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Johnston PR, Paris V, Rolff J. Immune gene regulation in the gut during metamorphosis in a holo- versus a hemimetabolous insect. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190073. [PMID: 31438821 PMCID: PMC6711282 DOI: 10.1098/rstb.2019.0073] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2019] [Indexed: 12/19/2022] Open
Abstract
During metamorphosis, holometabolous insects completely replace the larval gut and must control the microbiota to avoid septicaemia. Rapid induction of bactericidal activity in the insect gut at the onset of pupation has been described in numerous orders of the Holometabola and is best-studied in the Lepidoptera where it is under control of the 20-hydroxyecdysone (20E) moulting pathway. Here, using RNAseq, we compare the expression of immune effector genes in the gut during metamorphosis in a holometabolous (Galleria mellonella) and a hemimetabolous insect (Gryllus bimaculatus). We find that in G. mellonella, the expression of numerous immune effectors and the transcription factor GmEts are upregulated, with peak expression of three antimicrobial peptides (AMPs) and a lysozyme coinciding with delamination of the larval gut. By contrast, no such upregulation was detectable in the hemimetabolous Gr. bimaculatus. These findings support the idea that the upregulation of immune effectors at the onset of complete metamorphosis is an adaptive response, which controls the microbiota during gut replacement. This article is part of the theme issue 'The evolution of complete metamorphosis'.
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Affiliation(s)
- Paul R. Johnston
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Véronique Paris
- Evolutionary Biology, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Bio 21 Institute, University of Melbourne, Parkville VIC 3052, Australia
| | - Jens Rolff
- Evolutionary Biology, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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Karmacharya D, Manandhar P, Manandhar S, Sherchan AM, Sharma AN, Joshi J, Bista M, Bajracharya S, Awasthi NP, Sharma N, Llewellyn B, Waits LP, Thapa K, Kelly MJ, Vuyisich M, Starkenburg SR, Hero JM, Hughes J, Wultsch C, Bertola L, Fountain-Jones NM, Sinha AK. Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal. PLoS One 2019; 14:e0221868. [PMID: 31465520 PMCID: PMC6715213 DOI: 10.1371/journal.pone.0221868] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 08/17/2019] [Indexed: 02/01/2023] Open
Abstract
Bengal tigers (Panthera tigris tigris) serve a pivotal role as an apex predator in forest ecosystems. To increase our knowledge on factors impacting the viability and health of this endangered species, we studied the gut microbiota in 32 individual Bengal tigers from three geographically separated areas (Chitwan National Park (CNP), Bardia National Park (BNP) and Suklaphanta Wildlife Reserve (SWR)) in Nepal, using noninvasive genetic sampling methods. Gut microbiota influence the immune system, impact various physiological functions, and modulates metabolic reactions, that ultimately impact the host health, behavior and development. Across the tiger populations in Nepal, we found significant differences in the composition of microbial communities based on their geographic locations. Specifically, we detected significant differences between CNP and the other two protected areas (CNP vs BNP: pseudo t = 1.944, P = 0.006; CNP vs SWR: pseudo t = 1.9942, P = 0.0071), but no differences between BNP and SWR. This mirrors what has been found for tiger gene flow in the same populations, suggesting gut microbiota composition and host gene flow may be linked. Furthermore, predictive metagenome functional content analysis (PICRUSt) revealed a higher functional enrichment and diversity for significant gut microbiota in the Chitwan tiger population and the lowest enrichment and diversity in Suklaphanta. The CNP tiger population contained higher proportions of microbiota that are associated with predicted functions relevant for metabolism of amino acid, lipid, xenobiotics biodegradation, terpenoides and polyketides than the SWR population. We conclude the tiger population structure, gut microbiota profile and associated functional metabolic categories are correlated, with geographically most separated CNP and SWR tiger population having the most distinct and different host genotype and microbiota profiles. Our work dramatically expands the understanding of tiger microbiota in wild populations and provides a valuable case study on how to investigate genetic diversity at different hierarchical levels, including hosts as well as their microbial communities.
