1
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Łukasik P, Kolasa MR. With a little help from my friends: the roles of microbial symbionts in insect populations and communities. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230122. [PMID: 38705185 PMCID: PMC11070262 DOI: 10.1098/rstb.2023.0122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/14/2023] [Indexed: 05/07/2024] Open
Abstract
To understand insect abundance, distribution and dynamics, we need to understand the relevant drivers of their populations and communities. While microbial symbionts are known to strongly affect many aspects of insect biology, we lack data on their effects on populations or community processes, or on insects' evolutionary responses at different timescales. How these effects change as the anthropogenic effects on ecosystems intensify is an area of intense research. Recent developments in sequencing and bioinformatics permit cost-effective microbial diversity surveys, tracking symbiont transmission, and identification of functions across insect populations and multi-species communities. In this review, we explore how different functional categories of symbionts can influence insect life-history traits, how these effects could affect insect populations and their interactions with other species, and how they may affect processes and patterns at the level of entire communities. We argue that insect-associated microbes should be considered important drivers of insect response and adaptation to environmental challenges and opportunities. We also outline the emerging approaches for surveying and characterizing insect-associated microbiota at population and community scales. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Michał R. Kolasa
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
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2
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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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3
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Brockhurst MA, Cameron DD, Beckerman AP. Fitness trade-offs and the origins of endosymbiosis. PLoS Biol 2024; 22:e3002580. [PMID: 38607979 PMCID: PMC11014431 DOI: 10.1371/journal.pbio.3002580] [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: 04/14/2024] Open
Abstract
Endosymbiosis drives evolutionary innovation and underpins the function of diverse ecosystems. The mechanistic origins of symbioses, however, remain unclear, in part because early evolutionary events are obscured by subsequent evolution and genetic drift. This Essay highlights how experimental studies of facultative, host-switched, and synthetic symbioses are revealing the important role of fitness trade-offs between within-host and free-living niches during the early-stage evolution of new symbiotic associations. The mutational targets underpinning such trade-offs are commonly regulatory genes, such that single mutations have major phenotypic effects on multiple traits, thus enabling and reinforcing the transition to a symbiotic lifestyle.
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Affiliation(s)
- Michael A. Brockhurst
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Duncan D. Cameron
- Department of Environmental and Earth Sciences, School of Natural Sciences, University of Manchester, Manchester, United Kingdom
| | - Andrew P. Beckerman
- School of Biosciences, Ecology and Evolutionary Biology, University of Sheffield, Sheffield, United Kingdom
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4
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Tsukimi T, Obana N, Shigemori S, Arakawa K, Miyauchi E, Yang J, Song I, Ashino Y, Wakayama M, Soga T, Tomita M, Ohno H, Mori H, Fukuda S. Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet. mSystems 2024; 9:e0112323. [PMID: 38205998 PMCID: PMC10878103 DOI: 10.1128/msystems.01123-23] [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: 10/23/2023] [Accepted: 11/15/2023] [Indexed: 01/12/2024] Open
Abstract
Mammalian gut microbes colonize the intestinal tract of their host and adapt to establish a microbial ecosystem. The host diet changes the nutrient profile of the intestine and has a high impact on microbiota composition. Genetic mutations in Escherichia coli, a prevalent species in the human gut, allow for adaptation to the mammalian intestine, as reported in previous studies. However, the extent of colonization fitness in the intestine elevated by genetic mutation and the effects of diet change on these mutations in E. coli are still poorly known. Here, we show that notable mutations in sugar metabolism-related genes (gatC, araC, and malI) were detected in the E. coli K-12 genome just 2 weeks after colonization in the germ-free mouse intestine. In addition to elevated fitness by deletion of gatC, as previously reported, deletion of araC and malI also elevated E. coli fitness in the murine intestine in a host diet-dependent manner. In vitro cultures of medium containing nutrients abundant in the intestine (e.g., galactose, N-acetylglucosamine, and asparagine) also showed increased E. coli fitness after deletion of the genes-of-interest associated with their metabolism. Furthermore, the host diet was found to influence the developmental trajectory of gene mutations in E. coli. Taken together, we suggest that genetic mutations in E. coli are selected in response to the intestinal environment, which facilitates efficient utilization of nutrients abundant in the intestine under laboratory conditions. Our study offers some insight into the possible adaptation mechanisms of gut microbes.IMPORTANCEThe gut microbiota is closely associated with human health and is greatly impacted by the host diet. Bacteria such as Escherichia coli live in the gut all throughout the life of a human host and adapt to the intestinal environment. Adaptive mutations in E. coli are reported to enhance fitness in the mammalian intestine, but to what extent is still poorly known. It is also unknown whether the host diet affects what genes are mutated and to what extent fitness is affected. This study suggests that genetic mutations in the E. coli K-12 strain are selected in response to the intestinal environment and facilitate efficient utilization of abundant nutrients in the germ-free mouse intestine. Our study provides a better understanding of these intestinal adaptation mechanisms of gut microbes.
