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Magesh S, Schrope JH, Soto NM, Li C, Hurley AI, Huttenlocher A, Beebe DJ, Handelsman J. Co-zorbs: Motile, multispecies biofilms aid transport of diverse bacterial species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.29.607786. [PMID: 39257784 PMCID: PMC11383685 DOI: 10.1101/2024.08.29.607786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Biofilms are three-dimensional structures containing one or more bacterial species embedded in extracellular polymeric substances. Although most biofilms are stationary, Flavobacterium johnsoniae forms a motile spherical biofilm called a zorb, which is propelled by its base cells and contains a polysaccharide core. Here, we report formation of spatially organized, motile, multispecies biofilms, designated "co-zorbs," that are distinguished by a core-shell structure. F. johnsoniae forms zorbs whose cells collect other bacterial species and transport them to the zorb core, forming a co-zorb. Live imaging revealed that co-zorbs also form in zebrafish, thereby demonstrating a new type of bacterial movement in vivo. This discovery opens new avenues for understanding community behaviors, the role of biofilms in bulk bacterial transport, and collective strategies for microbial success in various environments.
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Affiliation(s)
- Shruthi Magesh
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison; Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison; Madison, WI, USA
| | - Jonathan H Schrope
- Department of Biomedical Engineering, University of Wisconsin-Madison; Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison; Madison, WI, USA
| | - Nayanna Mercado Soto
- Microbiology Doctoral Training Program, University of Wisconsin-Madison; Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison; Madison, WI, USA
| | - Chao Li
- Carbone Cancer Center, University of Wisconsin-Madison; Madison, WI, USA
| | - Amanda I Hurley
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison; Madison, WI, USA
- Avantiqor, 800 Wharf St SW, Washington, DC 20024
| | - Anna Huttenlocher
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison; Madison, WI, USA
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin-Madison; Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison; Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin-Madison; Madison, WI, USA
| | - Jo Handelsman
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison; Madison, WI, USA
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2
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Alexakis K, Baliou S, Ioannou P. Predatory Bacteria in the Treatment of Infectious Diseases and Beyond. Infect Dis Rep 2024; 16:684-698. [PMID: 39195003 DOI: 10.3390/idr16040052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/29/2024] Open
Abstract
Antimicrobial resistance (AMR) is an increasing problem worldwide, with significant associated morbidity and mortality. Given the slow production of new antimicrobials, non-antimicrobial methods for treating infections with significant AMR are required. This review examines the potential of predatory bacteria to combat infectious diseases, particularly those caused by pathogens with AMR. Predatory bacteria already have well-known applications beyond medicine, such as in the food industry, biocontrol, and wastewater treatment. Regarding their potential for use in treating infections, several in vitro studies have shown their potential in eliminating various pathogens, including those resistant to multiple antibiotics, and they also suggest minimal immune stimulation and cytotoxicity by predatory bacteria. In vivo animal studies have demonstrated safety and efficacy in reducing bacterial burden in various infection models. However, results can be inconsistent, suggesting dependence on factors like the animal model and the infecting bacteria. Until now, no clinical study in humans exists, but as experience with predatory bacteria grows, future studies including clinical studies in humans could be designed to evaluate their efficacy and safety in humans, thus leading to the potential for approval of a novel method for treating infectious diseases by bacteria.
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Affiliation(s)
| | - Stella Baliou
- School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Petros Ioannou
- School of Medicine, University of Crete, 71003 Heraklion, Greece
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3
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Subedi K, Roy PC, Saiz B, Basile F, Wall D. Cell-cell transfer of adaptation traits benefits kin and actor in a cooperative microbe. Proc Natl Acad Sci U S A 2024; 121:e2402559121. [PMID: 39012831 PMCID: PMC11287280 DOI: 10.1073/pnas.2402559121] [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: 02/09/2024] [Accepted: 06/14/2024] [Indexed: 07/18/2024] Open
Abstract
Microbes face many physical, chemical, and biological insults from their environments. In response, cells adapt, but whether they do so cooperatively is poorly understood. Here, we use a model social bacterium, Myxococcus xanthus, to ask whether adapted traits are transferable to naïve kin. To do so we isolated cells adapted to detergent stresses and tested for trait transfer. In some cases, strain-mixing experiments increased sibling fitness by transferring adaptation traits. This cooperative behavior depended on a kin recognition system called outer membrane exchange (OME) because mutants defective in OME could not transfer adaptation traits. Strikingly, in mixed stressed populations, the transferred trait also benefited the adapted (actor) cells. This apparently occurred by alleviating a detergent-induced stress response in kin that otherwise killed actor cells. Additionally, this adaptation trait when transferred also conferred resistance against a lipoprotein toxin delivered to targeted kin. Based on these and other findings, we propose a model for stress adaptation and how OME in myxobacteria promotes cellular cooperation in response to environmental stresses.
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Affiliation(s)
- Kalpana Subedi
- Department of Molecular Biology, University of Wyoming, Laramie, WY82071
- Department of Chemistry, University of Wyoming, Laramie, WY82071
| | - Pravas C. Roy
- Department of Molecular Biology, University of Wyoming, Laramie, WY82071
| | - Brandon Saiz
- Department of Chemistry, University of Wyoming, Laramie, WY82071
| | - Franco Basile
- Department of Chemistry, University of Wyoming, Laramie, WY82071
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, Laramie, WY82071
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4
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Pérez-Burgos M, Herfurth M, Kaczmarczyk A, Harms A, Huber K, Jenal U, Glatter T, Søgaard-Andersen L. A deterministic, c-di-GMP-dependent program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis. Nat Commun 2024; 15:6014. [PMID: 39019889 PMCID: PMC11255338 DOI: 10.1038/s41467-024-50444-4] [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: 02/18/2024] [Accepted: 07/10/2024] [Indexed: 07/19/2024] Open
Abstract
Phenotypic heterogeneity in bacteria can result from stochastic processes or deterministic programs. The deterministic programs often involve the versatile second messenger c-di-GMP, and give rise to daughter cells with different c-di-GMP levels by deploying c-di-GMP metabolizing enzymes asymmetrically during cell division. By contrast, less is known about how phenotypic heterogeneity is kept to a minimum. Here, we identify a deterministic c-di-GMP-dependent program that is hardwired into the cell cycle of Myxococcus xanthus to minimize phenotypic heterogeneity and guarantee the formation of phenotypically similar daughter cells during division. Cells lacking the diguanylate cyclase DmxA have an aberrant motility behaviour. DmxA is recruited to the cell division site and its activity is switched on during cytokinesis, resulting in a transient increase in the c-di-GMP concentration. During cytokinesis, this c-di-GMP burst ensures the symmetric incorporation and allocation of structural motility proteins and motility regulators at the new cell poles of the two daughters, thereby generating phenotypically similar daughters with correct motility behaviours. Thus, our findings suggest a general c-di-GMP-dependent mechanism for minimizing phenotypic heterogeneity, and demonstrate that bacteria can ensure the formation of dissimilar or similar daughter cells by deploying c-di-GMP metabolizing enzymes to distinct subcellular locations.
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Affiliation(s)
- María Pérez-Burgos
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Marco Herfurth
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Andrea Harms
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Katrin Huber
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland
| | - Timo Glatter
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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5
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Chin WC, Zhou YZ, Wang HY, Feng YT, Yang RY, Huang ZF, Yang YL. Bacterial polyynes uncovered: a journey through their bioactive properties, biosynthetic mechanisms, and sustainable production strategies. Nat Prod Rep 2024; 41:977-989. [PMID: 38284321 DOI: 10.1039/d3np00059a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Covering: up to 2023Conjugated polyynes are natural compounds characterized by alternating single and triple carbon-carbon bonds, endowing them with distinct physicochemical traits and a range of biological activities. While traditionally sourced mainly from plants, recent investigations have revealed many compounds originating from bacterial strains. This review synthesizes current research on bacterial-derived conjugated polyynes, delving into their biosynthetic routes, underscoring the variety in their molecular structures, and examining their potential applications in biotechnology. Additionally, we outline future directions for metabolic and protein engineering to establish more robust and stable platforms for their production.
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Affiliation(s)
- Wei-Chih Chin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yang-Zhi Zhou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Hao-Yung Wang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Department of Wood Based Materials and Design, National Chiayi University, Chiayi, Taiwan
| | - Yu-Ting Feng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Ru-Yin Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Zih-Fang Huang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
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6
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Stoy KS, Ratcliff WC. Uncovering the hidden complexity of multicellular magnetotactic bacteria. PLoS Biol 2024; 22:e3002695. [PMID: 38995981 PMCID: PMC11244792 DOI: 10.1371/journal.pbio.3002695] [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] [Indexed: 07/14/2024] Open
Abstract
Multicellular magnetotactic bacteria (MMB) have a surprisingly complex multicellular lifestyle. A new study in PLOS Biology combines genomics, microscopy, and isotopic labeling to show that MMB form obligately multicellular consortia of genetically diverse cells with rudimentary division of labor.
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Affiliation(s)
- Kayla S. Stoy
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - William C. Ratcliff
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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7
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Brown CL, Maile-Moskowitz A, Lopatkin AJ, Xia K, Logan LK, Davis BC, Zhang L, Vikesland PJ, Pruden A. Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment. Nat Commun 2024; 15:5412. [PMID: 38926391 PMCID: PMC11208604 DOI: 10.1038/s41467-024-49742-8] [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: 11/03/2023] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Activated sludge is the centerpiece of biological wastewater treatment, as it facilitates removal of sewage-associated pollutants, fecal bacteria, and pathogens from wastewater through semi-controlled microbial ecology. It has been hypothesized that horizontal gene transfer facilitates the spread of antibiotic resistance genes within the wastewater treatment plant, in part because of the presence of residual antibiotics in sewage. However, there has been surprisingly little evidence to suggest that sewage-associated antibiotics select for resistance at wastewater treatment plants via horizontal gene transfer or otherwise. We addressed the role of sewage-associated antibiotics in promoting antibiotic resistance using lab-scale sequencing batch reactors fed field-collected wastewater, metagenomic sequencing, and our recently developed bioinformatic tool Kairos. Here, we found confirmatory evidence that fluctuating levels of antibiotics in sewage are associated with horizontal gene transfer of antibiotic resistance genes, microbial ecology, and microdiversity-level differences in resistance gene fate in activated sludge.
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Affiliation(s)
- Connor L Brown
- Dept. of Civil and Environmental Engineering, Virginia Tech, Blacksburg, USA
| | | | | | - Kang Xia
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, USA
| | | | - Benjamin C Davis
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, USA
| | - Liqing Zhang
- Dept. of Computer Science, Virginia Tech, Blacksburg, USA
| | - Peter J Vikesland
- Dept. of Civil and Environmental Engineering, Virginia Tech, Blacksburg, USA.
| | - Amy Pruden
- Dept. of Civil and Environmental Engineering, Virginia Tech, Blacksburg, USA.
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8
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Black ME, Fei C, Alert R, Wingreen NS, Shaevitz JW. Capillary interactions drive the self-organization of bacterial colonies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596252. [PMID: 38853967 PMCID: PMC11160631 DOI: 10.1101/2024.05.28.596252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Many bacteria inhabit thin layers of water on solid surfaces both naturally in soils or on hosts or textiles and in the lab on agar hydrogels. In these environments, cells experience capillary forces, yet an understanding of how these forces shape bacterial collective behaviors remains elusive. Here, we show that the water menisci formed around bacteria lead to capillary attraction between cells while still allowing them to slide past one another. We develop an experimental apparatus that allows us to control bacterial collective behaviors by varying the strength and range of capillary forces. Combining 3D imaging and cell tracking with agent-based modeling, we demonstrate that capillary attraction organizes rod-shaped bacteria into densely packed, nematic groups, and profoundly influences their collective dynamics and morphologies. Our results suggest that capillary forces may be a ubiquitous physical ingredient in shaping microbial communities in partially hydrated environments.
