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Renoz F. The nutritional dimension of facultative bacterial symbiosis in aphids: Current status and methodological considerations for future research. CURRENT RESEARCH IN INSECT SCIENCE 2023; 5:100070. [PMID: 38222793 PMCID: PMC10787254 DOI: 10.1016/j.cris.2023.100070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/22/2023] [Accepted: 12/11/2023] [Indexed: 01/16/2024]
Abstract
Aphids are valuable models for studying the functional diversity of bacterial symbiosis in insects. In addition to their ancestral obligate nutritional symbiont Buchnera aphidicola, these insects can host a myriad of so-called facultative symbionts. The diversity of these heritable bacterial associates is now well known, and some of the ecologically important traits associated with them have been well documented. Some twenty years ago, it was suggested that facultative symbionts could play an important role in aphid nutrition, notably by improving feeding performance on specific host plants, thus influencing the adaptation of these insects to host plants. However, the underlying mechanisms have never been elucidated, and the nutritional role that facultative symbionts might perform in aphids remains enigmatic. In this opinion piece, I put forward a series of arguments in support of the hypothesis that facultative symbionts play a central role in aphid nutrition and emphasize methodological considerations for testing this hypothesis in future work. In particular, I hypothesize that the metabolic capacities of B. aphidicola alone may not always be able to counterbalance the nutritional deficiencies of phloem sap. The association with one or several facultative symbionts with extensive metabolic capabilities would then be necessary to buffer the insect from host plant-derived nutrient deficiencies, thus enabling it to gain access to certain host plants.
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Affiliation(s)
- François Renoz
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
- Biodiversity Research Centre, Earth and Life Institute, UCLouvain, Croix du Sud 4-5, 1348, Louvain-la-Neuve, Belgium
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2
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Cho H, Rohlfs M. Transmission of beneficial yeasts accompanies offspring production in Drosophila-An initial evolutionary stage of insect maternal care through manipulation of microbial load? Ecol Evol 2023; 13:e10184. [PMID: 37332518 PMCID: PMC10276349 DOI: 10.1002/ece3.10184] [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: 01/18/2023] [Revised: 04/28/2023] [Accepted: 05/26/2023] [Indexed: 06/20/2023] Open
Abstract
Parent-to-offspring transmission of beneficial microorganisms is intimately interwoven with the evolution of social behaviors. Ancestral stages of complex sociality-microbe vectoring interrelationships may be characterized by high costs of intensive parental care and hence only a weak link between the transmission of microbial symbionts and offspring production. We investigate the relationship between yeast symbiont transmission and egg-laying, as well as some general factors thought to drive the "farming" of microscopic fungi by the fruit fly Drosophila melanogaster, an insect with no obvious parental care but which is highly dependent on dietary microbes during offspring development. The process of transmitting microbes involves flies ingesting microbes from their previous environment, storing and vectoring them, and finally depositing them to a new environment. This study revealed that fecal materials of adult flies play a significant role in this process, as they contain viable yeast cells that support larval development. During single patch visits, egg-laying female flies transmitted more yeast cells than non-egg-laying females, suggesting that dietary symbiont transmission is not random, but linked to offspring production. The crop, an extension of the foregut, was identified as an organ capable of storing viable yeast cells during travel between egg-laying sites. However, the amount of yeast in the crop reduced rapidly during periods of starvation. Although females starved for 24 h deposited a smaller amount of yeast than those starved for 6 h, the yeast inoculum produced still promoted the development of larval offspring. The results of these experiments suggest that female Drosophila fruit flies have the ability to store and regulate the transfer of microorganisms beneficial to their offspring via the shedding of fecal material. We argue that our observation may represent an initial evolutionary stage of maternal care through the manipulation of microbial load, from which more specialized feedbacks of sociality and microbe management may evolve.
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Affiliation(s)
- Hanna Cho
- Institute of Ecology, Insect and Chemical Ecology GroupUniversity of BremenBremenGermany
| | - Marko Rohlfs
- Institute of Ecology, Insect and Chemical Ecology GroupUniversity of BremenBremenGermany
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3
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Ma Y, He J, Sieber M, von Frieling J, Bruchhaus I, Baines JF, Bickmeyer U, Roeder T. The microbiome of the marine flatworm Macrostomum lignano provides fitness advantages and exhibits circadian rhythmicity. Commun Biol 2023; 6:289. [PMID: 36934156 PMCID: PMC10024726 DOI: 10.1038/s42003-023-04671-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 03/07/2023] [Indexed: 03/20/2023] Open
Abstract
The close association between animals and their associated microbiota is usually beneficial for both partners. Here, we used a simple marine model invertebrate, the flatworm Macrostomum lignano, to characterize the host-microbiota interaction in detail. This analysis revealed that the different developmental stages each harbor a specific microbiota. Studies with gnotobiotic animals clarified the physiological significance of the microbiota. While no fitness benefits were mediated by the microbiota when food was freely available, animals with microbiota showed significantly increased fitness with a reduced food supply. The microbiota of M. lignano shows circadian rhythmicity, affecting both the total bacterial load and the behavior of specific taxa. Moreover, the presence of the worm influences the composition of the bacterial consortia in the environment. In summary, the Macrostomum-microbiota system described here can serve as a general model for host-microbe interactions in marine invertebrates.
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Affiliation(s)
- Yuanyuan Ma
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany
| | - Jinru He
- Kiel University, Zoological Institute, Cell and Developmental Biology, Kiel, Germany
| | - Michael Sieber
- Max-Planck Institute for Evolutionary Biology, Dept. Evolutionary Theory, Plön, Germany
| | - Jakob von Frieling
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany
| | - Iris Bruchhaus
- Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - John F Baines
- Kiel University, Medical Faculty, Institute for Experimental Medicine, Kiel, Germany
- Max-Planck Institute for Evolutionary Biology, Group Evolutionary Medicine, Plön, Germany
| | - Ulf Bickmeyer
- Alfred-Wegener-Institute, Biosciences, Ecological Chemistry, Bremerhaven, Germany
| | - Thomas Roeder
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany.
- German Center for Lung Research (DZL), Airway Research Center North, Kiel, Germany.
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4
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Quides KW, Lee Y, Hur T, Atamian HS. Evaluation of qPCR to Detect Shifts in Population Composition of the Rhizobial Symbiont Mesorhizobium japonicum during Serial in Planta Transfers. BIOLOGY 2023; 12:biology12020277. [PMID: 36829553 PMCID: PMC9953586 DOI: 10.3390/biology12020277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/12/2023]
Abstract
Microbial symbionts range from mutualistic to commensal to antagonistic. While these roles are distinct in their outcome, they are also fluid in a changing environment. Here, we used the Lotus japonicus-Mesorhizobium japonicum symbiosis to investigate short-term and long-term shifts in population abundance using an effective, fast, and low-cost tracking methodology for M. japonicum. We use quantitative polymerase chain reaction (qPCR) to track previously generated signature-tagged M. japonicum mutants targeting the Tn5 transposon insertion and the flanking gene. We used a highly beneficial wild type and moderately beneficial and non-beneficial mutants of M. japonicum sp. nov. to demonstrate the specificity of these primers to estimate the relative abundance of each genotype within individual nodules and after serial transfers to new hosts. For the moderate and non-beneficial genotypes, qPCR allowed us to differentiate genotypes that are phenotypically indistinguishable and investigate host control with suboptimal symbionts. We consistently found the wild type increasing in the proportion of the population, but our data suggest a potential reproductive trade-off between the moderate and non-beneficial genotypes. The multi-generation framework we used, coupled with qPCR, can easily be scaled up to track dozens of M. japonicum mutants simultaneously. Moreover, these mutants can be used to explore M. japonicum genotype abundance in the presence of a complex soil community.