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Affiliation(s)
- Tomoya Tsukimi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Nozomu Obana
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Suguru Shigemori
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Eiji Miyauchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Jiayue Yang
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Isaiah Song
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Yujin Ashino
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masataka Wakayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hirotada Mori
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
- Institute of Animal Sciences, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
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5
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Shao Y, Mason CJ, Felton GW. Toward an Integrated Understanding of the Lepidoptera Microbiome. ANNUAL REVIEW OF ENTOMOLOGY 2024; 69:117-137. [PMID: 37585608 DOI: 10.1146/annurev-ento-020723-102548] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Research over the past 30 years has led to a widespread acceptance that insects establish widespread and diverse associations with microorganisms. More recently, microbiome research has been accelerating in lepidopteran systems, leading to a greater understanding of both endosymbiont and gut microorganisms and how they contribute to integral aspects of the host. Lepidoptera are associated with a robust assemblage of microorganisms, some of which may be stable and routinely detected in larval and adult hosts, while others are ephemeral and transient. Certain microorganisms that populate Lepidoptera can contribute significantly to the hosts' performance and fitness, while others are inconsequential. We emphasize the context-dependent nature of the interactions between players. While our review discusses the contemporary literature, there are major avenues yet to be explored to determine both the fundamental aspects of host-microbe interactions and potential applications for the lepidopteran microbiome; we describe these avenues after our synthesis.
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Affiliation(s)
- Yongqi Shao
- Max Planck Partner Group, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China;
| | - Charles J Mason
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye US Pacific Basin Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, Hilo, Hawaii, USA;
| | - Gary W Felton
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, USA;
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6
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Fourie A, Venter SN, Slippers B, Fourie G. Pantoea bathycoeliae sp. nov and Sodalis sp. are core gut microbiome symbionts of the two-spotted stink bug. Front Microbiol 2023; 14:1284397. [PMID: 38098653 PMCID: PMC10720322 DOI: 10.3389/fmicb.2023.1284397] [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: 08/28/2023] [Accepted: 10/04/2023] [Indexed: 12/17/2023] Open
Abstract
Stink bug species (Pentatomoidea superfamily) have developed an interdependence with obligate bacterial gut symbionts in specialized midgut crypts (M4 sub-region). Species of the Enterobacteriaceae family (predominantly Pantoea) are vertically transferred to their offspring and provide nutrients that cannot be obtained from plant sap food sources. However, the bacteria in the other gut compartments of stink bugs have rarely been investigated. The two-spotted stink bug, Bathycoelia distincta, is a serious pest of macadamias in South Africa. Nothing is currently known regarding its gut microbiome or how symbionts are transferred between insect generations. In this study, the consistency of B. distincta gut bacteria across geographic locations and life stages was determined with 16S rRNA metabarcoding, considering both the M4 and other gut compartments. A novel Pantoea species was found to be the primary M4 gut symbiont and is vertically transferred to the offspring. The other gut compartments had a low bacterial diversity and genera varied between stink bug populations but a Sodalis species was prominent in all populations. Sequence data of the M4 compartment were used to produce high-quality metagenome-assembled genomes (MAGs) for the Pantoea and Sodalis species. Functional analyses suggested a similar role in nutrient provision for the host, yet also unique metabolites produced by each species. The Sodalis sp. also had additional traits, such as secretion systems, that likely allowed it to establish itself in the host. The Pantoea species was described as Pantoea bathycoeliae sp. nov based on the rules of the SeqCode.