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Affiliation(s)
- Dibesh Karmacharya
- Center for Molecular Dynamics Nepal, Kathmandu, Nepal
- School of Environment, Griffith University, Brisbane, Queensland, Australia
| | | | | | | | | | - Jyoti Joshi
- Center for Molecular Dynamics Nepal, Kathmandu, Nepal
| | - Manisha Bista
- Center for Molecular Dynamics Nepal, Kathmandu, Nepal
| | | | | | - Netra Sharma
- Environment Team, U.S. Agency for International Development, Kathmandu, Nepal
| | - Bronwyn Llewellyn
- Environment Team, U.S. Agency for International Development, Kathmandu, Nepal
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Kanchan Thapa
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Momchilo Vuyisich
- Applied Genomics, Los Alamos National Lab, Los Alamos, New Mexico, United States of America
| | - Shawn R. Starkenburg
- Applied Genomics, Los Alamos National Lab, Los Alamos, New Mexico, United States of America
| | - Jean-Marc Hero
- School of Science & Education, University of the Sunshine Coast, Sunshine Coast, Queensland, Australia
| | - Jane Hughes
- School of Environment, Griffith University, Brisbane, Queensland, Australia
| | - Claudia Wultsch
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, United States of America
- Bioinformatics and Computational Genomics Laboratory, Hunter College, City University of New York, New York, United States of America
| | - Laura Bertola
- Department of Biology, City College of New York, New York, United States of America
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Nicholas M. Fountain-Jones
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Amit K. Sinha
- Center for Molecular Dynamics Nepal, Kathmandu, Nepal
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Laviad-Shitrit S, Izhaki I, Lalzar M, Halpern M. Comparative Analysis of Intestine Microbiota of Four Wild Waterbird Species. Front Microbiol 2019; 10:1911. [PMID: 31481943 PMCID: PMC6711360 DOI: 10.3389/fmicb.2019.01911] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/05/2019] [Indexed: 01/07/2023] Open
Abstract
Waterbirds are ubiquitous and globally distributed. Yet, studies on wild waterbirds' gut microbiota are still rare. Our aim was to explore and compare the gut microbial community composition of wild waterbird species. Four wild waterbird species that are either wintering or all-year residents in Israel were studied: great cormorants, little egrets, black-crowned night herons and black-headed gulls. For each bird, three intestinal sections were sampled; anterior, middle and posterior. No significant differences were found among the microbiota compositions in the three intestine sections of each individual bird. Each waterbird species had a unique microbial composition. The gut microbiota of the black-headed gulls' fundamentally deviated from that of the other bird species, probably due to a very high abundance (58.8%) of the genus Catellicoccus (Firmicutes). Our results suggest a correlation between the waterbird species' phylogeny and their intestine microbial community hierarchical tree, which evinced phylosymbiosis. This recent coinage stands for eco-evolutionary patterns between the host phylogeny and its microbiota composition. We conclude that eco-evolutionary processes termed phylosymbiosis may occur between wild waterbird species and their gut microbial community composition.
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Affiliation(s)
- Sivan Laviad-Shitrit
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Ido Izhaki
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Maya Lalzar
- Bioinformatics Service Unit, University of Haifa, Haifa, Israel
| | - Malka Halpern
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel.,Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa at Oranim, Tivon, Israel
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Gaona O, Gómez-Acata ES, Cerqueda-García D, Neri-Barrios CX, Falcón LI. Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae. PLoS One 2019; 14:e0219982. [PMID: 31318946 PMCID: PMC6639036 DOI: 10.1371/journal.pone.0219982] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/05/2019] [Indexed: 01/12/2023] Open
Abstract
In this study we analyzed the microbiota composition of fecal samples from the lesser-long nosed bat Leptonycteris yerbabuenae in different reproductive stages (juveniles and adult bats of both sexes as well as pregnant and lactating females). The V4 region of the 16s rRNA gene from 33 individuals was analyzed using alpha and beta diversity metrics. We found that microbiota diversity (expressed in Amplicon Sequence Variants) is higher in pregnant and lactating females. The microbiota of the juveniles and non-reproductive adults was dominated by Gammaproteobacteria and Firmicutes. Reproductive females had a much more diverse microbiota, with a significant increase in phyla such as Bacteroidetes and Alphaproteobacteria. There was no difference in fecal microbiota diversity between pregnant and lactating females and juveniles and non-reproductive adults. Results suggest that differences in microbiota diversity are related to reproduction. We infer that males maintain stable microbiota composition because they do not undergo the large physiological changes that females do during reproduction and maintain a more specialized diet throughout all life stages.