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Affiliation(s)
- Kenjiro W. Quides
- Biological Sciences Program, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Yoobeen Lee
- Biological Sciences Program, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
| | - Teresa Hur
- Biological Sciences Program, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
| | - Hagop S. Atamian
- Biological Sciences Program, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Correspondence:
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5
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Rodríguez‐Pastor R, Shafran Y, Knossow N, Gutiérrez R, Harrus S, Zaman L, Lenski RE, Barrick JE, Hawlena H. A road map for in vivo evolution experiments with blood-borne parasitic microbes. Mol Ecol Resour 2022; 22:2843-2859. [PMID: 35599628 PMCID: PMC9796859 DOI: 10.1111/1755-0998.13649] [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: 11/07/2021] [Revised: 03/14/2022] [Accepted: 05/13/2022] [Indexed: 01/07/2023]
Abstract
Laboratory experiments in which blood-borne parasitic microbes evolve in their animal hosts offer an opportunity to study parasite evolution and adaptation in real time and under natural settings. The main challenge of these experiments is to establish a protocol that is both practical over multiple passages and accurately reflects natural transmission scenarios and mechanisms. We provide a guide to the steps that should be considered when designing such a protocol, and we demonstrate its use via a case study. We highlight the importance of choosing suitable ancestral genotypes, treatments, number of replicates per treatment, types of negative controls, dependent variables, covariates, and the timing of checkpoints for the experimental design. We also recommend specific preliminary experiments to determine effective methods for parasite quantification, transmission, and preservation. Although these methodological considerations are technical, they also often have conceptual implications. To this end, we encourage other researchers to design and conduct in vivo evolution experiments with blood-borne parasitic microbes, despite the challenges that the work entails.
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Affiliation(s)
- Ruth Rodríguez‐Pastor
- Jacob Blaustein Center for Scientific Cooperation, The Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
| | - Yarden Shafran
- Mitrani Department of Desert Ecology, Swiss Institute for Dryland Environmental and Energy Research, The Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
| | - Nadav Knossow
- Mitrani Department of Desert Ecology, Swiss Institute for Dryland Environmental and Energy Research, The Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
| | - Ricardo Gutiérrez
- Koret School of Veterinary Medicine, Faculty of Agricultural, Nutritional and Environmental SciencesThe Hebrew University of JerusalemRehovotIsrael
| | - Shimon Harrus
- Koret School of Veterinary Medicine, Faculty of Agricultural, Nutritional and Environmental SciencesThe Hebrew University of JerusalemRehovotIsrael
| | - Luis Zaman
- Department of Ecology and Evolutionary Biology, The Center for the Study of Complex Systems (CSCS)University of MichiganAnn ArborMichiganUSA
| | - Richard E. Lenski
- Department of Microbiology and Molecular GeneticsMichigan State UniversityEast LansingMichiganUSA
| | - Jeffrey E. Barrick
- Department of Molecular BiosciencesThe University of Texas AustinAustinTexasUSA
| | - Hadas Hawlena
- Mitrani Department of Desert Ecology, Swiss Institute for Dryland Environmental and Energy Research, The Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
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6
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Koga R, Moriyama M, Onodera-Tanifuji N, Ishii Y, Takai H, Mizutani M, Oguchi K, Okura R, Suzuki S, Gotoh Y, Hayashi T, Seki M, Suzuki Y, Nishide Y, Hosokawa T, Wakamoto Y, Furusawa C, Fukatsu T. Single mutation makes Escherichia coli an insect mutualist. Nat Microbiol 2022; 7:1141-1150. [PMID: 35927448 PMCID: PMC9352592 DOI: 10.1038/s41564-022-01179-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/21/2022] [Indexed: 02/07/2023]
Abstract
Microorganisms often live in symbiosis with their hosts, and some are considered mutualists, where all species involved benefit from the interaction. How free-living microorganisms have evolved to become mutualists is unclear. Here we report an experimental system in which non-symbiotic Escherichia coli evolves into an insect mutualist. The stinkbug Plautia stali is typically associated with its essential gut symbiont, Pantoea sp., which colonizes a specialized symbiotic organ. When sterilized newborn nymphs were infected with E. coli rather than Pantoea sp., only a few insects survived, in which E. coli exhibited specific localization to the symbiotic organ and vertical transmission to the offspring. Through transgenerational maintenance with P. stali, several hypermutating E. coli lines independently evolved to support the host's high adult emergence and improved body colour; these were called 'mutualistic' E. coli. These mutants exhibited slower bacterial growth, smaller size, loss of flagellar motility and lack of an extracellular matrix. Transcriptomic and genomic analyses of 'mutualistic' E. coli lines revealed independent mutations that disrupted the carbon catabolite repression global transcriptional regulator system. Each mutation reproduced the mutualistic phenotypes when introduced into wild-type E. coli, confirming that single carbon catabolite repression mutations can make E. coli an insect mutualist. These findings provide an experimental system for future work on host-microbe symbioses and may explain why microbial mutualisms are omnipresent in nature.
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Affiliation(s)
- Ryuichi Koga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
| | - Minoru Moriyama
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Naoko Onodera-Tanifuji
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yoshiko Ishii
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hiroki Takai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Masaki Mizutani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Kohei Oguchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Reiko Okura
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Shingo Suzuki
- Center for Biosystem Dynamics Research, RIKEN, Osaka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahide Seki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yudai Nishide
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,National Agriculture and Food Research Organization, Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Takahiro Hosokawa
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Yuichi Wakamoto
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| | - Chikara Furusawa
- Center for Biosystem Dynamics Research, RIKEN, Osaka, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan. .,Department of Biological Sciences, The University of Tokyo, Tokyo, Japan. .,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
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7
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Host-Associated Rhizobial Fitness: Dependence on Nitrogen, Density, Community Complexity, and Legume Genotype. Appl Environ Microbiol 2022; 88:e0052622. [PMID: 35852362 PMCID: PMC9361818 DOI: 10.1128/aem.00526-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The environmental context of the nitrogen-fixing mutualism between leguminous plants and rhizobial bacteria varies over space and time. Variation in resource availability, population density, and composition likely affect the ecology and evolution of rhizobia and their symbiotic interactions with hosts. We examined how host genotype, nitrogen addition, rhizobial density, and community complexity affected selection on 68 rhizobial strains in the Sinorhizobium meliloti–Medicago truncatula mutualism. As expected, host genotype had a substantial effect on the size, number, and strain composition of root nodules (the symbiotic organ). The understudied environmental variable of rhizobial density had a stronger effect on nodule strain frequency than the addition of low nitrogen levels. Higher inoculum density resulted in a nodule community that was less diverse and more beneficial but only in the context of the more selective host genotype. Higher density resulted in more diverse and less beneficial nodule communities with the less selective host. Density effects on strain composition deserve additional scrutiny as they can create feedback between ecological and evolutionary processes. Finally, we found that relative strain rankings were stable across increasing community complexity (2, 3, 8, or 68 strains). This unexpected result suggests that higher-order interactions between strains are rare in the context of nodule formation and development. Our work highlights the importance of examining mechanisms of density-dependent strain fitness and developing theoretical predictions that incorporate density dependence. Furthermore, our results have translational relevance for overcoming establishment barriers in bioinoculants and motivating breeding programs that maintain beneficial plant-microbe interactions across diverse agroecological contexts. IMPORTANCE Legume crops establish beneficial associations with rhizobial bacteria that perform biological nitrogen fixation, providing nitrogen to plants without the economic and greenhouse gas emission costs of chemical nitrogen inputs. Here, we examine the influence of three environmental factors that vary in agricultural fields on strain relative fitness in nodules. In addition to manipulating nitrogen, we also use two biotic variables that have rarely been examined: the rhizobial community's density and complexity. Taken together, our results suggest that (i) breeding legume varieties that select beneficial strains despite environmental variation is possible, (ii) changes in rhizobial population densities that occur routinely in agricultural fields could drive evolutionary changes in rhizobial populations, and (iii) the lack of higher-order interactions between strains will allow the high-throughput assessments of rhizobia winners and losers during plant interactions.