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Affiliation(s)
| | | | | | - Gerda Fourie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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7
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Wiesmann CL, Wang NR, Zhang Y, Liu Z, Haney CH. Origins of symbiosis: shared mechanisms underlying microbial pathogenesis, commensalism and mutualism of plants and animals. FEMS Microbiol Rev 2023; 47:fuac048. [PMID: 36521845 PMCID: PMC10719066 DOI: 10.1093/femsre/fuac048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/17/2023] Open
Abstract
Regardless of the outcome of symbiosis, whether it is pathogenic, mutualistic or commensal, bacteria must first colonize their hosts. Intriguingly, closely related bacteria that colonize diverse hosts with diverse outcomes of symbiosis have conserved host-association and virulence factors. This review describes commonalities in the process of becoming host associated amongst bacteria with diverse lifestyles. Whether a pathogen, commensal or mutualist, bacteria must sense the presence of and migrate towards a host, compete for space and nutrients with other microbes, evade the host immune system, and change their physiology to enable long-term host association. We primarily focus on well-studied taxa, such as Pseudomonas, that associate with diverse model plant and animal hosts, with far-ranging symbiotic outcomes. Given the importance of opportunistic pathogens and chronic infections in both human health and agriculture, understanding the mechanisms that facilitate symbiotic relationships between bacteria and their hosts will help inform the development of disease treatments for both humans, and the plants we eat.
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Affiliation(s)
- Christina L Wiesmann
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nicole R Wang
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yue Zhang
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zhexian Liu
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Cara H Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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8
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Gomes AFF, de Almeida LG, Cônsoli FL. Comparative Genomics of Pesticide-Degrading Enterococcus Symbionts of Spodoptera frugiperda (Lepidoptera: Noctuidae) Leads to the Identification of Two New Species and the Reappraisal of Insect-Associated Enterococcus Species. MICROBIAL ECOLOGY 2023; 86:2583-2605. [PMID: 37433981 DOI: 10.1007/s00248-023-02264-0] [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: 04/19/2023] [Accepted: 07/05/2023] [Indexed: 07/13/2023]
Abstract
Enterococcus species have been described as core members of the microbial community of Spodoptera frugiperda (Lepidoptera: Noctuidae) and have been previously reported as insecticide degrading agents. This study aimed to investigate the molecular composition of these microbial symbionts of S. frugiperda to better understand their association with the host and their potential for insecticide metabolization. Through phenotypic assays and comparative genomic analyses of several pesticide-degrading Enterococcus isolated from the gut of S. frugiperda larvae, we identified two new species: Enterococcus entomosocium n. sp. and Enterococcus spodopteracolus n. sp. Their identities as new species were confirmed by whole genome alignment, utilizing cut-offs of 95-96% for the average nucleotide identity (ANI) and 70% for the digital DNA: DNA hybridization (dDDH) values. The systematic positioning of these new species within the genus Enterococcus was resolved using genome-based analysis, revealing Enterococcus casseliflavus as a sister group of E. entomosocium n. sp., and Enterococcus mundtii as a sister group of E. spodopteracolus n. sp. Comparative genomic analyses of several isolates of E. entomosocium n. sp. and E. spodopteracolus n. sp. provided a better assessment of the interactions established in the symbiotic association with S. frugiperda and led to the discovery of misidentified new species of Enterococcus associated with insects. Our analyses indicated that the potential of E. entomosocium n. sp. and E. spodopteracolus n. sp. to metabolize different pesticides arises from molecular mechanisms that result in rapid evolution of new phenotypes in response to environmental stressors, in this case, the pesticides their host insect is exposed to.
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Affiliation(s)
- Ana Flávia Freitas Gomes
- Luiz de Queiroz College of Agriculture, Department of Entomology and Acarology, Insect Interactions Laboratory, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Luís Gustavo de Almeida
- Luiz de Queiroz College of Agriculture, Department of Entomology and Acarology, Insect Interactions Laboratory, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Fernando Luis Cônsoli
- Luiz de Queiroz College of Agriculture, Department of Entomology and Acarology, Insect Interactions Laboratory, University of São Paulo, Piracicaba, São Paulo, Brazil.
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9
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Hendry TA, Gallagher KA. Cyclic-di-GMP promotes bacteria-host association. Nat Microbiol 2023; 8:1758-1759. [PMID: 37679598 DOI: 10.1038/s41564-023-01479-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Affiliation(s)
- Tory A Hendry
- Department of Microbiology, Cornell University, Ithaca, NY, USA.