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9
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Meng Y, Zhang X, Zhai Y, Li Y, Shao Z, Liu S, Zhang C, Xing XH, Zheng H. Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis. MICROBIOME 2024; 12:93. [PMID: 38778376 PMCID: PMC11112851 DOI: 10.1186/s40168-024-01813-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/09/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND The gut microbiota and their hosts profoundly affect each other's physiology and evolution. Identifying host-selected traits is crucial to understanding the processes that govern the evolving interactions between animals and symbiotic microbes. Current experimental approaches mainly focus on the model bacteria, like hypermutating Escherichia coli or the evolutionary changes of wild stains by host transmissions. A method called atmospheric and room temperature plasma (ARTP) may overcome the bottleneck of low spontaneous mutation rates while maintaining mild conditions for the gut bacteria. RESULTS We established an experimental symbiotic system with gnotobiotic bee models to unravel the molecular mechanisms promoting host colonization. By in vivo serial passage, we tracked the genetic changes of ARTP-treated Snodgrassella strains from Bombus terrestris in the non-native honeybee host. We observed that passaged isolates showing genetic changes in the mutual gliding locus have a competitive advantage in the non-native host. Specifically, alleles in the orphan mglB, the GTPase activating protein, promoted colonization potentially by altering the type IV pili-dependent motility of the cells. Finally, competition assays confirmed that the mutations out-competed the ancestral strain in the non-native honeybee gut but not in the native host. CONCLUSIONS Using the ARTP mutagenesis to generate a mutation library of gut symbionts, we explored the potential genetic mechanisms for improved gut colonization in non-native hosts. Our findings demonstrate the implication of the cell mutual-gliding motility in host association and provide an experimental system for future study on host-microbe interactions. Video Abstract.
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Affiliation(s)
- Yujie Meng
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China
- MGI Tech, Qingdao, 266426, China
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100083, China
| | - Yifan Zhai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Yuan Li
- MGI Tech, Qingdao, 266426, China
| | | | | | - Chong Zhang
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xin-Hui Xing
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Hao Zheng
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
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10
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Radford EJ, Whitworth DE. The genetic basis of predation by myxobacteria. Adv Microb Physiol 2024; 85:1-55. [PMID: 39059819 DOI: 10.1016/bs.ampbs.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Myxobacteria (phylum Myxococcota) are abundant and virtually ubiquitous microbial predators. Facultatively multicellular organisms, they are able to form multicellular fruiting bodies and swarm across surfaces, cooperatively hunting for prey. Myxobacterial communities are able to kill a wide range of prey microbes, assimilating their biomass to fuel population growth. Their mechanism of predation is exobiotic - hydrolytic enzymes and toxic metabolites are secreted into the extracellular environment, killing and digesting prey cells from without. However, recent observations of single-cell predation and contact-dependent prey killing challenge the dogma of myxobacterial predation being obligately cooperative. Regardless of their predatory mechanisms, myxobacteria have a broad prey range, which includes Gram-negative bacteria, Gram-positive bacteria and fungi. Pangenome analyses have shown that their extremely large genomes are mainly composed of accessory genes, which are not shared by all members of their species. It seems that the diversity of accessory genes in different strains provides the breadth of activity required to prey upon such a smorgasbord of microbes, and also explains the considerable strain-to-strain variation in predatory efficiency against specific prey. After providing a short introduction to general features of myxobacterial biology which are relevant to predation, this review brings together a rapidly growing body of work into the molecular mechanisms and genetic basis of predation, presenting a summary of current knowledge, highlighting trends in research and suggesting strategies by which we can potentially exploit myxobacterial predation in the future.
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Affiliation(s)
- Emily J Radford
- Department of Life Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom
| | - David E Whitworth
- Department of Life Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom.
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11
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Eren E, Watts NR, Conway JF, Wingfield PT. Myxococcus xanthus encapsulin cargo protein EncD is a flavin-binding protein with ferric reductase activity. Proc Natl Acad Sci U S A 2024; 121:e2400426121. [PMID: 38748579 PMCID: PMC11126975 DOI: 10.1073/pnas.2400426121] [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: 01/08/2024] [Accepted: 04/18/2024] [Indexed: 05/27/2024] Open
Abstract
Encapsulins are protein nanocompartments that regulate cellular metabolism in several bacteria and archaea. Myxococcus xanthus encapsulins protect the bacterial cells against oxidative stress by sequestering cytosolic iron. These encapsulins are formed by the shell protein EncA and three cargo proteins: EncB, EncC, and EncD. EncB and EncC form rotationally symmetric decamers with ferroxidase centers (FOCs) that oxidize Fe+2 to Fe+3 for iron storage in mineral form. However, the structure and function of the third cargo protein, EncD, have yet to be determined. Here, we report the x-ray crystal structure of EncD in complex with flavin mononucleotide. EncD forms an α-helical hairpin arranged as an antiparallel dimer, but unlike other flavin-binding proteins, it has no β-sheet, showing that EncD and its homologs represent a unique class of bacterial flavin-binding proteins. The cryo-EM structure of EncA-EncD encapsulins confirms that EncD binds to the interior of the EncA shell via its C-terminal targeting peptide. With only 100 amino acids, the EncD α-helical dimer forms the smallest flavin-binding domain observed to date. Unlike EncB and EncC, EncD lacks a FOC, and our biochemical results show that EncD instead is a NAD(P)H-dependent ferric reductase, indicating that the M. xanthus encapsulins act as an integrated system for iron homeostasis. Overall, this work contributes to our understanding of bacterial metabolism and could lead to the development of technologies for iron biomineralization and the production of iron-containing materials for the treatment of various diseases associated with oxidative stress.
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Affiliation(s)
- Elif Eren
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD20892
| | - Norman R. Watts
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD20892
| | - James F. Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15260
| | - Paul T. Wingfield
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD20892
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12
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Han J, Dong Z, Ji W, Lv W, Luo M, Fu B. From predator to protector: Myxococcus fulvus WCH05 emerges as a potent biocontrol agent for fire blight. Front Microbiol 2024; 15:1378288. [PMID: 38650871 PMCID: PMC11033317 DOI: 10.3389/fmicb.2024.1378288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
Fire blight, caused by the Gram-negative bacterium Erwinia amylovora, poses a substantial threat to pome fruit production worldwide. Despite existing control strategies, a pressing need remains for sustainable and environmentally friendly fire blight management. Myxobacteria, renowned for their predatory behavior and potent enzymes, emerge as a groundbreaking biocontrol approach with significant potential. Here, we report the biocontrol potential of a novel Myxococcus fulvus WCH05, against E. amylovora. Using various in vitro and planta assays, we demonstrated the multifaceted biocontrol abilities of strain WCH05. In plate predation assays, strain WCH05 exhibited not only strong predation against E. amylovora but also broad-spectrum activities against other plant pathogenic bacteria. Pre-treatment with strain WCH05 significantly decreased pear blossom blight incidence in detached inflorescence assays, achieving a controlled efficacy of 76.02% that rivaled the antibiotic streptomycin (79.79%). In greenhouse trials, strain WCH05 effectively reduced the wilting rate and disease index in young pear seedlings, exhibiting both protective (73.68%) and curative (68.66%) control. Further investigation revealed that the biocontrol activity of strain WCH05 relies on both direct contact and extracellular enzyme secretion. While cell extracts lacked inhibitory activity, ammonium sulfate-precipitated secreted proteins displayed potent lytic activity against E. amylovora. Substrate spectrum analysis identified peptidases, lipases, and glycosidases among the secreted enzymes, suggesting their potential roles in pathogen degradation and biocontrol efficacy. This study presents the first evidence of Myxococcus fulvus WCH05 as a biocontrol agent against fire blight. Its potent predatory abilities and enzymatic arsenal highlight its potential for sustainable disease management in pome fruit production. Future research will focus on identifying and characterizing specific lytic enzymes and optimizing strain WCH05 application strategies for field efficacy.
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Affiliation(s)
- Jian Han
- Department of Plant Pathology, College of Agronomy, Xinjiang Agriculture University/Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of Xinjiang Uygur Autonomous Region, Urumqi, China
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Urumqi, China
| | - Zhiming Dong
- Department of Plant Pathology, College of Agronomy, Xinjiang Agriculture University/Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of Xinjiang Uygur Autonomous Region, Urumqi, China
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Urumqi, China
| | - Wenbo Ji
- Department of Plant Pathology, College of Agronomy, Xinjiang Agriculture University/Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of Xinjiang Uygur Autonomous Region, Urumqi, China
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Urumqi, China
| | - Wen Lv
- Department of Plant Pathology, College of Agronomy, Xinjiang Agriculture University/Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of Xinjiang Uygur Autonomous Region, Urumqi, China
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Urumqi, China
| | - Ming Luo
- Department of Plant Pathology, College of Agronomy, Xinjiang Agriculture University/Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of Xinjiang Uygur Autonomous Region, Urumqi, China
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Urumqi, China
| | - Benzhong Fu
- Department of Plant Pathology, College of Agronomy, Xinjiang Agriculture University/Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of Xinjiang Uygur Autonomous Region, Urumqi, China
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Urumqi, China
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13
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Odelgard A, Hägglund E, Guy L, Andersson SGE. Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota. Genome Biol Evol 2024; 16:evae068. [PMID: 38547507 PMCID: PMC11032199 DOI: 10.1093/gbe/evae068] [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] [Accepted: 03/23/2024] [Indexed: 04/22/2024] Open
Abstract
The recently isolated bacterium "Candidatus Uabimicrobium amorphum" is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that "Ca. Uabimicrobium amorphum" represents an early diverging lineage that clusters with the Saltatorellus clade within the phylum Planctomycetota. A gene flux analysis indicated a gain of 126 protein families for signal transduction functions in "Ca. Uabimicrobium amorphum", of which 66 families contained eukaryotic-like Serine/Threonine kinases with Pkinase domains. In total, we predicted 525 functional Serine/Threonine kinases in "Ca. Uabimicrobium amorphum", which represent 8% of the proteome and is the highest fraction of Serine/Threonine kinases in a bacterial proteome. The majority of Serine/Threonine kinases in this species are membrane proteins and 30% contain long, tandem arrays of WD40 or TPR domains. The pKinase domain was predicted to be located in the cytoplasm, while the WD40 and TPR domains were predicted to be located in the periplasm. Such domain combinations were also identified in the Serine/Threonine kinases of other species in the Planctomycetota, although in much lower abundances. A phylogenetic analysis of the Serine/Threonine kinases in the Planctomycetota inferred from the Pkinase domain alone provided support for lineage-specific expansions of the Serine/Threonine kinases in "Ca. Uabimicrobium amorphum". The results imply that expansions of eukaryotic-like signal transduction systems are not restricted to multicellular organisms, but have occurred in parallel in prokaryotes with predatory lifestyles and phagocytotic-like behaviors.