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Affiliation(s)
- Osiris Gaona
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Instituto de Ecología, UNAM, Mexico City, México
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, UNAM, Parque Científico y Tecnológico de Yucatán, Mérida, Yucatán, México
| | - Elizabeth Selene Gómez-Acata
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, UNAM, Parque Científico y Tecnológico de Yucatán, Mérida, Yucatán, México
| | - Daniel Cerqueda-García
- Consorcio de Investigación del Golfo de México (CIGOM), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del Mar, Mérida, Yucatán, México
| | - Carla Ximena Neri-Barrios
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, UNAM, Parque Científico y Tecnológico de Yucatán, Mérida, Yucatán, México
| | - Luisa I. Falcón
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, UNAM, Parque Científico y Tecnológico de Yucatán, Mérida, Yucatán, México
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Abstract
Phylosymbiosis is defined as microbial community relationships that recapitulate the phylogeny of hosts. As evidence for phylosymbiosis rapidly accumulates in different vertebrate and invertebrate holobionts, a central question is what evolutionary forces cause this pattern. We use intra- and interspecific gut microbiota transplants to test for evidence of selective pressures that contribute to phylosymbiosis. We leverage three closely related species of the parasitoid wasp model Nasonia that recently diverged between 0.4 and 1 million years ago: N. vitripennis, N. giraulti, and N. longicornis Upon exposure of germfree larvae to heat-inactivated microbiota from intra- or interspecific larvae, we measure larval growth, pupation rate, and adult reproductive capacity. We report three key findings: (i) larval growth significantly slows when hosts receive an interspecific versus intraspecific gut microbiota, (ii) marked decreases in pupation and resulting adult survival occur from interspecific gut microbiota exposure, and (iii) adult reproductive capacities including male fertility and longevity are unaffected by early life exposure to an interspecific microbiota. Overall, these findings reveal developmental and survival costs to Nasonia upon larval exposures to interspecific microbiota and provide evidence that selective pressures on phenotypes produced by host-microbiota interactions may underpin phylosymbiosis.IMPORTANCE Phylosymbiosis is an ecoevolutionary hypothesis and emerging pattern in animal-microbiota studies whereby the host phylogenetic relationships parallel the community relationships of the host-associated microbiota. A central prediction of phylosymbiosis is that closely related hosts exhibit a lower microbiota beta diversity than distantly related hosts. While phylosymbiosis has emerged as a widespread trend in a field often challenged to find trends across systems, two critical and understudied questions are whether or not phylosymbiosis is consequential to host biology and if adaptive evolutionary forces underpin the pattern. Here, using germfree rearing in the phylosymbiosis model Nasonia, we demonstrate that early life exposure to heat-inactivated microbiota from more distantly related species poses more severe developmental and survival costs than microbiota from closely related or the same species. This study advances a functional understanding of the consequences and potential selective pressures underpinning phylosymbiosis.
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Martínez-Rodríguez P, Rolán-Alvarez E, Del Mar Pérez-Ruiz M, Arroyo-Yebras F, Carpena-Catoira C, Carvajal-Rodríguez A, Bella JL. Geographic and Temporal Variation of Distinct Intracellular Endosymbiont Strains of Wolbachia sp. in the Grasshopper Chorthippus parallelus: a Frequency-Dependent Mechanism? MICROBIAL ECOLOGY 2019; 77:1036-1047. [PMID: 30762095 DOI: 10.1007/s00248-019-01338-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Abstract
Wolbachia is an intracellular endosymbiont that can produce a range of effects on host fitness, but the temporal dynamics of Wolbachia strains have rarely been experimentally evaluated. We compare interannual strain frequencies along a geographical region for understanding the forces that shape Wolbachia strain frequency in natural populations of its host, Chorthippus parallelus (Orthoptera, Acrididae). General linear models show that strain frequency changes significantly across geographical and temporal scales. Computer simulation allows to reject the compatibility of the observed patterns with either genetic drift or sampling errors. We use consecutive years to estimate total Wolbachia strain fitness. Our estimation of Wolbachia fitness is significant in most cases, within locality and between consecutive years, following a negatively frequency-dependent trend. Wolbachia spp. B and F strains show a temporal pattern of variation that is compatible with a negative frequency-dependent natural selection mechanism. Our results suggest that such a mechanism should be at least considered in future experimental and theoretical research strategies that attempt to understand Wolbachia biodiversity.
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Affiliation(s)
- Paloma Martínez-Rodríguez
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | | | - M Del Mar Pérez-Ruiz
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Francisca Arroyo-Yebras
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | | | | | - José L Bella
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain.
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58
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Genome Sequence of Enterococcus faecalis NVIT04, Isolated from Nasonia vitripennis. Microbiol Resour Announc 2019; 8:MRA01156-18. [PMID: 30714029 PMCID: PMC6357635 DOI: 10.1128/mra.01156-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/04/2019] [Indexed: 11/20/2022] Open
Abstract
Enterococcus faecalis is a Gram-positive, lactic acid-producing coccus which can be found as a member of the gut microbiome in many animal species and is a potential pathogen in humans. Here, we describe the genome sequence of an E. faecalis strain isolated from the gut microbiome of the hymenopteran model Nasonia vitripennis. Enterococcus faecalis is a Gram-positive, lactic acid-producing coccus which can be found as a member of the gut microbiome in many animal species and is a potential pathogen in humans. Here, we describe the genome sequence of an E. faecalis strain isolated from the gut microbiome of the hymenopteran model Nasonia vitripennis.
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Genome Sequence of Providencia rettgeri NVIT03, Isolated from Nasonia vitripennis. Microbiol Resour Announc 2019; 8:MRA01157-18. [PMID: 30687816 PMCID: PMC6346148 DOI: 10.1128/mra.01157-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/11/2018] [Indexed: 11/20/2022] Open
Abstract
Providencia rettgeri is a common insect-associated Gram-negative bacterium. Here, we present the draft genome sequence of P. rettgeri NVIT03, the most common bacterial symbiont of the insect hymenopteran model Nasonia vitripennis. This symbiont is also part of the Sarcophaga bullata pupal microbiome that Nasonia spp. parasitize and that critically influences the development of the wasp.
