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Magesh S, Hurley AI, Nepper JF, Chevrette MG, Schrope JH, Li C, Beebe DJ, Handelsman J. Surface colonization by Flavobacterium johnsoniae promotes its survival in a model microbial community. mBio 2024; 15:e0342823. [PMID: 38329367 PMCID: PMC10936215 DOI: 10.1128/mbio.03428-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024] Open
Abstract
Flavobacterium johnsoniae is a ubiquitous soil and rhizosphere bacterium, but despite its abundance, the factors contributing to its success in communities are poorly understood. Using a model microbial community, The Hitchhikers of the Rhizosphere (THOR), we determined the effects of colonization on the fitness of F. johnsoniae in the community. Insertion sequencing, a massively parallel transposon mutant screen, on sterile sand identified 25 genes likely to be important for surface colonization. We constructed in-frame deletions of candidate genes predicted to be involved in cell membrane biogenesis, motility, signal transduction, and transport of amino acids and lipids. All mutants poorly colonized sand, glass, and polystyrene and produced less biofilm than the wild type, indicating the importance of the targeted genes in surface colonization. Eight of the nine colonization-defective mutants were also unable to form motile biofilms or zorbs, thereby suggesting that the affected genes play a role in group movement and linking stationary and motile biofilm formation genetically. Furthermore, we showed that the deletion of colonization genes in F. johnsoniae affected its behavior and survival in THOR on surfaces, suggesting that the same traits are required for success in a multispecies microbial community. Our results provide insight into the mechanisms of surface colonization by F. johnsoniae and form the basis for further understanding its ecology in the rhizosphere. IMPORTANCE Microbial communities direct key environmental processes through multispecies interactions. Understanding these interactions is vital for manipulating microbiomes to promote health in human, environmental, and agricultural systems. However, microbiome complexity can hinder our understanding of the underlying mechanisms in microbial community interactions. As a first step toward unraveling these interactions, we explored the role of surface colonization in microbial community interactions using The Hitchhikers Of the Rhizosphere (THOR), a genetically tractable model community of three bacterial species, Flavobacterium johnsoniae, Pseudomonas koreensis, and Bacillus cereus. We identified F. johnsoniae genes important for surface colonization in solitary conditions and in the THOR community. Understanding the mechanisms that promote the success of bacteria in microbial communities brings us closer to targeted manipulations to achieve outcomes that benefit agriculture, the environment, and human health.
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Affiliation(s)
- Shruthi Magesh
- Department of Plant Pathology, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amanda I. Hurley
- Department of Plant Pathology, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Julia F. Nepper
- Department of Plant Pathology, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marc G. Chevrette
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
- University of Florida Genetics Institute, Gainesville, Florida, USA
| | - Jonathan H. Schrope
- Department of Biomedical Engineering, University of Wisconsin Madison, Madison, Wisconsin, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Chao Li
- Carbone Cancer Center, University of Wisconsin Madison, Madison, Wisconsin, USA
| | - David J. Beebe
- Department of Biomedical Engineering, University of Wisconsin Madison, Madison, Wisconsin, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Carbone Cancer Center, University of Wisconsin Madison, Madison, Wisconsin, USA
| | - Jo Handelsman
- Department of Plant Pathology, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Clawson ED, Blair V, Nepper JF, Stilwell MD, Tangen T, Weibel DB. Laboratory Activity Using Accessible Microfluidics to Study Nematode Behavior in an Electrical Field. J Microbiol Biol Educ 2018; 19:jmbe-19-58. [PMID: 29904558 PMCID: PMC5969444 DOI: 10.1128/jmbe.v19i1.1551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/07/2018] [Indexed: 06/08/2023]
Abstract
Microfluidic devices are used in a broad range of technological applications, from creating ingredients for cosmetics to discovering new medicines. The small size of microfluidic channels makes it possible to isolate individual cells, collections of cells, and multicellular organisms and study their biology, ecology, and behavior. Microfluidics is particularly well suited to teaching students concepts from different fields of science. A challenge with conventional microfluidic devices is that they are difficult and expensive to make, which has been a barrier for their entry into curricula and classrooms. We describe a simple and low-cost method for creating microfluidic devices and use them to study the behavior of nematodes in an electrical field. Nematodes are ecologically and agriculturally important organisms that respond robustly to various environmental cues. In this activity, we demonstrate that nematodes swim through liquid in microfluidic channels in response to an applied electric field and describe student responses to this activity.
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Affiliation(s)
| | - Val Blair
- Morgridge Institute for Research, Madison, WI 53715
| | - Julia F. Nepper
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Matthew D. Stilwell
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Travis Tangen
- Wisconsin Alumni Research Foundation, Madison, WI 53726
| | - Douglas B. Weibel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706
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