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Affiliation(s)
- Anna Odelgard
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Emil Hägglund
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala University, Uppsala, Sweden
| | - Siv G E Andersson
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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14
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Zhu LL, Yang Q, Wang DG, Niu L, Pan Z, Li S, Li YZ, Zhang W, Wu C. Deciphering the Biosynthesis and Physiological Function of 5-Methylated Pyrazinones Produced by Myxobacteria. ACS CENTRAL SCIENCE 2024; 10:555-568. [PMID: 38559311 PMCID: PMC10979478 DOI: 10.1021/acscentsci.3c01363] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/25/2023] [Accepted: 01/16/2024] [Indexed: 04/04/2024]
Abstract
Myxobacteria are a prolific source of secondary metabolites with sheer chemical complexity, intriguing biosynthetic enzymology, and diverse biological activities. In this study, we report the discovery, biosynthesis, biomimetic total synthesis, physiological function, structure-activity relationship, and self-resistance mechanism of the 5-methylated pyrazinone coralinone from a myxobacterium Corallococcus exiguus SDU70. A single NRPS/PKS gene corA was genetically and biochemically demonstrated to orchestrate coralinone, wherein the integral PKS part is responsible for installing the 5-methyl group. Intriguingly, coralinone exacerbated cellular aggregation of myxobacteria grown in liquid cultures by enhancing the secretion of extracellular matrix, and the 5-methylation is indispensable for the alleged activity. We provided an evolutionary landscape of the corA-associated biosynthetic gene clusters (BGCs) distributed in the myxobacterial realm, revealing the divergent evolution for the diversity-oriented biosynthesis of 5-alkyated pyrazinones. This phylogenetic contextualization provoked us to identify corB located in the proximity of corA as a self-resistance gene. CorB was experimentally verified to be a protease that hydrolyzes extracellular proteins to antagonize the agglutination-inducing effect of coralinone. Overall, we anticipate these findings will provide new insights into the chemical ecology of myxobacteria and lay foundations for the maximal excavation of these largely underexplored resources.
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Affiliation(s)
| | | | | | - Luo Niu
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Zhuo Pan
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Shengying Li
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Wei Zhang
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
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15
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França TC, Saïdi F, Ajamian A, Islam ST, LaPlante SR. Molecular Dynamics of Outer Membrane-Embedded Polysaccharide Secretion Porins Reveals Closed Resting-State Surface Gates Targetable by Virtual Fragment Screening for Drug Hotspot Identification. ACS OMEGA 2024; 9:13217-13226. [PMID: 38524450 PMCID: PMC10955716 DOI: 10.1021/acsomega.3c09970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 03/26/2024]
Abstract
Recent advances in iterative neural network analyses (e.g., AlphaFold2 and RoseTTA fold) have been revolutionary for protein 3D structure prediction, especially for difficult-to-manipulate α-helical/β-barrel integral membrane proteins. These model structures are calculated based on the coevolution of amino acids within the protein of interest and similarities to existing protein structures; the local effects of the membrane on folding and stability of the calculated model structures are not considered. We recently reported the discovery, 3D modeling, and characterization of 18-β-stranded outer-membrane (OM) WzpX, WzpS, and WzpB β-barrel secretion porins for the exopolysaccharide (EPS), major spore coat polysaccharide (MASC), and biosurfactant polysaccharide (BPS) pathways (respectively) in the Gram-negative social predatory bacterium Myxococcus xanthus DZ2. However, information was not obtained regarding the dynamic behavior of surface-gating WzpX/S/B loop domains or on potential treatments to inactivate these porins. Herein, we developed a molecular dynamics (MD) protocol to study the core stability and loop dynamism of neural network-based integral membrane protein structure models embedded in an asymmetric OM bilayer, using the M. xanthus WzpX, WzpS, and WzpB proteins as test candidates. This was accomplished through integration of the CHARMM-graphical user interface (GUI) and Molecular Operating Environment (MOE) workflows to allow for a rapid simulation system setup and facilitate data analysis. In addition to serving as a method of model structure validation, our molecular dynamics simulations revealed a minimal movement of extracellular WzpX/S/B loops in the absence of an external stimulus as well as druggable cavities between the loops. Virtual screening of a commercial fragment library against these cavities revealed putative fragment-binding hotspots on the cell-surface face of each β-barrel, along with key interacting residues, and identified promising hits for the design of potential binders capable of plugging the β-barrels and inhibiting polysaccharide secretion.
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Affiliation(s)
- Tanos
C. C. França
- Institut
National de la Recherche Scientifique (INRS), Centre Armand-Frappier
Santé Biotechnologie, Université
du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, QC G1V 0A6, Canada
- Laboratory
of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro 22290-270, Brazil
- Department
of Chemistry, Faculty of Science, University
of Hradec Kralove, Rokitanskeho
62, 50003 Hradec
Kralove, Czech Republic
| | - Fares Saïdi
- Institut
National de la Recherche Scientifique (INRS), Centre Armand-Frappier
Santé Biotechnologie, Université
du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, QC G1V 0A6, Canada
| | - Alain Ajamian
- Chemical
Computing Group, Montreal, Quebec H3A 2R7, Canada
| | - Salim T. Islam
- Institut
National de la Recherche Scientifique (INRS), Centre Armand-Frappier
Santé Biotechnologie, Université
du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, QC G1V 0A6, Canada
| | - Steven R. LaPlante
- Institut
National de la Recherche Scientifique (INRS), Centre Armand-Frappier
Santé Biotechnologie, Université
du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, QC G1V 0A6, Canada
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16
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Zhou X, Zhou X, Zhang X, Dong H, Dong Y, Zhu H. Secretory CAZymes profile and GH19 enzymes analysis of Corallococcus silvisoli c25j21. Front Microbiol 2024; 15:1324153. [PMID: 38374914 PMCID: PMC10875029 DOI: 10.3389/fmicb.2024.1324153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/15/2024] [Indexed: 02/21/2024] Open
Abstract
Extracellular enzymes play important roles in myxobacteria degrading macromolecules and preying on other microorganisms. Glycoside hydrolases 19 (GH19) are widely present in myxobacteria, but their evolution and biological functions have not been fully elucidated. Here we investigated the comparative secretory proteome of Corallococcus silvisoli c25j21 in the presence of cellulose and chitin. A total of 313 proteins were detected, including 16 carbohydrate-active enzymes (CAZymes), 7 of which were induced by cellulose or chitin, such as GH6, GH13, GH19, AA4, and CBM56. We further analyzed the sequence and structural characteristics of its three GH19 enzymes to understand their potential functions. The results revealed that myxobacterial GH19 enzymes are evolutionarily divided into two clades with different appended modules, and their different amino acid compositions in the substrate binding pockets lead to the differences in molecular surface electrostatic potentials, which may, in turn, affect their substrate selectivity and biological functions. Our study is helpful for further understanding the biological functions and catalytic mechanisms of myxobacterial CAZymes.
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Affiliation(s)
| | | | | | | | | | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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17
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Contreras-Moreno FJ, Pérez J, Muñoz-Dorado J, Moraleda-Muñoz A, Marcos-Torres FJ. Myxococcus xanthus predation: an updated overview. Front Microbiol 2024; 15:1339696. [PMID: 38328431 PMCID: PMC10849154 DOI: 10.3389/fmicb.2024.1339696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
Bacterial predators are widely distributed across a variety of natural environments. Understanding predatory interactions is of great importance since they play a defining role in shaping microbial communities in habitats such as soils. Myxococcus xanthus is a soil-dwelling bacterial predator that can prey on Gram-positive and Gram-negative bacteria and even on eukaryotic microorganisms. This model organism has been studied for many decades for its unusual lifecycle, characterized by the formation of multicellular fruiting bodies filled with myxospores. However, less is known about its predatory behavior despite being an integral part of its lifecycle. Predation in M. xanthus is a multifactorial process that involves several mechanisms working synergistically, including motility systems to efficiently track and hunt prey, and a combination of short-range and contact-dependent mechanisms to achieve prey death and feed on them. In the short-range attack, M. xanthus is best known for the collective production of secondary metabolites and hydrolytic enzymes to kill prey and degrade cellular components. On the other hand, contact-dependent killing is a cell-to-cell process that relies on Tad-like and type III secretion systems. Furthermore, recent research has revealed that metals also play an important role during predation, either by inducing oxidative stress in the prey, or by competing for essential metals. In this paper, we review the current knowledge about M. xanthus predation, focusing on the different mechanisms used to hunt, kill, and feed on its prey, considering the most recent discoveries and the transcriptomic data available.
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Affiliation(s)
| | | | | | - Aurelio Moraleda-Muñoz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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18
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Contreras-Moreno FJ, Moraleda-Muñoz A, Marcos-Torres FJ, Cuéllar V, Soto MJ, Pérez J, Muñoz-Dorado J. Siderophores and competition for iron govern myxobacterial predation dynamics. THE ISME JOURNAL 2024; 18:wrae077. [PMID: 38696719 PMCID: PMC11388931 DOI: 10.1093/ismejo/wrae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/04/2024]
Abstract
Bacterial predators are decisive organisms that shape microbial ecosystems. In this study, we investigated the role of iron and siderophores during the predatory interaction between two rhizosphere bacteria: Myxococcus xanthus, an epibiotic predator, and Sinorhizobium meliloti, a bacterium that establishes nitrogen-fixing symbiosis with legumes. The results show that iron enhances the motility of the predator and facilitates its predatory capability, and that intoxication by iron is not used by the predator to prey, although oxidative stress increases in both bacteria during predation. However, competition for iron plays an important role in the outcome of predatory interactions. Using combinations of predator and prey mutants (nonproducers and overproducers of siderophores), we have investigated the importance of competition for iron in predation. The results demonstrate that the competitor that, via the production of siderophores, obtains sufficient iron for growth and depletes metal availability for the opponent will prevail in the interaction. Consequently, iron fluctuations in soils may modify the composition of microbial communities by altering the activity of myxobacterial predators. In addition, siderophore overproduction during predation can alter soil properties, affecting the productivity and sustainability of agricultural operations.
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Affiliation(s)
| | - Aurelio Moraleda-Muñoz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, E-18071 Granada, Spain
| | | | - Virginia Cuéllar
- Departamento de Biotecnología y Protección Ambiental, Estación Experimental del Zaidín, CSIC, E-18008 Granada, Spain
| | - María José Soto
- Departamento de Biotecnología y Protección Ambiental, Estación Experimental del Zaidín, CSIC, E-18008 Granada, Spain
| | - Juana Pérez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, E-18071 Granada, Spain
| | - José Muñoz-Dorado
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, E-18071 Granada, Spain
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19
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Chen Y, Topo EJ, Nan B, Chen J. Mathematical modeling of mechanosensitive reversal control in Myxococcus xanthus. Front Microbiol 2024; 14:1294631. [PMID: 38260904 PMCID: PMC10803039 DOI: 10.3389/fmicb.2023.1294631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Adjusting motility patterns according to environmental cues is important for bacterial survival. Myxococcus xanthus, a bacterium moving on surfaces by gliding and twitching mechanisms, modulates the reversal frequency of its front-back polarity in response to mechanical cues like substrate stiffness and cell-cell contact. In this study, we propose that M. xanthus's gliding machinery senses environmental mechanical cues during force generation and modulates cell reversal accordingly. To examine our hypothesis, we expand an existing mathematical model for periodic polarity reversal in M. xanthus, incorporating the experimental data on the intracellular dynamics of the gliding machinery and the interaction between the gliding machinery and a key polarity regulator. The model successfully reproduces the dependence of cell reversal frequency on substrate stiffness observed in M. xanthus gliding. We further propose reversal control networks between the gliding and twitching motility machineries to explain the opposite reversal responses observed in wild type M. xanthus cells that possess both motility mechanisms. These results provide testable predictions for future experimental investigations. In conclusion, our model suggests that the gliding machinery in M. xanthus can function as a mechanosensor, which transduces mechanical cues into a cell reversal signal.