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Dinges ZM, Phillips RK, Lively CM, Bashey F. Post‐association barrier to host switching maintained despite strong selection in a novel mutualism. Ecol Evol 2022; 12:e9011. [PMID: 35784049 PMCID: PMC9204852 DOI: 10.1002/ece3.9011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 11/25/2022] Open
Abstract
Following a host shift, repeated co‐passaging of a mutualistic pair is expected to increase fitness over time in one or both species. Without adaptation, a novel association may be evolutionarily short‐lived as it is likely to be outcompeted by native pairings. Here, we test whether experimental evolution can rescue a low‐fitness novel pairing between two sympatric species of Steinernema nematodes and their symbiotic Xenorhabdus bacteria. Despite low mean fitness in the novel association, considerable variation in nematode reproduction was observed across replicate populations. We selected the most productive infections, co‐passaging this novel mutualism nine times to determine whether selection could improve the fitness of either or both partners. We found that neither partner showed increased fitness over time. Our results suggest that the variation in association success was not heritable and that mutational input was insufficient to allow evolution to facilitate this host shift. Thus, post‐association costs of host switching may represent a formidable barrier to novel partnerships among sympatric mutualists.
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Affiliation(s)
- Zoe M. Dinges
- Department of Biology Indiana University Bloomington Indiana USA
| | | | - Curtis M. Lively
- Department of Biology Indiana University Bloomington Indiana USA
| | - Farrah Bashey
- Department of Biology Indiana University Bloomington Indiana USA
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9
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Hoang KL, Choi H, Gerardo NM, Morran LT. Coevolution's conflicting role in the establishment of beneficial associations. Evolution 2022; 76:1073-1081. [PMID: 35304743 PMCID: PMC9310579 DOI: 10.1111/evo.14472] [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: 08/18/2021] [Revised: 01/28/2022] [Accepted: 02/14/2022] [Indexed: 01/21/2023]
Abstract
Reciprocal adaptation between hosts and symbionts can drive the maintenance of symbioses, resulting in coevolution and beneficial genotypic interactions. Consequently, hosts may experience decreased fitness when paired with nonsympatric partners compared to sympatric symbionts. However, coevolution does not preclude conflict-host and symbiont can act to advance their own fitness interests, which do not necessarily align with those of their partner. Despite coevolution's importance in extant symbioses, we know little about its role in shaping the origin of symbioses. Here, we tested the role of coevolution in establishing a novel association by experimentally (co)evolving a host with a protective bacterium under environmental stress. Although evolution in the presence of nonevolving bacteria facilitated host adaptation, co-passaged hosts did not exhibit greater adaptation rates than hosts paired with nonevolving bacteria. Furthermore, co-passaged hosts exhibited greater fecundity when paired with sympatric, co-passaged bacteria compared to co-passaged bacteria with which they did not share an evolutionary history. Thus, shared evolutionary history between the hosts and microbes actually reduced host fitness and has the potential to impede evolution of new beneficial associations.
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Affiliation(s)
- Kim L. Hoang
- Department of BiologyEmory UniversityAtlantaGeorgia30322
| | - Heidi Choi
- Department of BiologyEmory UniversityAtlantaGeorgia30322
| | | | - Levi T. Morran
- Department of BiologyEmory UniversityAtlantaGeorgia30322
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10
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Hoang KL, King KC. Symbiont-mediated immune priming in animals through an evolutionary lens. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35442184 DOI: 10.1099/mic.0.001181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Protective symbionts can defend hosts from parasites through several mechanisms, from direct interference to modulating host immunity, with subsequent effects on host and parasite fitness. While research on symbiont-mediated immune priming (SMIP) has focused on ecological impacts and agriculturally important organisms, the evolutionary implications of SMIP are less clear. Here, we review recent advances made in elucidating the ecological and molecular mechanisms by which SMIP occurs. We draw on current works to discuss the potential for this phenomenon to drive host, parasite, and symbiont evolution. We also suggest approaches that can be used to address questions regarding the impact of immune priming on host-microbe dynamics and population structures. Finally, due to the transient nature of some symbionts involved in SMIP, we discuss what it means to be a protective symbiont from ecological and evolutionary perspectives and how such interactions can affect long-term persistence of the symbiosis.
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Affiliation(s)
- Kim L Hoang
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Kayla C King
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
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11
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Henry LP, Bruijning M, Forsberg SKG, Ayroles JF. The microbiome extends host evolutionary potential. Nat Commun 2021; 12:5141. [PMID: 34446709 PMCID: PMC8390463 DOI: 10.1038/s41467-021-25315-x] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 08/03/2021] [Indexed: 02/07/2023] Open
Abstract
The microbiome shapes many host traits, yet the biology of microbiomes challenges traditional evolutionary models. Here, we illustrate how integrating the microbiome into quantitative genetics can help untangle complexities of host-microbiome evolution. We describe two general ways in which the microbiome may affect host evolutionary potential: by shifting the mean host phenotype and by changing the variance in host phenotype in the population. We synthesize the literature across diverse taxa and discuss how these scenarios could shape the host response to selection. We conclude by outlining key avenues of research to improve our understanding of the complex interplay between hosts and microbiomes.
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Affiliation(s)
- Lucas P. Henry
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA ,grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
| | - Marjolein Bruijning
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA
| | - Simon K. G. Forsberg
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA ,grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA ,grid.8993.b0000 0004 1936 9457Dept. of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Julien F. Ayroles
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA ,grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
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12
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Henry LP, Ayroles JF. Meta-analysis suggests the microbiome responds to Evolve and Resequence experiments in Drosophila melanogaster. BMC Microbiol 2021; 21:108. [PMID: 33836662 PMCID: PMC8034159 DOI: 10.1186/s12866-021-02168-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 03/31/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Experimental evolution has a long history of uncovering fundamental insights into evolutionary processes, but has largely neglected one underappreciated component--the microbiome. As eukaryotic hosts evolve, the microbiome may also respond to selection. However, the microbial contribution to host evolution remains poorly understood. Here, we re-analyzed genomic data to characterize the metagenomes from ten Evolve and Resequence (E&R) experiments in Drosophila melanogaster to determine how the microbiome changed in response to host selection. RESULTS Bacterial diversity was significantly different in 5/10 studies, primarily in traits associated with metabolism or immunity. Duration of selection did not significantly influence bacterial diversity, highlighting the importance of associations with specific host traits. CONCLUSIONS Our genomic re-analysis suggests the microbiome often responds to host selection; thus, the microbiome may contribute to the response of Drosophila in E&R experiments. We outline important considerations for incorporating the microbiome into E&R experiments. The E&R approach may provide critical insights into host-microbiome interactions and fundamental insight into the genomic basis of adaptation.