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Mazel F, Davis KM, Loudon A, Kwong WK, Groussin M, Parfrey LW. Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life? mSystems 2018; 3:e00097-18. [PMID: 30417109 PMCID: PMC6208643 DOI: 10.1128/msystems.00097-18] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 12/13/2022] Open
Abstract
Host-associated microbiota composition can be conserved over evolutionary time scales. Indeed, closely related species often host similar microbiota; i.e., the composition of their microbiota harbors a phylogenetic signal, a pattern sometimes referred to as "phylosymbiosis." Elucidating the origins of this pattern is important to better understand microbiota ecology and evolution. However, this is hampered by our lack of theoretical expectations and a comprehensive overview of phylosymbiosis prevalence in nature. Here, we use simulations to provide a simple expectation for when we should expect this pattern to occur and then review the literature to document the prevalence and strength of phylosymbiosis across the host tree of life. We demonstrate that phylosymbiosis can readily emerge from a simple ecological filtering process, whereby a given host trait (e.g., gut pH) that varies with host phylogeny (i.e., harbors a phylogenetic signal) filters preadapted microbes. We found marked differences between methods used to detect phylosymbiosis, so we proposed a series of practical recommendations based on using multiple best-performing approaches. Importantly, we found that, while the prevalence of phylosymbiosis is mixed in nature, it appears to be stronger for microbiotas living in internal host compartments (e.g., the gut) than those living in external compartments (e.g., the rhizosphere). We show that phylosymbiosis can theoretically emerge without any intimate, long-term coevolutionary mechanisms and that most phylosymbiosis patterns observed in nature are compatible with a simple ecological process. Deviations from baseline ecological expectations might be used to further explore more complex hypotheses, such as codiversification. IMPORTANCE Phylosymbiosis is a pattern defined as the tendency of closely related species to host microbiota whose compositions resemble each other more than host species drawn at random from the same tree. Understanding the mechanisms behind phylosymbiosis is important because it can shed light on rules governing the assembly of host-associated microbiotas and, potentially, their coevolutionary dynamics with hosts. For example, is phylosymbiosis a result of coevolution, or can it be generated by simple ecological filtering processes? Beyond qualitative theoretical models, quantitative theoretical expectations can provide new insights. For example, deviations from a simple baseline of ecological filtering may be used to test more-complex hypotheses (e.g., coevolution). Here, we use simulations to provide evidence that simple host-related ecological filtering can readily generate phylosymbiosis, and we contrast these predictions with real-world data. We find that while phylosymbiosis is widespread in nature, phylosymbiosis patterns are compatible with a simple ecological model in the majority of taxa. Internal compartments of hosts, such as the animal gut, often display stronger phylosymbiosis than expected from a purely ecological filtering process, suggesting that other mechanisms are also involved.
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Affiliation(s)
- Florent Mazel
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Katherine M. Davis
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Loudon
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Waldan K. Kwong
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mathieu Groussin
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Laura Wegener Parfrey
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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Li J, Zhan S, Liu X, Lin Q, Jiang J, Li X. Divergence of Fecal Microbiota and Their Associations With Host Phylogeny in Cervinae. Front Microbiol 2018; 9:1823. [PMID: 30214431 PMCID: PMC6125396 DOI: 10.3389/fmicb.2018.01823] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
Gastrointestinal microbiota may shape the adaptation of their hosts to different habitats and lifestyles, thereby driving their evolutionary diversification. It remains unknown if gastrointestinal microbiota diverge in congruence with the phylogenetic relationships of their hosts. To evaluate the phylosymbiotic relationships, here we analyzed the compositions of fecal microbiota of seven Cervinae species raised in the Chengdu Zoo. All sampled animals were kept in the same environmental condition and fed identical fodder for years. Results showed that Firmicutes and Bacteroidetes were dominant in their fecal microbiota. Even though some bacteria (e.g., Ruminococcaceae) were found to be common in the feces of all investigated species, some genera (e.g., Sharpea and Succinivibrio) were only observed in animals with particular digestive systems. As for the intraspecies variations of microbial communities, only a few operational taxonomic units (OTUs) were shared among replicates of the same host species although they accounted for most of the total abundance. Correlation was observed between the fecal microbiota divergence and host phylogeny, but they were not congruent completely. This may shed new light on the coevolution of host species and their microbiota.