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10
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Obeng N, Czerwinski A, Schütz D, Michels J, Leipert J, Bansept F, García García MJ, Schultheiß T, Kemlein M, Fuß J, Tholey A, Traulsen A, Sondermann H, Schulenburg H. Bacterial c-di-GMP has a key role in establishing host-microbe symbiosis. Nat Microbiol 2023; 8:1809-1819. [PMID: 37653009 PMCID: PMC10522488 DOI: 10.1038/s41564-023-01468-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 08/10/2023] [Indexed: 09/02/2023]
Abstract
Most microbes evolve faster than their hosts and should therefore drive evolution of host-microbe interactions. However, relatively little is known about the characteristics that define the adaptive path of microbes to host association. Here we identified microbial traits that mediate adaptation to hosts by experimentally evolving the free-living bacterium Pseudomonas lurida with the nematode Caenorhabditis elegans as its host. After ten passages, we repeatedly observed the evolution of beneficial host-specialist bacteria, with improved persistence in the nematode being associated with increased biofilm formation. Whole-genome sequencing revealed mutations that uniformly upregulate the bacterial second messenger, cyclic diguanylate (c-di-GMP). We subsequently generated mutants with upregulated c-di-GMP in different Pseudomonas strains and species, which consistently increased host association. Comparison of pseudomonad genomes from various environments revealed that c-di-GMP underlies adaptation to a variety of hosts, from plants to humans. This study indicates that c-di-GMP is fundamental for establishing host association.
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Affiliation(s)
- Nancy Obeng
- Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany
| | - Anna Czerwinski
- Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany
| | - Daniel Schütz
- Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany
| | - Jan Michels
- Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany
| | - Jan Leipert
- Department of Systematic Proteome Research and Bioanalytics, University of Kiel, Kiel, Germany
| | | | - María J García García
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Thekla Schultheiß
- Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany
- Institute of Toxicology and Pharmacology, University of Kiel, Kiel, Germany
| | - Melinda Kemlein
- Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany
| | - Janina Fuß
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Andreas Tholey
- Department of Systematic Proteome Research and Bioanalytics, University of Kiel, Kiel, Germany
| | - Arne Traulsen
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Holger Sondermann
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Section of Biology, University of Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany.
- Max Planck Institute for Evolutionary Biology, Plön, Germany.
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11
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Lv T, Zhan C, Pan Q, Xu H, Fang H, Wang M, Matsumoto H. Plant pathogenesis: Toward multidimensional understanding of the microbiome. IMETA 2023; 2:e129. [PMID: 38867927 PMCID: PMC10989765 DOI: 10.1002/imt2.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 06/14/2024]
Abstract
Single pathogen-targeted disease management measure has shown drawbacks in field efficacy under the scenario of global change. An in-depth understanding of plant pathogenesis will provide a promising solution but faces the challenges of the emerging paradigm involving the plant microbiome. While the beneficial impact of the plant microbiome is well characterized, their potential role in facilitating pathological processes has so far remained largely overlooked. To address these unsolved controversies and emerging challenges, we hereby highlight the pathobiome, the disease-assisting portion hidden in the plant microbiome, in the plant pathogenesis paradigm. We review the detrimental actions mediated by the pathobiome at multiple scales and further discuss how natural and human triggers result in the prevalence of the plant pathobiome, which would probably provide a clue to the mitigation of plant disease epidemics. Collectively, the article would advance the current insight into plant pathogenesis and also pave a new way to cope with the upward trends of plant disease by designing the pathobiome-targeted measure.
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Affiliation(s)
- Tianxing Lv
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Chengfang Zhan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Qianqian Pan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Haorong Xu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Hongda Fang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Global Education Program for AgriScience Frontiers, Graduate School of AgricultureHokkaido UniversitySapporoJapan
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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12
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Roy A, Houot B, Kushwaha S, Anderson P. Impact of transgenerational host switch on gut bacterial assemblage in generalist pest, Spodoptera littoralis (Lepidoptera: Noctuidae). Front Microbiol 2023; 14:1172601. [PMID: 37520373 PMCID: PMC10374326 DOI: 10.3389/fmicb.2023.1172601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/15/2023] [Indexed: 08/01/2023] Open
Abstract
Diet composition is vital in shaping gut microbial assemblage in many insects. Minimal knowledge is available about the influence of transgenerational diet transition on gut microbial community structure and function in polyphagous pests. This study investigated transgenerational diet-induced changes in Spodoptera littoralis larval gut bacteriome using 16S ribosomal sequencing. Our data revealed that 88% of bacterial populations in the S. littoralis larval gut comprise Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The first diet transition experiment from an artificial diet (F0) to a plant diet (F1), cabbage and cotton, caused an alteration of bacterial communities in the S. littoralis larval gut. The second transgenerational diet switch, where F1 larvae feed on the same plant in the F2 generation, displayed a significant variation suggesting further restructuring of the microbial communities in the Spodoptera larval gut. F1 larvae were also challenged with the plant diet transition at the F2 generation (cabbage to cotton or cotton to cabbage). After feeding on different plant diets, the microbial assemblage of F2 larvae pointed to considerable differences from other F2 larvae that continued on the same diet. Our results showed that S. littoralis larval gut bacteriome responds rapidly and inexplicably to different diet changes. Further experiments must be conducted to determine the developmental and ecological consequences of such changes. Nevertheless, this study improves our perception of the impact of transgenerational diet switches on the resident gut bacteriome in S. littoralis larvae and could facilitate future research to understand the importance of symbiosis in lepidopteran generalists better.