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Affiliation(s)
- Lucas P Henry
- Department of Ecology & Evolutionary Biology, 150 Carl Icahn Laboratory, Princeton University, Princeton, NJ, 08544, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
| | - Julien F Ayroles
- Department of Ecology & Evolutionary Biology, 150 Carl Icahn Laboratory, Princeton University, Princeton, NJ, 08544, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
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13
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Hoang KL, Gerardo NM, Morran LT. Association with a novel protective microbe facilitates host adaptation to a stressful environment. Evol Lett 2021; 5:118-129. [PMID: 33868708 PMCID: PMC8045907 DOI: 10.1002/evl3.223] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 02/02/2021] [Accepted: 02/18/2021] [Indexed: 01/19/2023] Open
Abstract
Protective symbionts can allow hosts to occupy otherwise uninhabitable niches. Despite the importance of symbionts in host evolution, we know little about how these associations arise. Encountering a microbe that can improve host fitness in a stressful environment may favor persistent interactions with that microbe, potentially facilitating a long-term association. The bacterium Bacillus subtilis protects Caenorhabditis elegans nematodes from heat shock by increasing host fecundity compared to the nonprotective Escherichia coli. In this study, we ask how the protection provided by the bacterium affects the host's evolutionary trajectory. Because of the stark fitness contrast between hosts heat shocked on B. subtilis versus E. coli, we tested whether the protection conferred by the bacteria could increase the rate of host adaptation to a stressful environment. We passaged nematodes on B. subtilis or E. coli, under heat stress or standard conditions for 20 host generations of selection. When assayed under heat stress, we found that hosts exhibited the greatest fitness increase when evolved with B. subtilis under stress compared to when evolved with E. coli or under standard (nonstressful) conditions. Furthermore, despite not directly selecting for increased B. subtilis fitness, we found that hosts evolved to harbor more B. subtilis as they adapted to heat stress. Our findings demonstrate that the context under which hosts evolve is important for the evolution of beneficial associations and that protective microbes can facilitate host adaptation to stress. In turn, such host adaptation can benefit the microbe.
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Affiliation(s)
- Kim L. Hoang
- Department of BiologyEmory UniversityAtlantaGeorgia30322USA
- Department of ZoologyUniversity of OxfordOxfordOX1 3SZUnited Kingdom
| | | | - Levi T. Morran
- Department of BiologyEmory UniversityAtlantaGeorgia30322USA
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14
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Larsen T, Jefferson C, Bartley A, Strassmann JE, Queller DC. Inference of symbiotic adaptations in nature using experimental evolution. Evolution 2021; 75:945-955. [PMID: 33590884 DOI: 10.1111/evo.14193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/30/2021] [Indexed: 11/27/2022]
Abstract
Microbes must adapt to the presence of other species, but it can be difficult to recreate the natural context for these interactions in the laboratory. We describe a method for inferring the existence of symbiotic adaptations by experimentally evolving microbes that would normally interact in an artificial environment without access to other species. By looking for changes in the fitness effects microbes adapted to isolation have on their partners, we can infer the existence of ancestral adaptations that were lost during experimental evolution. The direction and magnitude of trait changes can offer useful insight as to whether the microbes have historically been selected to help or harm one another in nature. We apply our method to the complex symbiosis between the social amoeba Dictyostelium discoideum and two intracellular bacterial endosymbionts, Paraburkholderia agricolaris and Paraburkholderia hayleyella. Our results suggest P. hayleyella-but not P. agricolaris-has generally been selected to attenuate its virulence in nature, and that D. discoideum has evolved to antagonistically limit the growth of Paraburkholderia. The approach demonstrated here can be a powerful tool for studying adaptations in microbes, particularly when the specific natural context in which the adaptations evolved is unknown or hard to reproduce.
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Affiliation(s)
- Tyler Larsen
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Cara Jefferson
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Anthony Bartley
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Joan E Strassmann
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - David C Queller
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130
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15
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Phenotypic Parallelism during Experimental Adaptation of a Free-Living Bacterium to the Zebrafish Gut. mBio 2020; 11:mBio.01519-20. [PMID: 32817106 PMCID: PMC7439477 DOI: 10.1128/mbio.01519-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Although animals encounter many bacterial species throughout their lives, only a subset colonize vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. We used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host by serially passaging replicate populations of Shewanella oneidensis through the intestines of larval zebrafish (Danio rerio). Our results demonstrate that adaptation to the zebrafish gut is complex, with multiple evolutionary pathways capable of improving colonization, but that motility plays an important role during the onset of host association. Although animals encounter a plethora of bacterial species throughout their lives, only a subset colonize vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. However, our understanding of how bacteria initiate symbioses with animal hosts remains underexplored, and this process is central to the assembly and function of gut bacterial communities. Therefore, we used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host by serially passaging replicate populations of Shewanella oneidensis through the intestines of larval zebrafish (Danio rerio). After approximately 200 bacterial generations, isolates from evolved populations improved their ability to colonize larval zebrafish during competition against their unpassaged ancestor. Genome sequencing revealed unique sets of mutations in the two evolved isolates exhibiting the highest mean competitive fitness. One isolate exhibited increased swimming motility and decreased biofilm formation compared to the ancestor, and we identified a missense mutation in the mannose-sensitive hemagglutinin pilus operon that is sufficient to increase fitness and reproduce these phenotypes. The second isolate exhibited enhanced swimming motility but unchanged biofilm formation, and here the genetic basis for adaptation is less clear. These parallel enhancements in motility and fitness resemble the behavior of a closely related Shewanella strain previously isolated from larval zebrafish and suggest phenotypic convergence with this isolate. Our results demonstrate that adaptation to the zebrafish gut is complex, with multiple evolutionary pathways capable of improving colonization, but that motility plays an important role during the onset of host association.