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Affiliation(s)
- Jiaying Li
- Key Laboratory of Environmental and Applied Microbiology - Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China
| | | | - Xuanzhen Liu
- Chengdu Zoo, Chengdu Institute of Wildlife, Chengdu, China
| | - Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology - Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jianping Jiang
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangzhen Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
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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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Emmett BD, Youngblut ND, Buckley DH, Drinkwater LE. Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field. Front Microbiol 2017; 8:2414. [PMID: 29321763 PMCID: PMC5732146 DOI: 10.3389/fmicb.2017.02414] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/22/2017] [Indexed: 11/15/2022] Open
Abstract
Rhizosphere microbial communities are critically important for soil nitrogen cycling and plant productivity. There is evidence that plant species and genotypes select distinct rhizosphere communities, however, knowledge of the drivers and extent of this variation remains limited. We grew 11 annual species and 11 maize (Zea mays subsp. mays) inbred lines in a common garden experiment to assess the influence of host phylogeny, growth, and nitrogen metabolism on rhizosphere communities. Growth characteristics, bacterial community composition and potential activity of extracellular enzymes were assayed at time of flowering, when plant nitrogen demand is maximal. Bacterial community composition varied significantly between different plant species and genotypes. Rhizosphere beta-diversity was positively correlated with phylogenetic distance between plant species, but not genetic distance within a plant species. In particular, life history traits associated with plant resource acquisition (e.g., longer lifespan, high nitrogen use efficiency, and larger seed size) were correlated with variation in bacterial community composition and enzyme activity. These results indicate that plant evolutionary history and life history strategy influence rhizosphere bacterial community composition and activity. Thus, incorporating phylogenetic or functional diversity into crop rotations may be a tool to manipulate plant-microbe interactions in agricultural systems.
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Affiliation(s)
- Bryan D. Emmett
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Nicholas D. Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Daniel H. Buckley
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Laurie E. Drinkwater
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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64
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Näpflin K, Schmid-Hempel P. Host effects on microbiota community assembly. J Anim Ecol 2017; 87:331-340. [DOI: 10.1111/1365-2656.12768] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 08/31/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Kathrin Näpflin
- Institute of Integrative Biology (IBZ); ETH Zurich; Zurich Switzerland
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Captive bottlenose dolphins and killer whales harbor a species-specific skin microbiota that varies among individuals. Sci Rep 2017; 7:15269. [PMID: 29127421 PMCID: PMC5681658 DOI: 10.1038/s41598-017-15220-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/23/2017] [Indexed: 02/06/2023] Open
Abstract
Marine animals surfaces host diverse microbial communities, which play major roles for host’s health. Most inventories of marine animal surface microbiota have focused on corals and fishes, while cetaceans remain overlooked. The few studies focused on wild cetaceans, making difficult to distinguish intrinsic inter- and/or intraspecific variability in skin microbiota from environmental effects. We used high-throughput sequencing to assess the skin microbiota from 4 body zones of 8 bottlenose dolphins (Tursiops truncatus) and killer whales (Orcinus orca), housed in captivity (Marineland park, France). Overall, cetacean skin microbiota is more diverse than planktonic communities and is dominated by different phylogenetic lineages and functions. In addition, the two cetacean species host different skin microbiotas. Within each species, variability was higher between individuals than between body parts, suggesting a high individuality of cetacean skin microbiota. Overall, the skin microbiota of the assessed cetaceans related more to the humpback whale and fishes’ than to microbiotas of terrestrial mammals.
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66
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Zhukova M, Sapountzis P, Schiøtt M, Boomsma JJ. Diversity and Transmission of Gut Bacteria in Atta and Acromyrmex Leaf-Cutting Ants during Development. Front Microbiol 2017; 8:1942. [PMID: 29067008 PMCID: PMC5641371 DOI: 10.3389/fmicb.2017.01942] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/21/2017] [Indexed: 11/28/2022] Open
Abstract
The social Hymenoptera have distinct larval and adult stages separated by metamorphosis, which implies striking remodeling of external and internal body structures during the pupal stage. This imposes challenges to gut symbionts as existing cultures are lost and may or may not need to be replaced. To elucidate the extent to which metamorphosis interrupts associations between bacteria and hosts, we analyzed changes in gut microbiota during development and traced the transmission routes of dominant symbionts from the egg to adult stage in the leaf-cutting ants Acromyrmex echinatior and Atta cephalotes, which are both important functional herbivores in the New World tropics. Bacterial density remained similar across the developmental stages of Acromyrmex, but Atta brood had very low bacterial prevalences suggesting that bacterial gut symbionts are not actively maintained. We found that Wolbachia was the absolute dominant bacterial species across developmental stages in Acromyrmex and we confirmed that Atta lacks Wolbachia also in the immature stages, and had mostly Mollicutes bacteria in the adult worker guts. Wolbachia in Acromyrmex appeared to be transovarially transmitted similar to transmission in solitary insects. In contrast, Mollicutes were socially transmitted from old workers to newly emerged callows. We found that larval and pupal guts of both ant species contained Pseudomonas and Enterobacter bacteria that are also found in fungus gardens, but hardly or not in adult workers, suggesting they are beneficial only for larval growth and development. Our results reveal that transmission pathways for bacterial symbionts may be very different both between developmental stages and between sister genera and that identifying the mechanisms of bacterial acquisition and loss will be important to clarify their putative mutualistic functions.