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Affiliation(s)
- Yirui Chen
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
- Genetics, Bioinformatics and Computational Biology Graduate Program, Virginia Tech, Blacksburg, VA, United States
| | - Elias J. Topo
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Jing Chen
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, United States
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, United States
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20
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Zhou Y, Chen H, Jiang H, Yao Q, Zhu H. Characteristics of a lipase ArEstA with lytic activity against drug-resistant pathogen from a novel myxobacterium, Archangium lipolyticum sp. nov. Front Microbiol 2024; 14:1320827. [PMID: 38239728 PMCID: PMC10794672 DOI: 10.3389/fmicb.2023.1320827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/04/2023] [Indexed: 01/22/2024] Open
Abstract
Bacteriolytic myxobacteria are versatile micropredators and are proposed as potential biocontrol agents against diverse bacterial and fungal pathogens. Isolation of new myxobacteria species and exploration of effective predatory products are necessary for successful biocontrol of pathogens. In this study, a myxobacterium strain CY-1 was isolated from a soil sample of a pig farm using the Escherichia coli baiting method. Based on the morphological observation, physiological test, 16S rRNA gene sequence, and genomic data, strain CY-1 was identified as a novel species of the myxobacterial genus Archangium, for which the name Archangium lipolyticum sp. nov. was proposed. Subsequent predation tests indicated that the strain efficiently lysed drug-resistant pathogens, with a higher predatory activity against E. coli 64 than Staphylococcus aureus GDMCC 1.771 (MRSA). The lysis of extracellular proteins against ester-bond-containing substrates (tributyrin, tween 80, egg-yolk, and autoclaved drug-resistant pathogens) inspired the mining of secreted predatory products with lipolytic activity. Furthermore, a lipase ArEstA was identified from the genome of CY-1, and the heterologously expressed and purified enzyme showed bacteriolytic activity against Gram-negative bacteria E. coli 64 but not against Gram-positive MRSA, possibly due to different accessibility of enzyme to lipid substrates in different preys. Our research not only provided a novel myxobacterium species and a candidate enzyme for the development of new biocontrol agents but also reported an experimental basis for further study on different mechanisms of secreted predatory products in myxobacterial killing and degrading of Gram-negative and Gram-positive preys.
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Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Haixin Chen
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hongxia Jiang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Qing Yao
- College of Horticulture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, South China Agricultural University, Guangzhou, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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21
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Barlow EV, House CH, Liu MC, Wetherington MT, Van Kranendonk MJ. Distinctive microfossil supports early Paleoproterozoic rise in complex cellular organisation. GEOBIOLOGY 2024; 22:e12576. [PMID: 37803496 DOI: 10.1111/gbi.12576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 08/14/2023] [Accepted: 09/07/2023] [Indexed: 10/08/2023]
Abstract
The great oxidation event (GOE), ~2.4 billion years ago, caused fundamental changes to the chemistry of Earth's surface environments. However, the effect of these changes on the biosphere is unknown, due to a worldwide lack of well-preserved fossils from this time. Here, we investigate exceptionally preserved, large spherical aggregate (SA) microfossils permineralised in chert from the c. 2.4 Ga Turee Creek Group in Western Australia. Field and petrographic observations, Raman spectroscopic mapping, and in situ carbon isotopic analyses uncover insights into the morphology, habitat, reproduction and metabolism of this unusual form, whose distinctive, SA morphology has no known counterpart in the fossil record. Comparative analysis with microfossils from before the GOE reveals the large SA microfossils represent a step-up in cellular organisation. Morphological comparison to extant micro-organisms indicates the SAs have more in common with coenobial algae than coccoidal bacteria, emphasising the complexity of this microfossil form. The remarkable preservation here provides a unique window into the biosphere, revealing an increase in the complexity of life coinciding with the GOE.
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Affiliation(s)
- Erica V Barlow
- Australian Centre for Astrobiology, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
- Australian Research Council Centre of Excellence for Core to Crust Fluid Systems (CCFS), Macquarie University, Sydney, New South Wales, Australia
- Department of Geosciences and the Earth and Environmental Systems Institute, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Christopher H House
- Department of Geosciences and the Earth and Environmental Systems Institute, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ming-Chang Liu
- Department of Earth, Planetary, and Space Sciences, University of California at Los Angeles, Los Angeles, California, USA
- Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Maxwell T Wetherington
- Materials Research Institute and Department of Materials Science & Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Martin J Van Kranendonk
- Australian Centre for Astrobiology, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
- Australian Research Council Centre of Excellence for Core to Crust Fluid Systems (CCFS), Macquarie University, Sydney, New South Wales, Australia
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22
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Bich L. Integrating Multicellular Systems: Physiological Control and Degrees of Biological Individuality. Acta Biotheor 2023; 72:1. [PMID: 38151680 PMCID: PMC10752842 DOI: 10.1007/s10441-023-09476-4] [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: 08/29/2023] [Accepted: 12/17/2023] [Indexed: 12/29/2023]
Abstract
This paper focuses on physiological integration in multicellular systems, a notion often associated with biological individuality, but which has not received enough attention and needs a thorough theoretical treatment. Broadly speaking, physiological integration consists in how different components come together into a cohesive unit in which they are dependent on one another for their existence and activity. This paper argues that physiological integration can be understood by considering how the components of a biological multicellular system are controlled and coordinated in such a way that their activities can contribute to the maintenance of the system. The main implication of this perspective is that different ways of controlling their parts may give rise to multicellular organizations with different degrees of integration. After defining control, this paper analyses how control is realized in two examples of multicellular systems located at different ends of the spectrum of multicellularity: biofilms and animals. It focuses on differences in control ranges, and it argues that a high degree of integration implies control exerted at both medium and long ranges, and that insofar as biofilms lack long-range control (relative to their size) they can be considered as less integrated than other multicellular systems. It then discusses the implication of this account for the debate on physiological individuality and the idea that degrees of physiological integration imply degrees of individuality.
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Affiliation(s)
- Leonardo Bich
- Department of Philosophy, IAS-Research Centre for Life, Mind and Society, University of the Basque Country (UPV/EHU), Avenida de Tolosa 70, Donostia-San Sebastian, 20018, Spain.
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23
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López-Rojo A, Jackson SA, Bernal-Bernal D, Galbis-Martínez M, Fineran PC, Elías-Arnanz M. Genome sequences of Mx1, the first Myxococcus phage isolated, and Mx4, a generalized transducing myxophage. Microbiol Resour Announc 2023; 12:e0090423. [PMID: 38009928 PMCID: PMC10720576 DOI: 10.1128/mra.00904-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
Myxococcus xanthus is the best-studied member of the phylum Myxococcota, but the bacteriophages infecting it and their characterization remain limited. Here, we present complete genomes of Mx1, the first Myxococcus phage isolated, and of an Mx4 derivative widely used for generalized transduction, both unclassified Caudoviricetes with long, contractile tails.
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Affiliation(s)
- Alfonso López-Rojo
- Departamento de Genética y Microbiología, Área de Genética (Unidad asociada al IQFR-CSIC), Universidad de Murcia, Murcia, Spain
| | - Simon A. Jackson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Diego Bernal-Bernal
- Departamento de Genética y Microbiología, Área de Genética (Unidad asociada al IQFR-CSIC), Universidad de Murcia, Murcia, Spain
| | - Marisa Galbis-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad asociada al IQFR-CSIC), Universidad de Murcia, Murcia, Spain
| | - Peter C. Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad asociada al IQFR-CSIC), Universidad de Murcia, Murcia, Spain
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Zhang N, Li T, Pan H, Wang Y, Li Q, Luan J, He X, Shi W, Li Y, Wang C, Zhang F, Hu W. Genetic components of Escherichia coli involved in its complex prey-predator interaction with Myxococcus xanthus. Front Microbiol 2023; 14:1304874. [PMID: 38116529 PMCID: PMC10728724 DOI: 10.3389/fmicb.2023.1304874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
Myxococcus xanthus and Escherichia coli represent a well-studied microbial predator-prey pair frequently examined in laboratory settings. While significant progress has been made in comprehending the mechanisms governing M. xanthus predation, various aspects of the response and defensive mechanisms of E. coli as prey remain elusive. In this study, the E. coli MG1655 large-scale chromosome deletion library was screened, and a mutant designated as ME5012 was identified to possess significantly reduced susceptibility to predation by M. xanthus. Within the deleted region of ME5012 encompassing seven genes, the significance of dusB and fis genes in driving the observed phenotype became apparent. Specifically, the deletion of fis resulted in a notable reduction in flagellum production in E. coli, contributing to a certain level of resistance against predation by M. xanthus. Meanwhile, the removal of dusB in E. coli led to diminished inducibility of myxovirescin A production by M. xanthus, accompanied by a slight decrease in susceptibility to myxovirescin A. These findings shed light on the molecular mechanisms underlying the complex interaction between M. xanthus and E. coli in a predatory context.
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Affiliation(s)
- Ning Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Tingyi Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Hongwei Pan
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yipeng Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Qi Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Jia Luan
- Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, United States
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, United States
| | - Wenyuan Shi
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, United States
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Chuandong Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Fengyu Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
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25
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Müller S, DeLeon O, Atkinson SN, Saravia F, Kellogg S, Shank EA, Kirby JR. Thiocillin contributes to the ecological fitness of Bacillus cereus ATCC 14579 during interspecies interactions with Myxococcus xanthus. Front Microbiol 2023; 14:1295262. [PMID: 38075900 PMCID: PMC10704990 DOI: 10.3389/fmicb.2023.1295262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/09/2023] [Indexed: 02/12/2024] Open
Abstract
The soil-dwelling delta-proteobacterium Myxococcus xanthus is a model organism to study predation and competition. M. xanthus preys on a broad range of bacteria mediated by lytic enzymes, exopolysaccharides, Type-IV pilus-based motility, and specialized metabolites. Competition between M. xanthus and prey bacterial strains with various specialized metabolite profiles indicates a range of fitness, suggesting that specialized metabolites contribute to prey survival. To expand our understanding of how specialized metabolites affect predator-prey dynamics, we assessed interspecies interactions between M. xanthus and two strains of Bacillus cereus. While strain ATCC 14579 resisted predation, strain T was found to be highly sensitive to M. xanthus predation. The interaction between B. cereus ATCC 14579 and M. xanthus appears to be competitive, resulting in population loss for both predator and prey. Genome analysis revealed that ATCC 14579 belongs to a clade that possesses the biosynthetic gene cluster for production of thiocillins, whereas B. cereus strain T lacks those genes. Further, purified thiocillin protects B. cereus strains unable to produce this specialized metabolite, strengthening the finding that thiocillin protects against predation and contributes to the ecological fitness of B. cereus ATCC 14579. Lastly, strains that produce thiocillin appear to confer some level of protection to their own antibiotic by encoding an additional copy of the L11 ribosomal protein, a known target for thiopeptides. This work highlights the importance of specialized metabolites affecting predator-prey dynamics in soil microenvironments.