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16
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Fontaine SS, Kohl KD. Optimal integration between host physiology and functions of the gut microbiome. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190594. [PMID: 32772673 DOI: 10.1098/rstb.2019.0594] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Host-associated microbial communities have profound impacts on animal physiological function, especially nutrition and metabolism. The hypothesis of 'symmorphosis', which posits that the physiological systems of animals are regulated precisely to meet, but not exceed, their imposed functional demands, has been used to understand the integration of physiological systems across levels of biological organization. Although this idea has been criticized, it is recognized as having important heuristic value, even as a null hypothesis, and may, therefore, be a useful tool in understanding how hosts evolve in response to the function of their microbiota. Here, through a hologenomic lens, we discuss how the idea of symmorphosis may be applied to host-microbe interactions. Specifically, we consider scenarios in which host physiology may have evolved to collaborate with the microbiota to perform important functions, and, on the other hand, situations in which services have been completely outsourced to the microbiota, resulting in relaxed selection on host pathways. Following this theoretical discussion, we finally suggest strategies by which these currently speculative ideas may be explicitly tested to further our understanding of host evolution in response to their associated microbial communities. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Samantha S Fontaine
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
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17
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Sørensen MES, Lowe CD, Minter EJA, Wood AJ, Cameron DD, Brockhurst MA. The role of exploitation in the establishment of mutualistic microbial symbioses. FEMS Microbiol Lett 2020; 366:5528313. [PMID: 31271421 PMCID: PMC6638607 DOI: 10.1093/femsle/fnz148] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022] Open
Abstract
Evolutionary theory suggests that the conditions required for the establishment of mutualistic symbioses through mutualism alone are highly restrictive, often requiring the evolution of complex stabilising mechanisms. Exploitation, whereby initially the host benefits at the expense of its symbiotic partner and mutual benefits evolve subsequently through trade-offs, offers an arguably simpler route to the establishment of mutualistic symbiosis. In this review, we discuss the theoretical and experimental evidence supporting a role for host exploitation in the establishment and evolution of mutualistic microbial symbioses, including data from both extant and experimentally evolved symbioses. We conclude that exploitation rather than mutualism may often explain the origin of mutualistic microbial symbioses.
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Affiliation(s)
- Megan E S Sørensen
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Chris D Lowe
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| | - Ewan J A Minter
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - A Jamie Wood
- Department of Biology, University of York, York YO10 5DD, UK.,Department of Mathematics, University of York, York YO10 5DD, UK
| | - Duncan D Cameron
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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18
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19
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Abstract
Insects frequently harbor multiple symbionts that collectively provide them with essential nutrients. Comparing several recent and ancient associations revealed a strikingly parallel pattern, by which a new symbiont was integrated into a preexisting host-symbiont interaction.
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Affiliation(s)
- Christian Kost
- Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
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20
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Kohl KD. Ecological and evolutionary mechanisms underlying patterns of phylosymbiosis in host-associated microbial communities. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190251. [PMID: 32200746 PMCID: PMC7133527 DOI: 10.1098/rstb.2019.0251] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
Phylosymbiosis, where similarities in host-associated microbial communities recapitulate the phylogeny of their hosts, is a newly recognized yet pervasive pattern in the field of host-microbe interactions. While phylosymbiosis has been documented across many systems, we still have a poor understanding of the mechanisms that underlie this emergent pattern. Host selection of the microbiome is a widely cited mechanism, yet other basic ecological and evolutionary processes (dispersal, drift and diversification) may also be at play. This paper discusses the roles that each of these processes and their interactions may play in yielding phylosymbiotic signals across hosts. Finally, this paper will identify open questions and methods that are required to better understand the relative contributions of these basic processes to phylosymbiosis. Given that phylosymbiosis has been shown to relate to functional components of host fitness, understanding the processes that contribute to these patterns will be important for our understanding of the ecology and evolution of host-microbe interactions. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Kevin D. Kohl
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
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21
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Specific Eco-evolutionary Contexts in the Mouse Gut Reveal Escherichia coli Metabolic Versatility. Curr Biol 2020; 30:1049-1062.e7. [PMID: 32142697 DOI: 10.1016/j.cub.2020.01.050] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/21/2019] [Accepted: 01/15/2020] [Indexed: 02/08/2023]
Abstract
Members of the gut microbiota are thought to experience strong competition for nutrients. However, how such competition shapes their evolutionary dynamics and depends on intra- and interspecies interactions is poorly understood. Here, we test the hypothesis that Escherichia coli evolution in the mouse gut is more predictable across hosts in the absence of interspecies competition than in the presence of other microbial species. In support, we observed that lrp, a gene encoding a global regulator of amino acid metabolism, was repeatedly selected in germ-free mice 2 weeks after mono-colonization by this bacterium. We established that this specific genetic adaptation increased E. coli's ability to compete for amino acids, and analysis of gut metabolites identified serine and threonine as the metabolites preferentially consumed by E. coli in the mono-colonized mouse gut. Preference for serine consumption was further supported by testing a set of mutants that showed loss of advantage of an lrp mutant impaired in serine metabolism in vitro and in vivo. Remarkably, the presence of a single additional member of the microbiota, Blautia coccoides, was sufficient to alter the gut metabolome and, consequently, the evolutionary path of E. coli. In this environment, the fitness advantage of the lrp mutant bacteria is lost, and mutations in genes involved in anaerobic respiration were selected instead, recapitulating the eco-evolutionary context from mice with a complex microbiota. Together, these results highlight the metabolic plasticity and evolutionary versatility of E. coli, tailored to the specific ecology it experiences in the gut.
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22
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Cohen ML, Mashanova EV, Jagannathan SV, Soto W. Adaptation to pH stress by Vibrio fischeri can affect its symbiosis with the Hawaiian bobtail squid ( Euprymna scolopes). MICROBIOLOGY-SGM 2020; 166:262-277. [PMID: 31967537 PMCID: PMC7376262 DOI: 10.1099/mic.0.000884] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many microorganisms engaged in host-microbe interactions pendulate between a free-living phase and a host-affiliated stage. How adaptation to stress during the free-living phase affects host-microbe associations is unclear and understudied. To explore this topic, the symbiosis between Hawaiian bobtail squid (Euprymna scolopes) and the luminous bacterium Vibrio fischeri was leveraged for a microbial experimental evolution study. V. fischeri experienced adaptation to extreme pH while apart from the squid host. V. fischeri was serially passaged for 2000 generations to the lower and upper pH growth limits for this microorganism, which were pH 6.0 and 10.0, respectively. V. fischeri was also serially passaged for 2000 generations to vacillating pH 6.0 and 10.0. Evolution to pH stress both facilitated and impaired symbiosis. Microbial evolution to acid stress promoted squid colonization and increased bioluminescence for V. fischeri, while symbiont adaptation to alkaline stress diminished these two traits. Oscillatory selection to acid and alkaline stress also improved symbiosis for V. fischeri, but the facilitating effects were less than that provided by microbial adaptation to acid stress. In summary, microbial adaptation to harsh environments amid the free-living phase may impact the evolution of host-microbe interactions in ways that were not formerly considered.
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Affiliation(s)
- Meagan Leah Cohen
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - Ekaterina Vadimovna Mashanova
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - Sveta Vivian Jagannathan
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - William Soto
- College of William & Mary, Department of Biology, Integrated Science Center Rm 3035, 540 Landrum Dr., Williamsburg, VA 23185, USA
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23
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Abstract
Little is known about the establishment of symbioses. A new study finds that two independent protist-algae symbioses utilize convergent patterns of nutrient exchange, suggesting that certain complementary host and symbiont traits can increase the likelihood of establishing beneficial symbiotic interactions.
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Affiliation(s)
- Levi T Morran
- Department of Biology, Emory University, Atlanta, GA, USA.
