332 DOI: 10.1371/journal.pone.0279936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/17/2022] [Indexed: 01/05/2023] Open
Abstract
The genetic and molecular basis of flagellar motility has been investigated for several decades, with innovative research strategies propelling advances at a steady pace. Furthermore, as the phenomenon is examined in diverse bacteria, new taxon-specific regulatory and structural features are being elucidated. Motility is also a straightforward bacterial phenotype that can allow undergraduate researchers to explore the palette of molecular genetic tools available to microbiologists. This study, driven primarily by undergraduate researchers, evaluated hundreds of flagellar motility mutants in the Gram-negative plant-associated bacterium Agrobacterium fabrum. The nearly saturating screen implicates a total of 37 genes in flagellar biosynthesis, including genes of previously unknown function.
Collapse
Affiliation(s)
- Diana G. Calvopina-Chavez
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Robyn E. Howarth
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Audrey K. Memmott
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Oscar H. Pech Gonzalez
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Caleb B. Hafen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Kyson T. Jensen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Alex B. Benedict
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Jessica D. Altman
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Brittany S. Burnside
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Justin S. Childs
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Samuel W. Dallon
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Alexa C. DeMarco
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Kirsten C. Flindt
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Sarah A. Grover
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Elizabeth Heninger
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Christina S. Iverson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Abigail K. Johnson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Jack B. Lopez
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - McKay A. Meinzer
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Brook A. Moulder
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Rebecca I. Moulton
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Hyrum S. Russell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Tiana M. Scott
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Yuka Shiobara
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Mason D. Taylor
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Kathryn E. Tippets
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Kayla M. Vainerere
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Isabella C. Von Wallwitz
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Madison Wagley
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Megumi S. Wiley
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Naomi J. Young
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
- * E-mail:
| |
Collapse
|
7
|
Williams MA, Bouchier JM, Mason AK, Brown PJB. Activation of ChvG-ChvI regulon by cell wall stress confers resistance to β-lactam antibiotics and initiates surface spreading in Agrobacterium tumefaciens. PLoS Genet 2022; 18:e1010274. [PMID: 36480495 PMCID: PMC9731437 DOI: 10.1371/journal.pgen.1010274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/28/2022] [Indexed: 12/13/2022] Open
Abstract
A core component of nearly all bacteria, the cell wall is an ideal target for broad spectrum antibiotics. Many bacteria have evolved strategies to sense and respond to antibiotics targeting cell wall synthesis, especially in the soil where antibiotic-producing bacteria compete with one another. Here we show that cell wall stress caused by both chemical and genetic inhibition of the essential, bifunctional penicillin-binding protein PBP1a prevents microcolony formation and activates the canonical host-invasion two-component system ChvG-ChvI in Agrobacterium tumefaciens. Using RNA-seq, we show that depletion of PBP1a for 6 hours results in a downregulation in transcription of flagellum-dependent motility genes and an upregulation in transcription of type VI secretion and succinoglycan biosynthesis genes, a hallmark of the ChvG-ChvI regulon. Depletion of PBP1a for 16 hours, results in differential expression of many additional genes and may promote a stress response, resembling those of sigma factors in other bacteria. Remarkably, the overproduction of succinoglycan causes cell spreading and deletion of the succinoglycan biosynthesis gene exoA restores microcolony formation. Treatment with cefsulodin phenocopies depletion of PBP1a and we correspondingly find that chvG and chvI mutants are hypersensitive to cefsulodin. This hypersensitivity only occurs in response to treatment with β-lactam antibiotics, suggesting that the ChvG-ChvI pathway may play a key role in resistance to antibiotics targeting cell wall synthesis. Finally, we provide evidence that ChvG-ChvI likely has a conserved role in conferring resistance to cell wall stress within the Alphaproteobacteria that is independent of the ChvG-ChvI repressor ExoR.
Collapse
Affiliation(s)
- Michelle A. Williams
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - Jacob M. Bouchier
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - Amara K. Mason
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - Pamela J. B. Brown
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America
- * E-mail:
| |
Collapse
|