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Affiliation(s)
- Susanne Müller
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Orlando DeLeon
- Department of Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
| | - Samantha N. Atkinson
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Fatima Saravia
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Stephanie Kellogg
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Elizabeth A. Shank
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worchester, MA, United States
| | - John R. Kirby
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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26
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Lindig A, Schwarz J, Hubmann G, Rosenthal K, Lütz S. Bivariate One Strain Many Compounds Designs Expand the Secondary Metabolite Production Space in Corallococcus coralloides. Microorganisms 2023; 11:2592. [PMID: 37894250 PMCID: PMC10609524 DOI: 10.3390/microorganisms11102592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The scarcely investigated myxobacterium Corallococcus coralloides holds a large genome containing many uncharacterized biosynthetic gene clusters (BGCs) that potentially encode the synthesis of entirely new natural products. Despite its promising genomic potential, suitable cultivation conditions have not yet been found to activate the synthesis of new secondary metabolites (SMs). Finding the right cultivation conditions to activate BGCs in the genome remains a major bottleneck, and its full biosynthetic potential has so far not been determined. We therefore applied a bivariate "one strain many compounds" (OSMAC) approach, using a combination of two elicitor changes at once, for the activation of BGCs and concomitant SM production by C. coralloides. The screening was carried out in Duetz-System 24-well plates, applying univariate and bivariate OSMAC conditions. We combined biotic additives and organic solvents with a complex growth medium for univariate conditions and with minimal medium for bivariate conditions. The success in the activation of BGCs was evaluated by determining the number of new mass features detected in the respective extracts. We found synergistic effects in the bivariate OSMAC designs, evidenced by the detection of completely new mass features in the bivariate OSMAC experiments, which were not detected in the univariate OSMAC designs with only one elicitor. Overall, the bivariate OSMAC screening led to 55 new mass features, which were not detected in the univariate OSMAC design. Molecular networks revealed that these new mass features embody potential novel natural compounds and chemical derivatives like the N-acyl fatty amine N-pentyloctadecanamide and possibly sulfur-containing natural products. Hence, the presence of multiple elicitors in the bivariate OSMAC designs successfully activated the biosynthetic potential in C. coralloides. We propose bivariate OSMAC designs with a complex combination of elicitors as a straightforward strategy to robustly expand the SM space of microorganisms with large genomes.
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Affiliation(s)
- Anton Lindig
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227 Dortmund, Germany
| | - Jenny Schwarz
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227 Dortmund, Germany
| | - Georg Hubmann
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227 Dortmund, Germany
| | - Katrin Rosenthal
- School of Science, Constructor University, 28759 Bremen, Germany;
| | - Stephan Lütz
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227 Dortmund, Germany
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27
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Mun W, Choi SY, Upatissa S, Mitchell RJ. Predatory bacteria as potential biofilm control and eradication agents in the food industry. Food Sci Biotechnol 2023; 32:1729-1743. [PMID: 37780591 PMCID: PMC10533476 DOI: 10.1007/s10068-023-01310-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 10/03/2023] Open
Abstract
Biofilms are a major concern within the food industry since they have the potential to reduce productivity in situ (within the field), impact food stability and storage, and cause downstream food poisoning. Within this review, predatory bacteria as potential biofilm control and eradication agents are discussed, with a particular emphasis on the intraperiplasmic Bdellovibrio-and-like organism (BALO) grouping. After providing a brief overview of predatory bacteria and their activities, focus is given to how BALOs fulfill four attributes that are essential for biocontrol agents to be successful in the food industry: (1) Broad spectrum activity against pathogens, both plant and human; (2) Activity against biofilms; (3) Safety towards humans and animals; and (4) Compatibility with food. As predatory bacteria possess all of these characteristics, they represent a novel form of biofilm biocontrol that is ripe for use within the food industry.
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Affiliation(s)
- Wonsik Mun
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 South Korea
| | - Seong Yeol Choi
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 South Korea
| | - Sumudu Upatissa
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 South Korea
| | - Robert J. Mitchell
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 South Korea
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28
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Agaras BC, Grossi CEM, Ulloa RM. Unveiling the Secrets of Calcium-Dependent Proteins in Plant Growth-Promoting Rhizobacteria: An Abundance of Discoveries Awaits. PLANTS (BASEL, SWITZERLAND) 2023; 12:3398. [PMID: 37836138 PMCID: PMC10574481 DOI: 10.3390/plants12193398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023]
Abstract
The role of Calcium ions (Ca2+) is extensively documented and comprehensively understood in eukaryotic organisms. Nevertheless, emerging insights, primarily derived from studies on human pathogenic bacteria, suggest that this ion also plays a pivotal role in prokaryotes. In this review, our primary focus will be on unraveling the intricate Ca2+ toolkit within prokaryotic organisms, with particular emphasis on its implications for plant growth-promoting rhizobacteria (PGPR). We undertook an in silico exploration to pinpoint and identify some of the proteins described in the existing literature, including prokaryotic Ca2+ channels, pumps, and exchangers that are responsible for regulating intracellular Calcium concentration ([Ca2+]i), along with the Calcium-binding proteins (CaBPs) that play a pivotal role in sensing and transducing this essential cation. These investigations were conducted in four distinct PGPR strains: Pseudomonas chlororaphis subsp. aurantiaca SMMP3, P. donghuensis SVBP6, Pseudomonas sp. BP01, and Methylobacterium sp. 2A, which have been isolated and characterized within our research laboratories. We also present preliminary experimental data to evaluate the influence of exogenous Ca2+ concentrations ([Ca2+]ex) on the growth dynamics of these strains.
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Affiliation(s)
- Betina Cecilia Agaras
- Laboratory of Physiology and Genetics of Plant Probiotic Bacteria (LFGBBP), Centre of Biochemistry and Microbiology of Soils, National University of Quilmes, Bernal B1876BXD, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina;
| | - Cecilia Eugenia María Grossi
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina;
- Laboratory of Plant Signal Transduction, Institute of Genetic Engineering and Molecular Biology (INGEBI), National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina
| | - Rita María Ulloa
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina;
- Laboratory of Plant Signal Transduction, Institute of Genetic Engineering and Molecular Biology (INGEBI), National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina
- Biochemistry Department, Faculty of Exact and Natural Sciences, University of Buenos Aires (FCEN-UBA), Buenos Aires C1428EGA, Argentina
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29
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Rombouts S, Mas A, Le Gall A, Fiche JB, Mignot T, Nollmann M. Multi-scale dynamic imaging reveals that cooperative motility behaviors promote efficient predation in bacteria. Nat Commun 2023; 14:5588. [PMID: 37696789 PMCID: PMC10495355 DOI: 10.1038/s41467-023-41193-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 08/21/2023] [Indexed: 09/13/2023] Open
Abstract
Many species, such as fish schools or bird flocks, rely on collective motion to forage, prey, or escape predators. Likewise, Myxococcus xanthus forages and moves collectively to prey and feed on other bacterial species. These activities require two distinct motility machines enabling adventurous (A) and social (S) gliding, however when and how these mechanisms are used has remained elusive. Here, we address this long-standing question by applying multiscale semantic cell tracking during predation. We show that: (1) foragers and swarms can comprise A- and S-motile cells, with single cells exchanging frequently between these groups; (2) A-motility is critical to ensure the directional movement of both foragers and swarms; (3) the combined action of A- and S-motile cells within swarms leads to increased predation efficiencies. These results challenge the notion that A- and S-motilities are exclusive to foragers and swarms, and show that these machines act synergistically to enhance predation efficiency.
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Affiliation(s)
- Sara Rombouts
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090, Montpellier, France
| | - Anna Mas
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090, Montpellier, France
| | - Antoine Le Gall
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090, Montpellier, France.
| | - Jean-Bernard Fiche
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090, Montpellier, France
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne, Marseille, France
| | - Marcelo Nollmann
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090, Montpellier, France.
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30
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Riley R, Bowers RM, Camargo AP, Campbell A, Egan R, Eloe-Fadrosh EA, Foster B, Hofmeyr S, Huntemann M, Kellom M, Kimbrel JA, Oliker L, Yelick K, Pett-Ridge J, Salamov A, Varghese NJ, Clum A. Terabase-Scale Coassembly of a Tropical Soil Microbiome. Microbiol Spectr 2023; 11:e0020023. [PMID: 37310219 PMCID: PMC10434106 DOI: 10.1128/spectrum.00200-23] [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: 01/12/2023] [Accepted: 05/24/2023] [Indexed: 06/14/2023] Open
Abstract
Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life. Metagenome coassembly, in which many metagenomic samples from an environment are simultaneously analyzed to infer the underlying genomes' sequences, is an essential tool for achieving this goal. We applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 terabases (Tbp) of metagenome data from a tropical soil in the Luquillo Experimental Forest (LEF), Puerto Rico. The resulting coassembly yielded 39 high-quality (>90% complete, <5% contaminated, with predicted 23S, 16S, and 5S rRNA genes and ≥18 tRNAs) metagenome-assembled genomes (MAGs), including two from the candidate phylum Eremiobacterota. Another 268 medium-quality (≥50% complete, <10% contaminated) MAGs were extracted, including the candidate phyla Dependentiae, Dormibacterota, and Methylomirabilota. In total, 307 medium- or higher-quality MAGs were assigned to 23 phyla, compared to 294 MAGs assigned to nine phyla in the same samples individually assembled. The low-quality (<50% complete, <10% contaminated) MAGs from the coassembly revealed a 49% complete rare biosphere microbe from the candidate phylum FCPU426 among other low-abundance microbes, an 81% complete fungal genome from the phylum Ascomycota, and 30 partial eukaryotic MAGs with ≥10% completeness, possibly representing protist lineages. A total of 22,254 viruses, many of them low abundance, were identified. Estimation of metagenome coverage and diversity indicates that we may have characterized ≥87.5% of the sequence diversity in this humid tropical soil and indicates the value of future terabase-scale sequencing and coassembly of complex environments. IMPORTANCE Petabases of reads are being produced by environmental metagenome sequencing. An essential step in analyzing these data is metagenome assembly, the computational reconstruction of genome sequences from microbial communities. "Coassembly" of metagenomic sequence data, in which multiple samples are assembled together, enables more complete detection of microbial genomes in an environment than "multiassembly," in which samples are assembled individually. To demonstrate the potential for coassembling terabases of metagenome data to drive biological discovery, we applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 Tbp of reads from a humid tropical soil environment. The resulting coassembly, its functional annotation, and analysis are presented here. The coassembly yielded more, and phylogenetically more diverse, microbial, eukaryotic, and viral genomes than the multiassembly of the same data. Our resource may facilitate the discovery of novel microbial biology in tropical soils and demonstrates the value of terabase-scale metagenome sequencing.
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Affiliation(s)
- Robert Riley
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Robert M. Bowers
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Antonio Pedro Camargo
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Ashley Campbell
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Rob Egan
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | | | - Brian Foster
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Steven Hofmeyr
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marcel Huntemann
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Matthew Kellom
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Jeffrey A. Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Leonid Oliker
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Katherine Yelick
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, California, USA
| | - Asaf Salamov
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Neha J. Varghese
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Alicia Clum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
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31
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Han E, Fei C, Alert R, Copenhagen K, Koch MD, Wingreen NS, Shaevitz JW. Local polar order controls mechanical stress and triggers layer formation in developing Myxococcus xanthus colonies. ARXIV 2023:arXiv:2308.00368v1. [PMID: 37576128 PMCID: PMC10418523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Colonies of the social bacterium Myxococcus xanthus go through a morphological transition from a thin colony of cells to three-dimensional droplet-like fruiting bodies as a strategy to survive starvation. The biological pathways that control the decision to form a fruiting body have been studied extensively. However, the mechanical events that trigger the creation of multiple cell layers and give rise to droplet formation remain poorly understood. By measuring cell orientation, velocity, polarity, and force with cell-scale resolution, we reveal a stochastic local polar order in addition to the more obvious nematic order. Average cell velocity and active force at topological defects agree with predictions from active nematic theory, but their fluctuations are anomalously large due to polar active forces generated by the self-propelled rod-shaped cells. We find that M. xanthus cells adjust their reversal frequency to tune the magnitude of this local polar order, which in turn controls the mechanical stresses and triggers layer formation in the colonies.
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Affiliation(s)
- Endao Han
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Chenyi Fei
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ricard Alert
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstraße 38, 01187 Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstraße 108, 01307 Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, 01062, Dresden, Germany
| | - Katherine Copenhagen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Matthias D. Koch
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ned S. Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Joshua W. Shaevitz
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
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32
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Gomez JB, Waters CM. Switching on cyclic di-GMP heterogeneity in Pseudomonas aeruginosa biofilms. Nat Microbiol 2023; 8:1380-1381. [PMID: 37488256 PMCID: PMC10752495 DOI: 10.1038/s41564-023-01428-5] [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] [Indexed: 07/26/2023]
Abstract
Pseudomonas aeruginosa drives heterogeneity of cyclic di-GMP signalling in biofilms as a division-of-labour strategy to maximize colonization and dispersal using the protein HecE.