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24
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Quigley KM, Alvarez Roa C, Torda G, Bourne DG, Willis BL. Co-dynamics of Symbiodiniaceae and bacterial populations during the first year of symbiosis with Acropora tenuis juveniles. Microbiologyopen 2019; 9:e959. [PMID: 31670480 PMCID: PMC7002099 DOI: 10.1002/mbo3.959] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 02/04/2023] Open
Abstract
Interactions between corals and their associated microbial communities (Symbiodiniaceae and prokaryotes) are key to understanding corals' potential for and rate of acclimatory and adaptive responses. However, the establishment of microalgal and bacterial communities is poorly understood during coral ontogeny in the wild. We examined the establishment and co-occurrence between multiple microbial communities using 16S rRNA (bacterial) and ITS2 rDNA (Symbiodiniaceae) gene amplicon sequencing in juveniles of the common coral, Acropora tenuis, across the first year of development. Symbiodiniaceae communities in juveniles were dominated by Durusdinium trenchii and glynnii (D1 and D1a), with lower abundances of Cladocopium (C1, C1d, C50, and Cspc). Bacterial communities were more diverse and dominated by taxa within Proteobacteria, Cyanobacteria, and Planctomycetes. Both communities were characterized by significant changes in relative abundance and diversity of taxa throughout the year. D1, D1a, and C1 were significantly correlated with multiple bacterial taxa, including Alpha-, Deltra-, and Gammaproteobacteria, Planctomycetacia, Oxyphotobacteria, Phycisphaerae, and Rhizobiales. Specifically, D1a tended to associate with Oxyphotobacteria and D1 with Alphaproteobacteria, although these associations may represent correlational and not causal relationships. Bioenergetic modeling combined with physiological measurements of coral juveniles (surface area and Symbiodiniaceae cell densities) identified key periods of carbon limitation and nitrogen assimilation, potentially coinciding with shifts in microbial community composition. These results demonstrate that Symbiodiniaceae and bacterial communities are dynamic throughout the first year of ontology and may vary in tandem, with important fitness effects on host juveniles.
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Affiliation(s)
- Kate M Quigley
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, QLD, Australia.,Australian Institute of Marine Science, Townsville, QLD, Australia
| | | | - Greg Torda
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - David G Bourne
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, QLD, Australia.,Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Bette L Willis
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, QLD, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
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25
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Cohen ML, Mashanova EV, Rosen NM, Soto W. Adaptation to temperature stress by Vibrio fischeri facilitates this microbe's symbiosis with the Hawaiian bobtail squid (Euprymna scolopes). Evolution 2019; 73:1885-1897. [PMID: 31397886 DOI: 10.1111/evo.13819] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 08/02/2019] [Accepted: 08/03/2019] [Indexed: 11/29/2022]
Abstract
For microorganisms cycling between free-living and host-associated stages, where reproduction occurs in both of these lifestyles, an interesting inquiry is whether adaptation to stress during the free-living stage can impact microbial fitness in the host. To address this topic, the mutualism between the Hawaiian bobtail squid (Euprymna scolopes) and the marine bioluminescent bacterium Vibrio fischeri was utilized. Using microbial experimental evolution, V. fischeri was selected to low (8°C), high (34°C), and fluctuating temperature stress (8°C/34°C) for 2000 generations. The temperatures 8°C and 34°C were the lower and upper growth limits, respectively. V. fischeri was also selected to benign temperatures (21°C and 28°C) for 2000 generations, which served as controls. V. fischeri demonstrated significant adaptation to low, high, and fluctuating temperature stress. V. fischeri did not display significant adaptation to the benign temperatures. Adaptation to stressful temperatures facilitated V. fischeri's ability to colonize the squid host relative to the ancestral lines. Bioluminescence levels also increased. Evolution to benign temperatures did not manifest these results. In summary, microbial adaptation to stress during the free-living stage can promote coevolution between hosts and microorganisms.
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Affiliation(s)
- Meagan Leah Cohen
- Department of Biology, College of William & Mary, Williamsburg, Virginia, 23185
| | | | | | - William Soto
- Department of Biology, College of William & Mary, Williamsburg, Virginia, 23185
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26
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McDonald MJ. Microbial Experimental Evolution - a proving ground for evolutionary theory and a tool for discovery. EMBO Rep 2019; 20:e46992. [PMID: 31338963 PMCID: PMC6680118 DOI: 10.15252/embr.201846992] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 03/23/2019] [Accepted: 06/28/2019] [Indexed: 01/21/2023] Open
Abstract
Microbial experimental evolution uses controlled laboratory populations to study the mechanisms of evolution. The molecular analysis of evolved populations enables empirical tests that can confirm the predictions of evolutionary theory, but can also lead to surprising discoveries. As with other fields in the life sciences, microbial experimental evolution has become a tool, deployed as part of the suite of techniques available to the molecular biologist. Here, I provide a review of the general findings of microbial experimental evolution, especially those relevant to molecular microbiologists that are new to the field. I also relate these results to design considerations for an evolution experiment and suggest future directions for those working at the intersection of experimental evolution and molecular biology.
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Affiliation(s)
- Michael J McDonald
- School of Biological Sciences, Monash University, Melbourne, Vic., Australia
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27
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Watanabe K, Suzuki H, Nishida T, Mishima M, Tachibana M, Fujishima M, Shimizu T, Watarai M. Identification of novel Legionella genes required for endosymbiosis in Paramecium based on comparative genome analysis with Holospora spp. FEMS Microbiol Ecol 2019; 94:5074368. [PMID: 30124811 DOI: 10.1093/femsec/fiy162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/11/2018] [Indexed: 12/20/2022] Open
Abstract
The relationship between Legionella and protist hosts has a huge impact when considering the infectious risk in humans because it facilitates the long-term replication and survival of Legionella in the environment. The ciliate Paramecium is considered to be a protist host for Legionella in natural environments, but the details of their endosymbiosis are largely unknown. In this study, we determined candidate Legionella pneumophila genes that are likely to be involved in the establishment of endosymbiosis in Paramecium caudatum by comparing the genomes of Legionella spp. and Holospora spp. that are obligate endosymbiotic bacteria in Paramecium spp. Among the candidate genes, each single deletion mutant for five genes (lpg0492, lpg0522, lpg0523, lpg2141 and lpg2398) failed to establish endosymbiosis in P. caudatum despite showing intracellular growth in human macrophages. The mutants exhibited no characteristic changes in terms of their morphology, multiplication rate or capacity for modulating the phagosomes in which they were contained, but their resistance to lysozyme decreased significantly. This study provides insights into novel factors required by L. pneumophila for endosymbiosis in P. caudatum, and suggests that endosymbiotic organisms within conspecific hosts may have shared genes related to effective endosymbiosis establishment.
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Affiliation(s)
- Kenta Watanabe
- The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan.,Joint Faculty of Veterinary Medicine, Laboratory of Veterinary Public Health, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Takashi Nishida
- The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
| | - Manami Mishima
- Joint Faculty of Veterinary Medicine, Laboratory of Veterinary Public Health, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
| | - Masato Tachibana
- Graduate School of Medicine, Dentistry and Pharmaceutical Science, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Masahiro Fujishima
- Department of Sciences, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan.,Department of Research Infrastructure, National BioResource Project of Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Takashi Shimizu
- The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan.,Joint Faculty of Veterinary Medicine, Laboratory of Veterinary Public Health, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
| | - Masahisa Watarai
- The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan.,Joint Faculty of Veterinary Medicine, Laboratory of Veterinary Public Health, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
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28
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Remigi P, Masson-Boivin C, Rocha EP. Experimental Evolution as a Tool to Investigate Natural Processes and Molecular Functions. Trends Microbiol 2019; 27:623-634. [DOI: 10.1016/j.tim.2019.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 12/17/2022]
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29
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Vega NM. Experimental evolution reveals microbial traits for association with the host gut. PLoS Biol 2019; 17:e3000129. [PMID: 30716061 PMCID: PMC6375648 DOI: 10.1371/journal.pbio.3000129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/14/2019] [Indexed: 11/19/2022] Open
Abstract
Understanding how microbes adapt to their host is an enduring problem in microbiome ecology, and understanding the microbial traits that allow colonization of the host and increase adaptation to the host environment is of particular interest. In this study, Robinson and colleagues use experimental evolution to demonstrate adaptation of a commensal bacterium to its zebrafish host and describe the changes in phenotype that emerge during this evolutionary process. These results provide insight into the evolutionary problem of host adaptation and demonstrate the utility of simple models for understanding host–microbiome dynamics.