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Affiliation(s)
- Amit Roy
- Faculty of Forestry and Wood Sciences, EXTEMIT-K and EVA.4.0 Unit, Czech University of Life Sciences, Suchdol, Czechia
| | - Benjamin Houot
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Sandeep Kushwaha
- Department of Bioinformatics, National Institute of Animal Biotechnology (NIAB), Hyderabad, India
| | - Peter Anderson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Hosseinzadeh S, Heck M. Variations on a theme: factors regulating interaction between Diaphorina citri and "Candidatus Liberibacter asiaticus" vector and pathogen of citrus huanglongbing. CURRENT OPINION IN INSECT SCIENCE 2023; 56:101025. [PMID: 36990150 DOI: 10.1016/j.cois.2023.101025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Diaphorina citri, the Asian citrus psyllid, is a vector of Candidatus Liberibacter asiaticus (CLas), the causal agent of huanglongbing (HLB), the world's most serious disease of citrus. Owing to the relevancy and urgency of HLB research, the study of transmission biology in the HLB pathosystem has been a significant area of research. The focus of this article is to summarize and synthesize recent advancements in transmission biology between D. citri and CLas to create an updated view of the research landscape and to identify avenues for future research. Variability appears to play an important role in the transmission of CLas by D. citri. We advocate that it is important to understand the genetic basis for and environmental factors contributing to CLas transmission and how that variation may be exploited to develop and improve HLB control tactics.
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Affiliation(s)
- Saeed Hosseinzadeh
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Michelle Heck
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; Emerging Pests and Pathogens Research Unit, USDA Agricultural Research Service, Ithaca, NY 14853, USA.
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14
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Conrad B, Iseli C, Pirovino M. Energy-harnessing problem solving of primordial life: Modeling the emergence of catalytic host-nested parasite life cycles. PLoS One 2023; 18:e0281661. [PMID: 36972235 PMCID: PMC10042343 DOI: 10.1371/journal.pone.0281661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/29/2023] [Indexed: 03/29/2023] Open
Abstract
All life forms on earth ultimately descended from a primordial population dubbed the last universal common ancestor or LUCA via Darwinian evolution. Extant living systems share two salient functional features, a metabolism extracting and transforming energy required for survival, and an evolvable, informational polymer-the genome-conferring heredity. Genome replication invariably generates essential and ubiquitous genetic parasites. Here we model the energetic, replicative conditions of LUCA-like organisms and their parasites, as well as adaptive problem solving of host-parasite pairs. We show using an adapted Lotka-Volterra frame-work that three host-parasite pairs-individually a unit of a host and a parasite that is itself parasitized, therefore a nested parasite pair-are sufficient for robust and stable homeostasis, forming a life cycle. This nested parasitism model includes competition and habitat restriction. Its catalytic life cycle efficiently captures, channels and transforms energy, enabling dynamic host survival and adaptation. We propose a Malthusian fitness model for a quasispecies evolving through a host-nested parasite life cycle with two core features, rapid replacement of degenerate parasites and increasing evolutionary stability of host-nested parasite units from one to three pairs.