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Affiliation(s)
- Mariya Zhukova
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Panagiotis Sapountzis
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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67
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Prado-Irwin SR, Bird AK, Zink AG, Vredenburg VT. Intraspecific Variation in the Skin-Associated Microbiome of a Terrestrial Salamander. MICROBIAL ECOLOGY 2017; 74:745-756. [PMID: 28466089 PMCID: PMC5909955 DOI: 10.1007/s00248-017-0986-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 04/18/2017] [Indexed: 05/28/2023]
Abstract
Resident microbial communities living on amphibian skin can have significant effects on host health, yet the basic ecology of the host-microbiome relationship of many amphibian taxa is poorly understood. We characterized intraspecific variation in the skin microbiome of the salamander Ensatina eschscholtzii xanthoptica, a subspecies composed of four genetically distinct populations distributed throughout the San Francisco Bay Area and the Sierra Nevada mountains in California, USA. We found that salamanders from four geographically and genetically isolated populations harbor similar skin microbial communities, which are dominated by a common core set of bacterial taxa. Additionally, within a population, the skin microbiome does not appear to differ significantly between salamanders of different ages or sexes. In all cases, the salamander skin microbiomes were significantly different from those of the surrounding terrestrial environment. These results suggest that the relationship between E. e. xanthoptica salamanders and their resident skin microbiomes is conserved, possibly indicating a stable mutualism between the host and microbiome.
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Affiliation(s)
- Sofia R Prado-Irwin
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA.
| | - Alicia K Bird
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Andrew G Zink
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA, 94132, USA
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA, 94132, USA
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68
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Bowen JL, Kearns PJ, Byrnes JEK, Wigginton S, Allen WJ, Greenwood M, Tran K, Yu J, Cronin JT, Meyerson LA. Lineage overwhelms environmental conditions in determining rhizosphere bacterial community structure in a cosmopolitan invasive plant. Nat Commun 2017; 8:433. [PMID: 28874666 PMCID: PMC5585233 DOI: 10.1038/s41467-017-00626-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/13/2017] [Indexed: 02/01/2023] Open
Abstract
Plant-microbe interactions play crucial roles in species invasions but are rarely investigated at the intraspecific level. Here, we study these interactions in three lineages of a globally distributed plant, Phragmites australis. We use field surveys and a common garden experiment to analyze bacterial communities in the rhizosphere of P. australis stands from native, introduced, and Gulf lineages to determine lineage-specific controls on rhizosphere bacteria. We show that within-lineage bacterial communities are similar, but are distinct among lineages, which is consistent with our results in a complementary common garden experiment. Introduced P. australis rhizosphere bacterial communities have lower abundances of pathways involved in antimicrobial biosynthesis and degradation, suggesting a lower exposure to enemy attack than native and Gulf lineages. However, lineage and not rhizosphere bacterial communities dictate individual plant growth in the common garden experiment. We conclude that lineage is crucial for determination of both rhizosphere bacterial communities and plant fitness.Environmental factors often outweigh host heritable factors in structuring host-associated microbiomes. Here, Bowen et al. show that host lineage is crucial for determination of rhizosphere bacterial communities in Phragmites australis, a globally distributed invasive plant.
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Affiliation(s)
- Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 430 Nahant Road, Nahant, MA, 01908, USA.
| | - Patrick J Kearns
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 430 Nahant Road, Nahant, MA, 01908, USA
| | - Jarrett E K Byrnes
- University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA, 02125, USA
| | - Sara Wigginton
- Department of Natural Resources Science, University of Rhode Island, Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Warwick J Allen
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
- The Bio-Protection Research Centre, Lincoln University, PO Box 84, Lincoln, 7647, New Zealand
| | - Michael Greenwood
- University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA, 02125, USA
| | - Khang Tran
- University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA, 02125, USA
| | - Jennifer Yu
- University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA, 02125, USA
| | - James T Cronin
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Laura A Meyerson
- Department of Natural Resources Science, University of Rhode Island, Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
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69
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Abstract
Many aspects of an individual's biology derive from its interaction with symbiotic microbes, which further define many aspects of the ecology and evolution of the host species. The centrality of microbes in the function of individual organisms has given rise to the concept of the holobiont—that an individual's biology is best understood as a composite of the ‘host organism’ and symbionts within. This concept has been further elaborated to posit the holobiont as a unit of selection. In this review, I critically examine whether it is useful to consider holobionts as a unit of selection. I argue that microbial heredity—the direct passage of microbes from parent to offspring—is a key factor determining the degree to which the holobiont can usefully be considered a level of selection. Where direct vertical transmission (VT) is common, microbes form part of extended genomes whose dynamics can be modelled with simple population genetics, but that nevertheless have subtle quantitative distinctions from the classic mutation/selection model for nuclear genes. Without direct VT, the correlation between microbial fitness and host individual fitness erodes, and microbe fitness becomes associated with host survival only (rather than reproduction). Furthermore, turnover of microbes within a host may lessen associations between microbial fitness with host survival, and in polymicrobial communities, microbial fitness may derive largely from the ability to outcompete other microbes, to avoid host immune clearance and to minimize mortality through phage infection. These competing selection pressures make holobiont fitness a very minor consideration in determining symbiont evolution. Nevertheless, the importance of non-heritable microbes in organismal function is undoubted—and as such the evolutionary and ecological processes giving rise to variation and evolution of the microbes within and between host individuals represent a key research area in biology.