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Affiliation(s)
- Jasper B Gomez
- Department of Microbiology and Molecular Genetics, East Lansing, MI, USA
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33
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Waoo AA, Singh S, Pandey A, Kant G, Choure K, Amesho KT, Srivastava S. Microbial exopolysaccharides in the biomedical and pharmaceutical industries. Heliyon 2023; 9:e18613. [PMID: 37593641 PMCID: PMC10432183 DOI: 10.1016/j.heliyon.2023.e18613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 07/12/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
The most significant and renewable class of polymeric materials are extracellular exopolysaccharides (EPSs) produced by microorganisms. Because of their diverse chemical and structural makeup, EPSs play a variety of functions in a variety of industries, including the agricultural industry, dairy industry, biofilms, cosmetics, and others, demonstrating their biotechnological significance. EPSs are typically utilized in high-value applications, and current research has focused heavily on them because of their biocompatibility, biodegradability, and compatibility with both people and the environment. Due to their high production costs, only a few microbial EPSs have been commercially successful. The emergence of financial barriers and the growing significance of microbial EPSs in industrial and medical biotechnology has increased interest in exopolysaccharides. Since exopolysaccharides can be altered in a variety of ways, their use is expected to increase across a wide range of industries in the coming years. This review introduces some significant EPSs and their composites while concentrating on their biomedical uses.
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Affiliation(s)
| | - Sukhendra Singh
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura, India
| | - Ashutosh Pandey
- Department of Biotechnology, AKS University, Satna, India
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Gaurav Kant
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, India
| | - Kamlesh Choure
- Department of Biotechnology, AKS University, Satna, India
| | - Kassian T.T. Amesho
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
- Center for Emerging Contaminants Research, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
- The International University of Management, Centre for Environmental Studies, Main Campus, Dorado Park Ext 1, Windhoek, Namibia
- Destinies Biomass Energy and Farming Pty Ltd, P.O. Box 7387, Swakomund, Namibia
| | - Sameer Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, India
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34
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Vroomans RMA, Colizzi ES. Evolution of selfish multicellularity: collective organisation of individual spatio-temporal regulatory strategies. BMC Ecol Evol 2023; 23:35. [PMID: 37468829 PMCID: PMC10357660 DOI: 10.1186/s12862-023-02133-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 06/12/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND The unicellular ancestors of modern-day multicellular organisms were remarkably complex. They had an extensive set of regulatory and signalling genes, an intricate life cycle and could change their behaviour in response to environmental changes. At the transition to multicellularity, some of these behaviours were co-opted to organise the development of the nascent multicellular organism. Here, we focus on the transition to multicellularity before the evolution of stable cell differentiation, to reveal how the emergence of clusters affects the evolution of cell behaviour. RESULTS We construct a computational model of a population of cells that can evolve the regulation of their behavioural state - either division or migration - and study both a unicellular and a multicellular context. Cells compete for reproduction and for resources to survive in a seasonally changing environment. We find that the evolution of multicellularity strongly determines the co-evolution of cell behaviour, by altering the competition dynamics between cells. When adhesion cannot evolve, cells compete for survival by rapidly migrating towards resources before dividing. When adhesion evolves, emergent collective migration alleviates the pressure on individual cells to reach resources. This allows individual cells to maximise their own replication. Migrating adhesive clusters display striking patterns of spatio-temporal cell state changes that visually resemble animal development. CONCLUSIONS Our model demonstrates how emergent selection pressures at the onset of multicellularity can drive the evolution of cellular behaviour to give rise to developmental patterns.
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Affiliation(s)
- Renske M A Vroomans
- Informatics Institute, University of Amsterdam, Amsterdam, Netherlands.
- Origins Center, Groningen, Netherlands.
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
| | - Enrico Sandro Colizzi
- Origins Center, Groningen, Netherlands
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Mathematical Institute, Leiden University, Leiden, Netherlands
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Kaimer C, Weltzer ML, Wall D. Two reasons to kill: predation and kin discrimination in myxobacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001372. [PMID: 37494115 PMCID: PMC10433427 DOI: 10.1099/mic.0.001372] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/15/2023] [Indexed: 07/27/2023]
Abstract
Myxobacteria are social microbial predators that use cell-cell contacts to identify bacterial or fungal prey and to differentiate kin relatives to initiate cellular responses. For prey killing, they assemble Tad-like and type III-like secretion systems at contact sites. For kin discrimination (KD), they assemble outer membrane exchange complexes composed of the TraA and TraB receptors at contacts sites. A type VI secretion system and Rhs proteins also mediate KD. Following cellular recognition, these systems deliver appropriate effectors into target cells. For prey, this leads to cell death and lysis for nutrient consumption by myxobacteria. In KD, a panel of effectors are delivered, and if adjacent cells are clonal cells, resistance ensues because they express a cognate panel of immunity factors; while nonkin lack complete immunity and are intoxicated. This review compares and contrasts recent findings from these systems in myxobacteria.
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Affiliation(s)
- Christine Kaimer
- Department of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Michael L. Weltzer
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
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36
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Zhang L, Dong C, Wang J, Liu M, Wang J, Hu J, Liu L, Liu X, Xia C, Zhong L, Zhao Y, Ye X, Huang Y, Fan J, Cao H, Wang J, Li Y, Wall D, Li Z, Cui Z. Predation of oomycetes by myxobacteria via a specialized CAZyme system arising from adaptive evolution. THE ISME JOURNAL 2023; 17:1089-1103. [PMID: 37156836 PMCID: PMC10284895 DOI: 10.1038/s41396-023-01423-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/07/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023]
Abstract
As social micropredators, myxobacteria are studied for their abilities to prey on bacteria and fungi. However, their predation of oomycetes has received little attention. Here, we show that Archangium sp. AC19 secretes a carbohydrate-active enzyme (CAZyme) cocktail during predation on oomycetes Phytophthora. These enzymes include three specialized β-1,3-glucanases (AcGlu13.1, -13.2 and -13.3) that act as a cooperative consortium to target β-1,3-glucans of Phytophthora. However, the CAZymes showed no hydrolytic effects on fungal cells, even though fungi contain β-1,3-glucans. Heterologous expression of AcGlu13.1, -13.2 or -13.3 enzymes in Myxococcus xanthus DK1622, a model myxobacterium that antagonizes but does not predate on P. sojae, conferred a cooperative and mycophagous ability that stably maintains myxobacteria populations as a mixture of engineered strains. Comparative genomic analyses suggest that these CAZymes arose from adaptive evolution among Cystobacteriaceae myxobacteria for a specific prey killing behavior, whereby the presence of Phytophthora promotes growth of myxobacterial taxa by nutrient release and consumption. Our findings demonstrate that this lethal combination of CAZymes transforms a non-predatory myxobacterium into a predator with the ability to feed on Phytophthora, and provides new insights for understanding predator-prey interactions. In summary, our work extends the repertoire of myxobacteria predatory strategies and their evolution, and suggests that these CAZymes can be engineered as a functional consortium into strains for biocontrol of Phytophothora diseases and hence crop protection.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chaonan Dong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jihong Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Muxing Liu
- The Key Laboratory of Monitoring and Management of Plant Diseases ansingled Insects of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Nanjing Agriculture University, Nanjing, 210095, China
| | - Juying Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiexiong Hu
- The Key Laboratory of Monitoring and Management of Plant Diseases ansingled Insects of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Nanjing Agriculture University, Nanjing, 210095, China
| | - Lin Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinyu Liu
- The Key Laboratory of Monitoring and Management of Plant Diseases ansingled Insects of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Nanjing Agriculture University, Nanjing, 210095, China
| | - Chengyao Xia
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lingli Zhong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuqiang Zhao
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaqin Fan
- The Key Laboratory of Monitoring and Management of Plant Diseases ansingled Insects of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Nanjing Agriculture University, Nanjing, 210095, China
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingjing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, 1000 E University Avenue, Laramie, WY, 82071, USA
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
- Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China.
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37
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Soto MJ, Pérez J, Muñoz-Dorado J, Contreras-Moreno FJ, Moraleda-Muñoz A. Transcriptomic response of Sinorhizobium meliloti to the predatory attack of Myxococcus xanthus. Front Microbiol 2023; 14:1213659. [PMID: 37405170 PMCID: PMC10315480 DOI: 10.3389/fmicb.2023.1213659] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/01/2023] [Indexed: 07/06/2023] Open
Abstract
Bacterial predation impacts microbial community structures, which can have both positive and negative effects on plant and animal health and on environmental sustainability. Myxococcus xanthus is an epibiotic soil predator with a broad range of prey, including Sinorhizobium meliloti, which establishes nitrogen-fixing symbiosis with legumes. During the M. xanthus-S. meliloti interaction, the predator must adapt its transcriptome to kill and lyse the target (predatosome), and the prey must orchestrate a transcriptional response (defensome) to protect itself against the biotic stress caused by the predatory attack. Here, we describe the transcriptional changes taking place in S. meliloti in response to myxobacterial predation. The results indicate that the predator induces massive changes in the prey transcriptome with up-regulation of protein synthesis and secretion, energy generation, and fatty acid (FA) synthesis, while down-regulating genes required for FA degradation and carbohydrate transport and metabolism. The reconstruction of up-regulated pathways suggests that S. meliloti modifies the cell envelop by increasing the production of different surface polysaccharides (SPSs) and membrane lipids. Besides the barrier role of SPSs, additional mechanisms involving the activity of efflux pumps and the peptide uptake transporter BacA, together with the production of H2O2 and formaldehyde have been unveiled. Also, the induction of the iron-uptake machinery in both predator and prey reflects a strong competition for this metal. With this research we complete the characterization of the complex transcriptional changes that occur during the M. xanthus-S. meliloti interaction, which can impact the establishment of beneficial symbiosis with legumes.
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Affiliation(s)
- María José Soto
- Departamento de Biotecnología y Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juana Pérez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - José Muñoz-Dorado
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | | | - Aurelio Moraleda-Muñoz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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38
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Seidel M, Skotnicka D, Glatter T, Søgaard-Andersen L. During heat stress in Myxococcus xanthus, the CdbS PilZ domain protein, in concert with two PilZ-DnaK chaperones, perturbs chromosome organization and accelerates cell death. PLoS Genet 2023; 19:e1010819. [PMID: 37339150 PMCID: PMC10313047 DOI: 10.1371/journal.pgen.1010819] [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: 04/14/2023] [Revised: 06/30/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023] Open
Abstract
C-di-GMP is a bacterial second messenger that regulates diverse processes in response to environmental or cellular cues. The nucleoid-associated protein (NAP) CdbA in Myxococcus xanthus binds c-di-GMP and DNA in a mutually exclusive manner in vitro. CdbA is essential for viability, and CdbA depletion causes defects in chromosome organization, leading to a block in cell division and, ultimately, cell death. Most NAPs are not essential; therefore, to explore the paradoxical cdbA essentiality, we isolated suppressor mutations that restored cell viability without CdbA. Most mutations mapped to cdbS, which encodes a stand-alone c-di-GMP binding PilZ domain protein, and caused loss-of-function of cdbS. Cells lacking CdbA and CdbS or only CdbS were fully viable and had no defects in chromosome organization. CdbA depletion caused post-transcriptional upregulation of CdbS accumulation, and this CdbS over-accumulation was sufficient to disrupt chromosome organization and cause cell death. CdbA depletion also caused increased accumulation of CsdK1 and CsdK2, two unusual PilZ-DnaK chaperones. During CdbA depletion, CsdK1 and CsdK2, in turn, enabled the increased accumulation and toxicity of CdbS, likely by stabilizing CdbS. Moreover, we demonstrate that heat stress, possibly involving an increased cellular c-di-GMP concentration, induced the CdbA/CsdK1/CsdK2/CdbS system, causing a CsdK1- and CsdK2-dependent increase in CdbS accumulation. Thereby this system accelerates heat stress-induced chromosome mis-organization and cell death. Collectively, this work describes a unique system that contributes to regulated cell death in M. xanthus and suggests a link between c-di-GMP signaling and regulated cell death in bacteria.