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Affiliation(s)
- Nicole M. Vega
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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30
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Robinson CD, Klein HS, Murphy KD, Parthasarathy R, Guillemin K, Bohannan BJM. Experimental bacterial adaptation to the zebrafish gut reveals a primary role for immigration. PLoS Biol 2018; 16:e2006893. [PMID: 30532251 PMCID: PMC6301714 DOI: 10.1371/journal.pbio.2006893] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 12/20/2018] [Accepted: 11/21/2018] [Indexed: 02/07/2023] Open
Abstract
All animals live in intimate association with microorganisms that profoundly influence their health and development, yet the traits that allow microorganisms to establish and maintain host associations are not well understood. To date, most investigations aimed at identifying traits required for host association have focused on intrahost niches. Consequently, little is known about the relative contribution of extrahost factors such as environmental growth and survival and immigration into hosts from the external environment, as promoters of host association. To address this, we developed a tractable experimental evolution system that investigates both intra- and extrahost factors contributing to bacterial adaptation to the vertebrate gut. We passaged replicate lines of a zebrafish bacterial isolate, Aeromonas veronii, through populations of germ-free larval zebrafish (Danio rerio), each time using gut-associated Aeromonas populations to inoculate the aquatic environment of the next zebrafish population. We observed rapid increased adaptation to the host in all replicate lines. The initial adaptations present in early-evolved isolates did not increase intrahost fitness but rather enhanced both immigration from the environment and interhost transmission. Only in later-evolved isolates did we find evidence for intrahost-specific adaptations, as demonstrated by comparing their competitive fitness in the host genotype to which they evolved to that in a different genotype. Our results show how selection for bacterial transmission between hosts and their environment can shape bacterial-host association. This work illuminates the nature of selective forces present in host-microbe systems and reveals specific mechanisms of increased host association. Furthermore, our findings demonstrate that the entire host-microbe-environment system must be considered when identifying microbial traits that contribute to host adaptation.
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Affiliation(s)
- Catherine D. Robinson
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Helena S. Klein
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Kyleah D. Murphy
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, Oregon, United States of America
| | - Raghuveer Parthasarathy
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, Oregon, United States of America
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Brendan J. M. Bohannan
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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Tso GHW, Reales-Calderon JA, Tan ASM, Sem X, Le GTT, Tan TG, Lai GC, Srinivasan KG, Yurieva M, Liao W, Poidinger M, Zolezzi F, Rancati G, Pavelka N. Experimental evolution of a fungal pathogen into a gut symbiont. Science 2018; 362:589-595. [DOI: 10.1126/science.aat0537] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 09/12/2018] [Indexed: 12/21/2022]
Abstract
Gut microbes live in symbiosis with their hosts, but how mutualistic animal-microbe interactions emerge is not understood. By adaptively evolving the opportunistic fungal pathogenCandida albicansin the mouse gastrointestinal tract, we selected strains that not only had lost their main virulence program but also protected their new hosts against a variety of systemic infections. This protection was independent of adaptive immunity, arose as early as a single day postpriming, was dependent on increased innate cytokine responses, and was thus reminiscent of “trained immunity.” Because both the microbe and its new host gain some advantages from their interaction, this experimental system might allow direct study of the evolutionary forces that govern the emergence of mutualism between a mammal and a fungus.
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Bellis ES, Edlund RB, Berrios HK, Lessios HA, Denver DR. Molecular signatures of host specificity linked to habitat specialization in Exaiptasia sea anemones. Ecol Evol 2018; 8:5413-5426. [PMID: 29938062 PMCID: PMC6010850 DOI: 10.1002/ece3.4058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/24/2018] [Accepted: 02/27/2018] [Indexed: 12/17/2022] Open
Abstract
Rising ocean temperatures associated with global climate change induce breakdown of the symbiosis between coelenterates and photosynthetic microalgae of the genus Symbiodinium. Association with more thermotolerant partners could contribute to resilience, but the genetic mechanisms controlling specificity of hosts for particular Symbiodinium types are poorly known. Here, we characterize wild populations of a sea anemone laboratory model system for anthozoan symbiosis, from contrasting environments in Caribbean Panama. Patterns of anemone abundance and symbiont diversity were consistent with specialization of holobionts for particular habitats, with Exaiptasia pallida/S. minutum (ITS2 type B1) abundant on vertical substrate in thermally stable, shaded environments but E. brasiliensis/Symbiodinium sp. (ITS2 clade A) more common in shallow areas subject to high temperature and irradiance. Population genomic sequencing revealed a novel E. pallida population from the Bocas del Toro Archipelago that only harbors S. minutum. Loci most strongly associated with divergence of the Bocas-specific population were enriched in genes with putative roles in cnidarian symbiosis, including activators of the complement pathway of the innate immune system, thrombospondin-type-1 repeat domain proteins, and coordinators of endocytic recycling. Our findings underscore the importance of unmasking cryptic diversity in natural populations and the role of long-term evolutionary history in mediating interactions with Symbiodinium.
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Affiliation(s)
- Emily S. Bellis
- Department of Integrative BiologyOregon State UniversityCorvallisOregon
| | - Reid. B. Edlund
- Department of Integrative BiologyOregon State UniversityCorvallisOregon
| | - Hazel K. Berrios
- Department of Biological SciencesArkansas State UniversityJonesboroArkansas
| | | | - Dee R. Denver
- Department of Integrative BiologyOregon State UniversityCorvallisOregon
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A Microbial Perspective on the Grand Challenges in Comparative Animal Physiology. mSystems 2018; 3:mSystems00146-17. [PMID: 29556549 PMCID: PMC5853186 DOI: 10.1128/msystems.00146-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/13/2017] [Indexed: 01/23/2023] Open
Abstract
Interactions with microbial communities can have profound influences on animal physiology, thereby impacting animal performance and fitness. Therefore, it is important to understand the diversity and nature of host-microbe interactions in various animal groups (invertebrates, fish, amphibians, reptiles, birds, and mammals). Interactions with microbial communities can have profound influences on animal physiology, thereby impacting animal performance and fitness. Therefore, it is important to understand the diversity and nature of host-microbe interactions in various animal groups (invertebrates, fish, amphibians, reptiles, birds, and mammals). In this perspective, I discuss how the field of host-microbe interactions can be used to address topics that have been identified as grand challenges in comparative animal physiology: (i) horizontal integration of physiological processes across organisms, (ii) vertical integration of physiological processes across organizational levels within organisms, and (iii) temporal integration of physiological processes during evolutionary change. Addressing these challenges will require the use of a variety of animal models and the development of systems approaches that can integrate large, multiomic data sets from both microbial communities and animal hosts. Integrating host-microbe interactions into the established field of comparative physiology represents an exciting frontier for both fields.