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Affiliation(s)
- Gregory D D Hurst
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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70
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Kohl KD, Varner J, Wilkening JL, Dearing MD. Gut microbial communities of American pikas (
O
chotona princeps
): Evidence for phylosymbiosis and adaptations to novel diets. J Anim Ecol 2017; 87:323-330. [DOI: 10.1111/1365-2656.12692] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 03/21/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Kevin D. Kohl
- Department of Biological Sciences Vanderbilt University Nashville TN USA
- Department of Biology University of Utah Salt Lake City UT USA
| | - Johanna Varner
- Department of Biology Colorado Mesa University Grand Junction CO USA
| | - Jennifer L. Wilkening
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
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71
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Groussin M, Mazel F, Sanders JG, Smillie CS, Lavergne S, Thuiller W, Alm EJ. Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nat Commun 2017; 8:14319. [PMID: 28230052 PMCID: PMC5331214 DOI: 10.1038/ncomms14319] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/08/2016] [Indexed: 12/28/2022] Open
Abstract
Whether mammal–microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny and major dietary shifts have affected the distribution of different gut bacterial lineages and did so on vastly different bacterial phylogenetic resolutions. Diet mostly influences the acquisition of ancient and large microbial lineages. Conversely, correlation with host phylogeny is mostly seen among more recently diverged bacterial lineages, consistent with processes operating at similar timescales to host evolution. Considering microbiomes at appropriate phylogenetic scales allows us to model their evolution along the mammalian tree and to infer ancient diets from the predicted microbiomes of mammalian ancestors. Phylogenetic analyses support co-speciation as having a significant role in the evolution of mammalian gut microbiome compositions. Highly co-speciating bacterial genera are also associated with immune diseases in humans, laying a path for future studies that probe these co-speciating bacteria for signs of co-evolution. Both host diet and phylogeny have been argued to shape mammalian microbiome communities. Here, the authors show that diet predicts the presence of ancient bacterial lineages in the microbiome, but that co-speciation between more recent bacterial lineages and their hosts may drive associations between microbiome composition and phylogeny.
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Affiliation(s)
- Mathieu Groussin
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Florent Mazel
- Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041, Grenoble Cedex 9, France
| | - Jon G Sanders
- Organismic and Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, Massachusetts 02138, USA
| | - Chris S Smillie
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,The Broad Institute of MIT and Harvard, 415 Main Street Cambridge, Massachusetts 02142, USA
| | - Sébastien Lavergne
- Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041, Grenoble Cedex 9, France
| | - Wilfried Thuiller
- Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041, Grenoble Cedex 9, France
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,The Broad Institute of MIT and Harvard, 415 Main Street Cambridge, Massachusetts 02142, USA
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72
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Nedoluzhko AV, Sharko FS, Tsygankova SV, Boulygina ES, Sokolov AS, Rastorguev SM, Kadnikov VV, Mardanov AV, Ravin NV, Mazur AM, Polilov AA, Gruzdeva NM, Prokhortchouk EB, Skryabin KG. Metagenomic analysis of microbial community of a parasitoid wasp Megaphragma amalphitanum. GENOMICS DATA 2016; 11:87-88. [PMID: 28066711 PMCID: PMC5200880 DOI: 10.1016/j.gdata.2016.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 12/08/2016] [Accepted: 12/11/2016] [Indexed: 11/29/2022]
Abstract
The vast majority of multicellular organisms coexist with bacterial symbionts that may play various roles during their life cycle. Parasitoid wasp Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae) belongs to the smallest known insects whose size is comparable with some bacteria. Using 16S rRNA gene sequencing and Whole Genome Sequencing (WGS), we described microbiota diversity for this arthropod and its potential impact on their lifecycle. Metagenomic sequences were deposited to SRA database which is available at NCBI with accession number SRX2363723 and SRX2363724. We found that small body size and limited lifespan do not lead to a significant reduction of bacterial symbionts diversity. At the same time, we show here a specific feature of microbiota composition in M. amalphitanum – the absence of the Rickettsiaceae family representatives that are known to cause sex-ratio distortion in arthropods and well represented in other populations of parasitoid wasps.