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Affiliation(s)
- Michael Seidel
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Dorota Skotnicka
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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39
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Black ME, Shaevitz JW. Rheological Dynamics of Active Myxococcus xanthus Populations during Development. PHYSICAL REVIEW LETTERS 2023; 130:218402. [PMID: 37295076 DOI: 10.1103/physrevlett.130.218402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/21/2023] [Indexed: 06/12/2023]
Abstract
The bacterium Myxococcus xanthus produces multicellular droplets called fruiting bodies when starved. These structures form initially through the active dewetting of a vegetative biofilm into surface-associated droplets. This motility-driven aggregation is succeeded by a primitive developmental process in which cells in the droplets mature into nonmotile spores. Here, we use atomic force microscopy to probe the mechanics of these droplets throughout their formation. Using a combination of time- and frequency-domain rheological experiments, we characterize and develop a simple model of the linear viscoelasticity of these aggregates. We then use this model to quantify how cellular behaviors predominant at different developmental times-motility during the dewetting phase and cellular sporulation during later development-manifest as decreased droplet viscosity and increased elasticity, respectively.
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Affiliation(s)
- Matthew E Black
- Joseph Henry Laboratories of Physics and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Joshua W Shaevitz
- Joseph Henry Laboratories of Physics and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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40
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Dong H, Gao R, Dong Y, Yao Q, Zhu H. Whole-genome sequencing of a biocontrol Myxococcus xanthus R31 isolate and comparative genomic analysis. Gene 2023; 863:147286. [PMID: 36804855 DOI: 10.1016/j.gene.2023.147286] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/01/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
Tomato bacterial wilt (TBW) caused by Ralstonia solanacearum is one of the most destructive soil-borne diseases. Myxococcus xanthus R31, isolated from healthy tomato rhizosphere soil using the R. solanacearum baiting method, exhibiting good biocontrol efficacy against TBW. However, the genomic information and evolutionary features of R31 are largely unclear. Here, the high-quality genome assembly of R31 was presented. Using Nanopore sequencing technology, we assembled the 9.25 Mb complete genome of R31 and identified several extracellular enzyme proteins, including carbohydrate-active enzymes (CAZymes) and peptidases. We also performed a comparative genome analysis of R31 and 17 other strains of M. xanthus with genome sequences in the NCBI database to gain insights into myxobacteria predation and genome size expansion. Average nucleotide identity and digital DNA-DNA hybridization calculation and phylogenetic analysis indicated that R31 was closely related to the species M. xanthus. Further comparative genomics analysis suggested that, in addition to characteristics of predatory microorganisms, R31 contains many strain-specific genes, which may provide a genetic basis for its proficient predatory ability. This study provides new insights into R31 and other closely related species and facilitates studies using genetic approaches to further elucidate the predation mechanism of myxobacteria.
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Affiliation(s)
- Honghong Dong
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Ruixiang Gao
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; College of Plant Protection, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangzhou 510642, China
| | - Yijie Dong
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangzhou 510642, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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41
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Smith WPJ, Wucher BR, Nadell CD, Foster KR. Bacterial defences: mechanisms, evolution and antimicrobial resistance. Nat Rev Microbiol 2023:10.1038/s41579-023-00877-3. [PMID: 37095190 DOI: 10.1038/s41579-023-00877-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 04/26/2023]
Abstract
Throughout their evolutionary history, bacteria have faced diverse threats from other microorganisms, including competing bacteria, bacteriophages and predators. In response to these threats, they have evolved sophisticated defence mechanisms that today also protect bacteria against antibiotics and other therapies. In this Review, we explore the protective strategies of bacteria, including the mechanisms, evolution and clinical implications of these ancient defences. We also review the countermeasures that attackers have evolved to overcome bacterial defences. We argue that understanding how bacteria defend themselves in nature is important for the development of new therapies and for minimizing resistance evolution.
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Affiliation(s)
- William P J Smith
- Division of Genomics, Infection and Evolution, University of Manchester, Manchester, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Benjamin R Wucher
- Department of Biological sciences, Dartmouth College, Hanover, NH, USA
| | - Carey D Nadell
- Department of Biological sciences, Dartmouth College, Hanover, NH, USA
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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42
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Complete Genome Sequence Assembly and Annotation for Myxococcus xanthus Strains DK1050 and DK101. Microbiol Resour Announc 2023; 12:e0102022. [PMID: 36749079 PMCID: PMC10019317 DOI: 10.1128/mra.01020-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Myxococcus xanthus is a social Gram-negative soil bacterium and the best studied member of the order Myxococcales in the class Deltaproteobacteria, which was recently reclassified as the phylum Myxococcota. Here, we report complete genomes, obtained using Illumina and PacBio sequencing, of M. xanthus strains DK1050 and DK101 (GenBank accession numbers CP104804 and CP104803, respectively).
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43
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Wang DG, Wang CY, Hu JQ, Wang JJ, Liu WC, Zhang WJ, Du XR, Wang H, Zhu LL, Sui HY, Li YZ, Wu C. Constructing a Myxobacterial Natural Product Database to Facilitate NMR-Based Metabolomics Bioprospecting of Myxobacteria. Anal Chem 2023; 95:5256-5266. [PMID: 36917632 DOI: 10.1021/acs.analchem.2c05145] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Myxobacteria are fascinating prokaryotes featuring a potent capacity for producing a wealth of bioactive molecules with intricate chemical topology as well as intriguing enzymology, and thus it is critical to developing an efficient pipeline for bioprospecting. Herein, we construct the database MyxoDB, the first public compendium solely dedicated to myxobacteria, which enabled us to provide an overview of the structural diversity and taxonomic distribution of known myxobacterial natural products. Moreover, we demonstrated that the cutting-edge NMR-based metabolomics was effective to differentiate the biosynthetic priority of myxobacteria, whereby MyxoDB could greatly streamline the dereplication of multifarious known compounds and accordingly speed up the discovery of new compounds. This led to the rapid identification of a class of linear di-lipopeptides (archangimins) and a rare rearranged sterol (corasterol) that were endowed with unique chemical architectures and/or biosynthetic enzymology. We also showcased that NMR-based metabolomics, MyxoDB, and genomics can also work concertedly to accelerate the targeted discovery of a polyketidic compound pyxipyrrolone C. All in all, this study sets the stage for the discovery of many more novel natural products from underexplored myxobacterial resources.
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Affiliation(s)
- De-Gao Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Chao-Yi Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jia-Qi Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jing-Jing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Wen-Chao Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Wen-Juan Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xin-Ran Du
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Han Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Le-Le Zhu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Hai-Yan Sui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
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44
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Dinet C, Mignot T. Unorthodox regulation of the MglA Ras-like GTPase controlling polarity in Myxococcus xanthus. FEBS Lett 2023; 597:850-864. [PMID: 36520515 DOI: 10.1002/1873-3468.14565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Motile cells have developed a large array of molecular machineries to actively change their direction of movement in response to spatial cues from their environment. In this process, small GTPases act as molecular switches and work in tandem with regulators and sensors of their guanine nucleotide status (GAP, GEF, GDI and effectors) to dynamically polarize the cell and regulate its motility. In this review, we focus on Myxococcus xanthus as a model organism to elucidate the function of an atypical small Ras GTPase system in the control of directed cell motility. M. xanthus cells direct their motility by reversing their direction of movement through a mechanism involving the redirection of the motility apparatus to the opposite cell pole. The reversal frequency of moving M. xanthus cells is controlled by modular and interconnected protein networks linking the chemosensory-like frizzy (Frz) pathway - that transmits environmental signals - to the downstream Ras-like Mgl polarity control system - that comprises the Ras-like MglA GTPase protein and its regulators. Here, we discuss how variations in the GTPase interactome landscape underlie single-cell decisions and consequently, multicellular patterns.
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Affiliation(s)
- Céline Dinet
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille University, France
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille University, France
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45
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A Diverged Transcriptional Network for Usage of Two Fe-S Cluster Biogenesis Machineries in the Delta-Proteobacterium Myxococcus xanthus. mBio 2023; 14:e0300122. [PMID: 36656032 PMCID: PMC9973013 DOI: 10.1128/mbio.03001-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Myxococcus xanthus possesses two Fe-S cluster biogenesis machineries, ISC (iron-sulfur cluster) and SUF (sulfur mobilization). Here, we show that in comparison to the phylogenetically distant Enterobacteria, which also have both machineries, M. xanthus evolved an independent transcriptional scheme to coordinately regulate the expression of these machineries. This transcriptional response is directed by RisR, which we show to belong to a phylogenetically distant and biochemically distinct subgroup of the Rrf2 transcription factor family, in comparison to IscR that regulates the isc and suf operons in Enterobacteria. We report that RisR harbors an Fe-S cluster and that holo-RisR acts as a repressor of both the isc and suf operons, in contrast to Escherichia coli, where holo-IscR represses the isc operon whereas apo-IscR activates the suf operon. In addition, we establish that the nature of the cluster and the DNA binding sites of RisR, in the isc and suf operons, diverge from those of IscR. We further show that in M. xanthus, the two machineries appear to be fully interchangeable in maintaining housekeeping levels of Fe-S cluster biogenesis and in synthesizing the Fe-S cluster for their common regulator, RisR. We also demonstrate that in response to oxidative stress and iron limitation, transcriptional upregulation of the M. xanthus isc and suf operons was mediated solely by RisR and that the contribution of the SUF machinery was greater than the ISC machinery. Altogether, these findings shed light on the diversity of homeostatic mechanisms exploited by bacteria to coordinately use two Fe-S cluster biogenesis machineries. IMPORTANCE Fe-S proteins are ubiquitous and control a wide variety of key biological processes; therefore, maintaining Fe-S cluster homeostasis is an essential task for all organisms. Here, we provide the first example of how a bacterium from the Deltaproteobacteria branch coordinates expression of two Fe-S cluster biogenesis machineries. The results revealed a new model of coordination, highlighting the unique and common features that have independently emerged in phylogenetically distant bacteria to maintain Fe-S cluster homeostasis in response to environmental changes. Regulation is orchestrated by a previously uncharacterized transcriptional regulator, RisR, belonging to the Rrf2 superfamily, whose members are known to sense diverse environmental stresses frequently encountered by bacteria. Understanding how M. xanthus maintains Fe-S cluster homeostasis via RisR regulation revealed a strategy reflective of the aerobic lifestyle of this organsim. This new knowledge also paves the way to improve production of Fe-S-dependent secondary metabolites using M. xanthus as a chassis.