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34
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Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments. Proc Natl Acad Sci U S A 2018; 115:2425-2430. [PMID: 29453274 DOI: 10.1073/pnas.1714246115] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Assays to accurately estimate relative fitness of bacteria growing in multistrain communities can advance our understanding of how selection shapes diversity within a lineage. Here, we present a variant of the "evolve and resequence" approach both to estimate relative fitness and to identify genetic variants responsible for fitness variation of symbiotic bacteria in free-living and host environments. We demonstrate the utility of this approach by characterizing selection by two plant hosts and in two free-living environments (sterilized soil and liquid media) acting on synthetic communities of the facultatively symbiotic bacterium Ensifer meliloti We find (i) selection that hosts exert on rhizobial communities depends on competition among strains, (ii) selection is stronger inside hosts than in either free-living environment, and (iii) a positive host-dependent relationship between relative strain fitness in multistrain communities and host benefits provided by strains in single-strain experiments. The greatest changes in allele frequencies in response to plant hosts are in genes associated with motility, regulation of nitrogen fixation, and host/rhizobia signaling. The approach we present provides a powerful complement to experimental evolution and forward genetic screens for characterizing selection in bacterial populations, identifying gene function, and surveying the functional importance of naturally occurring genomic variation.
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Sinnathamby G, Henderson G, Umair S, Janssen P, Bland R, Simpson H. The bacterial community associated with the sheep gastrointestinal nematode parasite Haemonchus contortus. PLoS One 2018; 13:e0192164. [PMID: 29420571 PMCID: PMC5805237 DOI: 10.1371/journal.pone.0192164] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/17/2018] [Indexed: 11/23/2022] Open
Abstract
Culture-independent methods were used to study the microbiota of adult worms, third-stage larvae and eggs, both in faeces and laid in vitro, of Haemonchus contortus, a nematode parasite of the abomasa of ruminants which is a major cause of production losses and ill-health. Bacteria were identified in eggs, the female reproductive tract and the gut of adult and third-stage larvae (L3). PCR amplification of 16S rRNA sequences, denaturing gradient gel electrophoresis (DGGE) and clone libraries were used to compare the composition of the microbial communities of the different life-cycle stages of the parasites, as well as parasites and their natural environments. The microbiomes of adult worms and L3 were different from those in the abomasum or faeces respectively. The H. contortus microbiota was mainly comprised of members of the phyla Proteobacteria, Firmicutes and Bacteroidetes. Bacteria were localised in the gut, inside eggs and within the uterus of adult female worms using the universal FISH Eub338 probe, which targets most bacteria, and were also seen in these tissues by light and transmission electron microscopy. Streptococcus/Lactococcus sp. were identified within the distal uterus with the probe Strc493. Sequences from the genera Weissella and Leuconostoc were found in all life-cycle stages, except eggs collected from faeces, in which most sequences belonged to Clostridium sp. Bacteria affiliated with Weissella/Leuconostoc were identified in both PCR-DGGE short sequences and clone libraries of nearly full length 16S rRNA bacterial sequences in all life-cycle stages and subsequently visualised in eggs by fluorescent in situ hybridisation (FISH) with group-specific probes. This strongly suggests they are vertically transmitted endosymbionts. As this study was carried out on a parasite strain which has been maintained in the laboratory, other field isolates will need to be examined to establish whether these bacteria are more widely dispersed and have potential as targets to control H. contortus infections.
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Affiliation(s)
- Gajenathirin Sinnathamby
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | | | - Saleh Umair
- AgResearch Ltd, Palmerston North, New Zealand
| | | | - Ross Bland
- AgResearch Ltd, Palmerston North, New Zealand
| | - Heather Simpson
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
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Gerardo N, Hurst G. Q&A: Friends (but sometimes foes) within: the complex evolutionary ecology of symbioses between host and microbes. BMC Biol 2017; 15:126. [PMID: 29282064 PMCID: PMC5744397 DOI: 10.1186/s12915-017-0455-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Over the past decade, there has been a pronounced shift in the study of host-microbe associations, with recognition that many of these associations are beneficial, and often critical, for a diverse array of hosts. There may also be pronounced benefits for the microbes, though this is less well empirically understood. Significant progress has been made in understanding how ecology and evolution shape simple associations between hosts and one or a few microbial species, and this work can serve as a foundation to study the ecology and evolution of host associations with their often complex microbial communities (microbiomes).
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Affiliation(s)
- Nicole Gerardo
- Department of Biology, Emory University, 1510 Clifton RD, Atlanta, Georgia, 30322, USA.
| | - Gregory Hurst
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
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37
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Sousa A, Frazão N, Ramiro RS, Gordo I. Evolution of commensal bacteria in the intestinal tract of mice. Curr Opin Microbiol 2017; 38:114-121. [PMID: 28591676 DOI: 10.1016/j.mib.2017.05.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/28/2017] [Accepted: 05/21/2017] [Indexed: 12/19/2022]
Abstract
Hundreds of different bacterial species inhabit our intestines and contribute to our health status, with significant loss of species diversity typically observed in disease conditions. Within each microbial species a great deal of diversity is hidden and such intra-specific variation is also key to the proper homeostasis between the host and its microbial inhabitants. Indeed, it is at this level that new mechanisms of antibiotic resistance emerge and pathogenic characteristics evolve. Yet, our knowledge on intra-species variation in the gut is still limited and an understanding of the evolutionary mechanisms acting on it is extremely reduced. Here we review recent work that has begun to reveal that adaptation of commensal bacteria to the mammalian intestine may be fast and highly repeatable, and that the time scales of evolutionary and ecological change can be very similar in these ecosystems.
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Affiliation(s)
- Ana Sousa
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, Oeiras, Portugal; iBiMED, Institute for Biomedicine, Universidade de Aveiro, Portugal
| | - Nelson Frazão
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, Oeiras, Portugal
| | - Ricardo S Ramiro
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, Oeiras, Portugal
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, Oeiras, Portugal.
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38
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Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations. ISME JOURNAL 2017; 11:2181-2194. [PMID: 28509909 DOI: 10.1038/ismej.2017.69] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/02/2017] [Accepted: 03/10/2017] [Indexed: 01/01/2023]
Abstract
Evolution is an on-going process, and it can be studied experimentally in organisms with rapid generations. My team has maintained 12 populations of Escherichia coli in a simple laboratory environment for >25 years and 60 000 generations. We have quantified the dynamics of adaptation by natural selection, seen some of the populations diverge into stably coexisting ecotypes, described changes in the bacteria's mutation rate, observed the new ability to exploit a previously untapped carbon source, characterized the dynamics of genome evolution and used parallel evolution to identify the genetic targets of selection. I discuss what the future might hold for this particular experiment, briefly highlight some other microbial evolution experiments and suggest how the fields of experimental evolution and microbial ecology might intersect going forward.
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39
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Tomberlin JK, Crippen TL, Tarone AM, Chaudhury MFB, Singh B, Cammack JA, Meisel RP. A Review of Bacterial Interactions With Blow Flies (Diptera: Calliphoridae) of Medical, Veterinary, and Forensic Importance. ANNALS OF THE ENTOMOLOGICAL SOCIETY OF AMERICA 2017; 110:19-36. [DOI: 10.1093/aesa/saw086] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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