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Affiliation(s)
| | - Christian Iseli
- Bioinformatics Competence Center, EPFL and Unil, Lausanne, Switzerland
| | - Magnus Pirovino
- OPIRO Consulting Ltd, Triesen, Principality of Liechtenstein
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15
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Giannotti D, Boscaro V, Husnik F, Vannini C, Keeling PJ. At the threshold of symbiosis: the genome of obligately endosymbiotic ' Candidatus Nebulobacter yamunensis' is almost indistinguishable from that of a cultivable strain. Microb Genom 2022; 8:mgen000909. [PMID: 36748607 PMCID: PMC9837558 DOI: 10.1099/mgen.0.000909] [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: 12/15/2022] Open
Abstract
Comparing obligate endosymbionts with their free-living relatives is a powerful approach to investigate the evolution of symbioses, and it has led to the identification of several genomic traits consistently associated with the establishment of symbiosis. 'Candidatus Nebulobacter yamunensis' is an obligate bacterial endosymbiont of the ciliate Euplotes that seemingly depends on its host for survival. A subsequently characterized bacterial strain with an identical 16S rRNA gene sequence, named Fastidiosibacter lacustris, can instead be maintained in pure culture. We analysed the genomes of 'Candidatus Nebulobacter' and Fastidiosibacter seeking to identify key differences between their functional traits and genomic structure that might shed light on a recent transition to obligate endosymbiosis. Surprisingly, we found almost no such differences: the two genomes share a high level of sequence identity, the same overall structure, and largely overlapping sets of genes. The similarities between the genomes of the two strains are at odds with their different ecological niches, confirmed here with a parallel growth experiment. Although other pairs of closely related symbiotic/free-living bacteria have been compared in the past, 'Candidatus Nebulobacter' and Fastidiosibacter represent an extreme example proving that a small number of (unknown) factors might play a pivotal role in the earliest stages of obligate endosymbiosis establishment.
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Affiliation(s)
- Daniele Giannotti
- Department of Biology, University of Pisa, Pisa, Italy,Department of Botany, University of British Columbia, Vancouver, Canada
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada,*Correspondence: Vittorio Boscaro,
| | - Filip Husnik
- Department of Botany, University of British Columbia, Vancouver, Canada,Okinawa Institute of Science and Technology, Okinawa, Japan
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Moriyama M, Fukatsu T. Host’s demand for essential amino acids is compensated by an extracellular bacterial symbiont in a hemipteran insect model. Front Physiol 2022; 13:1028409. [PMID: 36246139 PMCID: PMC9561257 DOI: 10.3389/fphys.2022.1028409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Plant sap is a nutritionally unbalanced diet that constitutes a challenge for insects that feed exclusively on it. Sap-sucking hemipteran insects generally overcome this challenge by harboring beneficial microorganisms in their specialized symbiotic organ, either intracellularly or extracellularly. Genomic information of these bacterial symbionts suggests that their primary role is to supply essential amino acids, but empirical evidence has been virtually limited to the intracellular symbiosis between aphids and Buchnera. Here we investigated the amino acid complementation by the extracellular symbiotic bacterium Ishikawaella harbored in the midgut symbiotic organ of the stinkbug Megacopta punctatissima. We evaluated amino acid compositions of the phloem sap of plants on which the insect feeds, as well as those of its hemolymph, whole body hydrolysate, and excreta. The results highlighted that the essential amino acids in the diet are apparently insufficient for the stinkbug development. Experimental symbiont removal caused severe shortfalls of some essential amino acids, including branched-chain and aromatic amino acids. In vitro culturing of the isolated symbiotic organ demonstrated that hemolymph-circulating metabolites, glutamine and trehalose, efficiently fuel the production of essential amino acids. Branched-chain amino acids and aromatic amino acids are the ones preferentially synthesized despite the symbiont’s synthetic capability of all essential amino acids. These results indicate that the symbiont-mediated amino acid compensation is quantitatively optimized in the stinkbug-Ishikawaella gut symbiotic association as in the aphid-Buchnera intracellular symbiotic association. The convergence of symbiont functions across distinct nutritional symbiotic systems provides insight into how host-symbiont interactions have been shaped over evolutionary time.
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Affiliation(s)
- Minoru Moriyama
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- *Correspondence: Minoru Moriyama, ; Takema Fukatsu,
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- *Correspondence: Minoru Moriyama, ; Takema Fukatsu,
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Vigneron A, Kaltenpoth M. Symbiosis: Creating a tractable intracellular insect-microbe association. Curr Biol 2022; 32:R943-R946. [PMID: 36167040 DOI: 10.1016/j.cub.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Endosymbioses are widespread among insects and have far-reaching implications for their hosts' ecology and evolution. However, the molecular underpinnings of symbiosis remain largely obscure. In a new study, Su et al. successfully established a transmissible synthetic symbiosis, opening up exciting new opportunities to explore the initial dynamics of endosymbiotic interactions.
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Affiliation(s)
- Aurélien Vigneron
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany.
| | - Martin Kaltenpoth
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany.
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18
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Fast track to mutualism. Nat Microbiol 2022; 7:1104-1105. [PMID: 35927447 DOI: 10.1038/s41564-022-01188-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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