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Navarrete AA, Aburto F, González-Rocha G, Guzmán CM, Schmidt R, Scow K. Anthropogenic degradation alter surface soil biogeochemical pools and microbial communities in an Andean temperate forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158508. [PMID: 36063938 DOI: 10.1016/j.scitotenv.2022.158508] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 08/14/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Soil microbial communities regulate a myriad of critical biogeochemical functions in forest ecosystems. Anthropogenic disturbances in natural forests could drive major shifts in plant and microbial communities resulting in substantial biogeochemical alterations. We evaluated the effect of anthropogenic disturbances in the soils of Andean temperate forests with different levels of degradation: i) mature forest (MF), ii) secondary forest (SF), iii) degraded forest (DF), and iv) deforested site converted into a prairie (DP). We quantified total soil carbon, nitrogen and phosphorous (TC, TN, and TP), and available nutrient stocks. The soil microbial community structure (i.e., composition, diversity, and abundance) was assessed under each condition from amplicon sequence variants (ASVs) obtained via NGS-Illumina sequencing and subsequent microbiome analysis. There were no significant differences in TC, TN, and TP across the forested states (MF, SF, DF). The deforested site condition presented significantly higher soil TC, TN, and TP and the lowest C:N, C:P, and N:P ratios. The DP soil microbiome was significantly more diverse in bacteria (D' = 0.47 ± 0.04); and fungi (H' = 5.11 ± 0.33). The bacterial microbiome was dominated by Proteobacteria (45.35 ± 0.89 %), Acidobacteria (20.73 ± 1.48 %), Actinobacteria (12.59 ± 0.34 %), and Bacteroidetes (7.32 ± 0.36 %) phyla in all sites. The soil fungal community was dominated by the phyla Ascomycota (42.11 ± 0.95 %), Mortierellomycota (28.74 ± 2.25 %), Basidiomycota (24.61 ± 0.52), and Mucoromycota (2.06 ± 0.43 %). Yet, there were significant differences at the genus level across conditions. Forest to prairie conversion facilitated the introduction of exotic bacterial and fungal taxa associated with agricultural activities and livestock grazing (∼50 % of DP core microbiome composed of unique ASVs). For example, the ammonia-oxidizing bacteria community emerged as a dominant group in the DP soils, along with a reduction in the ectomycorrhizal fungi community. The surface soil microbial community was surprisingly resistant to forest degradation and did not show a clear succession along the degradation gradient, but it was strongly altered after deforestation.
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Affiliation(s)
- Alejandro Atenas Navarrete
- Postgrado Facultad de Ciencias Forestales, Universidad de Concepción, Chile; Laboratorio de Investigación en Suelos, Aguas y Bosques (LISAB), Universidad de Concepción, Chile; Iniciativa Foresta Nativa, Universidad de Concepción, Concepción, Chile
| | - Felipe Aburto
- Soil and Crop Sciences Department, Texas A&M University, 370 Olsen Blvd. Heep Center, TX 77845, USA; Departamento de Planificación Territorial y Sistemas Urbanos, Facultad de Ciencias Ambientales, Universidad de Concepción, Chile.
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Carolina Merino Guzmán
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, BIOREN, Universidad de La Frontera, Chile
| | - Radomir Schmidt
- Working Lands Innovation Center at the Institute of the Environment, University of California, Davis, USA
| | - Kate Scow
- Soil Microbial Ecology Lab, Department of Land, Air and Water Resources, University of California, Davis, USA
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Wang C, Xiao Y, Wang Y, Liu Y, Yao Q, Zhu H. Comparative genomics and transcriptomics insight into myxobacterial metabolism potentials and multiple predatory strategies. Front Microbiol 2023; 14:1146523. [PMID: 37213496 PMCID: PMC10196010 DOI: 10.3389/fmicb.2023.1146523] [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] [Received: 01/17/2023] [Accepted: 04/19/2023] [Indexed: 05/23/2023] Open
Abstract
Myxobacteria are part of the phylum Myxococcota, encompassing four orders. Most of them display complex lifestyles and broad predation profiles. However, metabolic potential and predation mechanisms of different myxobacteria remains poorly understood. Herein, we used comparative genomics and transcriptomics to analyze metabolic potentials and differentially expressed gene (DEG) profiles of Myxococcus xanthus monoculture (Mx) compared to coculture with Escherichia coli (MxE) and Micrococcus luteus (MxM) prey. The results showed that myxobacteria had conspicuous metabolic deficiencies, various protein secretion systems (PSSs) and the common type II secretion system (T2SS). RNA-seq data demonstrated that M. xanthus overexpressed the potential predation DEGs, particularly those encoding T2SS, the tight adherence (Tad) pilus, different secondary metabolites (myxochelin A/B, myxoprincomide, myxovirescin A1, geosmin and myxalamide), glycosyl transferases and peptidase during predation. Furthermore, the myxalamide biosynthesis gene clusters, two hypothetical gene clusters and one arginine biosynthesis clusters were highly differential expressed in MxE versus MxM. Additionally, homologue proteins of the Tad (kil) system and five secondary metabolites were in different obligate or facultative predators. Finally, we provided a working model for exhibiting multiple predatory strategies when M. xanthus prey on M. luteus and E. coli. These results might spur application-oriented research on the development of novel antibacterial strategies.
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Affiliation(s)
- Chunling Wang
- College of Life Science, Huizhou University, Huizhou, Guangdong, China
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Yi Xiao
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Yong Wang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Yumin Liu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangzhou, Guangdong, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- *Correspondence: Honghui Zhu,
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Octaviana S, Primahana G, Mozef T, Borges LGA, Pieper DH, Wink J. Diversity of Myxobacteria Isolated from Indonesian Mangroves and Their Potential for New Antimicrobial Sources. Curr Microbiol 2022; 80:46. [PMID: 36538090 PMCID: PMC9768008 DOI: 10.1007/s00284-022-03066-2] [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: 01/10/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022]
Abstract
Mangroves are unique intertidal ecosystems that provide ecological niches to different microbes, which play various roles in nutrient recycling and diverse environmental activities. The association between myxobacteria and mangroves are hitherto poorly understood. The aim of our study was to evaluate the myxobacterial community composition as well as isolate myxobacteria and to characterize the antimicrobial activity of myxobacteria isolates from Indonesian mangroves. Twenty-five cultivable myxobacteria were affiliated in six genera: Myxococcus, Corallococcus, Archangium, Chondromyces, Racemicystis and Nannocystis of the order Myxococcales based on partial 16S rRNA gene sequences. Thirteen crude extracts showed moderate activities against at least one of human pathogenic microorganisms. The crude extract of Racemicystis sp. strain 503MSO indicated a novel compound, which has not been reported in the database yet and the identification of this compound needs further study. The myxobacterial communities of three different sampling sites were analyzed using primers adapted for the myxobacteria group identification. The results showed that myxobacterial communities are more diverse than assumed. Therefore, our study has highlighted the importance of the mangrove habitat as promising harbor of myxobacteria as well as novel antimicrobial compounds with activity against pathogenic microorganisms.
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Affiliation(s)
- Senlie Octaviana
- Helmholtz Center for Infection Research, Microbial Strain Collection, Braunschweig, Germany
- Research Center for Applied Microbiology BRIN, Cibinong, Jawa Barat, Indonesia
| | - Gian Primahana
- Microbial Drug, Helmholtz Center for Infection Research, Braunschweig, Germany
- Research Center for Pharmaceutical Ingredients and Traditional Medicines BRIN, Cibinong, Jawa Barat, Indonesia
| | - Tjandrawati Mozef
- Research Center for Pharmaceutical Ingredients and Traditional Medicines BRIN, Cibinong, Jawa Barat, Indonesia
| | - Luiz G A Borges
- Microbial Interactions and Processes, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Joachim Wink
- Helmholtz Center for Infection Research, Microbial Strain Collection, Braunschweig, Germany.
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Schaal KA, Yu YTN, Vasse M, Velicer GJ. Allopatric divergence of cooperators confers cheating resistance and limits effects of a defector mutation. BMC Ecol Evol 2022; 22:141. [PMID: 36510120 PMCID: PMC9746145 DOI: 10.1186/s12862-022-02094-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Social defectors may meet diverse cooperators. Genotype-by-genotype interactions may constrain the ranges of cooperators upon which particular defectors can cheat, limiting cheater spread. Upon starvation, the soil bacterium Myxococcus xanthus cooperatively develops into spore-bearing fruiting bodies, using a complex regulatory network and several intercellular signals. Some strains (cheaters) are unable to sporulate effectively in pure culture due to mutations that reduce signal production but can exploit and outcompete cooperators within mixed groups. RESULTS In this study, interactions between a cheater disrupted at the signaling gene csgA and allopatrically diversified cooperators reveal a very small cheating range. Expectedly, the cheater failed to cheat on all natural-isolate cooperators owing to non-cheater-specific antagonisms. Surprisingly, some lab-evolved cooperators had already exited the csgA mutant's cheating range after accumulating fewer than 20 mutations and without experiencing cheating during evolution. Cooperators might also diversify in the potential for a mutation to reduce expression of a cooperative trait or generate a cheating phenotype. A new csgA mutation constructed in several highly diverged cooperators generated diverse sporulation phenotypes, ranging from a complete defect to no defect, indicating that genetic backgrounds can limit the set of genomes in which a mutation creates a defector. CONCLUSIONS Our results demonstrate that natural populations may feature geographic mosaics of cooperators that have diversified in their susceptibility to particular cheaters, limiting defectors' cheating ranges and preventing them from spreading. This diversification may also lead to variation in the phenotypes generated by any given cooperation-gene mutation, further decreasing the chance of a cheater emerging which threatens the persistence of cooperation in the system.
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Affiliation(s)
- Kaitlin A. Schaal
- grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, 8092 Zurich, Switzerland
| | - Yuen-Tsu Nicco Yu
- grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, 8092 Zurich, Switzerland
| | - Marie Vasse
- grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, 8092 Zurich, Switzerland ,grid.121334.60000 0001 2097 0141Institute MIVEGEC (UMR 5290 CNRS, IRD, UM), 34394 Montpellier, France
| | - Gregory J. Velicer
- grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, 8092 Zurich, Switzerland
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Liau P, Kim C, Saxton MA, Malkin SY. Microbial succession in a marine sediment: Inferring interspecific microbial interactions with marine cable bacteria. Environ Microbiol 2022; 24:6348-6364. [PMID: 36178156 PMCID: PMC10092204 DOI: 10.1111/1462-2920.16230] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/27/2022] [Indexed: 01/12/2023]
Abstract
Cable bacteria are long, filamentous, multicellular bacteria that grow in marine sediments and couple sulfide oxidation to oxygen reduction over centimetre-scale distances via long-distance electron transport. Cable bacteria can strongly modify biogeochemical cycling and may affect microbial community networks. Here we examine interspecific interactions with marine cable bacteria (Ca. Electrothrix) by monitoring the succession of 16S rRNA amplicons (DNA and RNA) and cell abundance across depth and time, contrasting sediments with and without cable bacteria growth. In the oxic zone, cable bacteria activity was positively associated with abundant predatory bacteria (Bdellovibrionota, Myxococcota, Bradymonadales), indicating putative predation on cathodic cells. At suboxic depths, cable bacteria activity was positively associated with sulfate-reducing and magnetotactic bacteria, consistent with cable bacteria functioning as ecosystem engineers that modify their local biogeochemical environment, benefitting certain microbes. Cable bacteria activity was negatively associated with chemoautotrophic sulfur-oxidizing Gammaproteobacteria (Thiogranum, Sedimenticola) at oxic depths, suggesting competition, and positively correlated with these taxa at suboxic depths, suggesting syntrophy and/or facilitation. These observations are consistent with chemoautotrophic sulfur oxidizers benefitting from an oxidizing potential imparted by cable bacteria at suboxic depths, possibly by using cable bacteria as acceptors for electrons or electron equivalents, but by an as yet enigmatic mechanism.
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Affiliation(s)
- Pinky Liau
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, Maryland, USA
| | - Carol Kim
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, Maryland, USA
| | - Matthew A Saxton
- Department of Biological Sciences, Miami University, Middletown, Ohio, USA
| | - Sairah Y Malkin
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, Maryland, USA
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