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Affiliation(s)
- A V Nedoluzhko
- National Research Centre "Kurchatov Institute", Russian Federation
| | - F S Sharko
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Russian Federation
| | - S V Tsygankova
- National Research Centre "Kurchatov Institute", Russian Federation
| | - E S Boulygina
- National Research Centre "Kurchatov Institute", Russian Federation
| | - A S Sokolov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Russian Federation
| | - S M Rastorguev
- National Research Centre "Kurchatov Institute", Russian Federation
| | - V V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Russian Federation
| | - A V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Russian Federation
| | - N V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Russian Federation; Lomonosov Moscow State University, Faculty of Biology, Russian Federation
| | - A M Mazur
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Russian Federation
| | - A A Polilov
- Lomonosov Moscow State University, Faculty of Biology, Russian Federation
| | - N M Gruzdeva
- National Research Centre "Kurchatov Institute", Russian Federation
| | - E B Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Russian Federation; Lomonosov Moscow State University, Faculty of Biology, Russian Federation
| | - K G Skryabin
- National Research Centre "Kurchatov Institute", Russian Federation; Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Russian Federation; Lomonosov Moscow State University, Faculty of Biology, Russian Federation
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73
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Brooks AW, Kohl KD, Brucker RM, van Opstal EJ, Bordenstein SR. Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History. PLoS Biol 2016; 14:e2000225. [PMID: 27861590 PMCID: PMC5115861 DOI: 10.1371/journal.pbio.2000225] [Citation(s) in RCA: 318] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/20/2016] [Indexed: 02/07/2023] Open
Abstract
Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern, whereby the ecological relatedness of host-associated microbial communities parallels the phylogeny of related host species. Here, we test the prevalence of phylosymbiosis and its functional significance under highly controlled conditions by characterizing the microbiota of 24 animal species from four different groups (Peromyscus deer mice, Drosophila flies, mosquitoes, and Nasonia wasps), and we reevaluate the phylosymbiotic relationships of seven species of wild hominids. We demonstrate three key findings. First, intraspecific microbiota variation is consistently less than interspecific microbiota variation, and microbiota-based models predict host species origin with high accuracy across the dataset. Interestingly, the age of host clade divergence positively associates with the degree of microbial community distinguishability between species within the host clades, spanning recent host speciation events (~1 million y ago) to more distantly related host genera (~108 million y ago). Second, topological congruence analyses of each group's complete phylogeny and microbiota dendrogram reveal significant degrees of phylosymbiosis, irrespective of host clade age or taxonomy. Third, consistent with selection on host–microbiota interactions driving phylosymbiosis, there are survival and performance reductions when interspecific microbiota transplants are conducted between closely related and divergent host species pairs. Overall, these findings indicate that the composition and functional effects of an animal's microbial community can be closely allied with host evolution, even across wide-ranging timescales and diverse animal systems reared under controlled conditions. Studies on the assembly and function of host-microbiota symbioses are inherently complicated by the diverse effects of diet, age, sex, host genetics, and endosymbionts. Central to unraveling one effect from the other is an experimental framework that reduces confounders. Using common rearing conditions across four animal groups (deer mice, flies, mosquitoes, and wasps) that span recent host speciation events to more distantly related host genera, this study tests whether microbial community assembly is generally random with respect to host relatedness or "phylosymbiotic," in which the phylogeny of the host group is congruent with ecological relationships of their microbial communities. Across all four animal groups and one external dataset of great apes, we apply several statistics for analyzing congruencies and demonstrate phylosymbiosis to varying degrees in each group. Moreover, consistent with selection on host–microbiota interactions driving phylosymbiosis, transplanting interspecific microbial communities in mice significantly decreased their ability to digest food. Similarly, wasps that received transplants of microbial communities from different wasp species had lower survival than those given their own microbiota. Overall, this experimental and statistical framework shows how microbial community assembly and functionality across related species can be linked to animal evolution, health, and survival.
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Affiliation(s)
- Andrew W. Brooks
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kevin D. Kohl
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Robert M. Brucker
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- The Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
| | - Edward J. van Opstal
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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74
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Berg M, Zhou XY, Shapira M. Host-Specific Functional Significance of Caenorhabditis Gut Commensals. Front Microbiol 2016; 7:1622. [PMID: 27799924 PMCID: PMC5066524 DOI: 10.3389/fmicb.2016.01622] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/29/2016] [Indexed: 12/27/2022] Open
Abstract
The gut microbiota is an important contributor to host health and fitness. Given its importance, microbiota composition should not be left to chance. However, what determines this composition is far from clear, with results supporting contributions of both environmental factors and host genetics. To gauge the relative contributions of host genetics and environment, specifically the microbial diversity, we characterized the gut microbiotas of Caenorhabditis species spanning 200-300 million years of evolution, and raised on different composted soil environments. Comparisons were based on 16S rDNA deep sequencing data, as well as on functional evaluation of gut isolates. Worm microbiotas were distinct from those in their respective soil environment, and included bacteria previously identified as part of the C. elegans core microbiota. Microbiotas differed between experiments initiated with different soil communities, but within each experiment, worm microbiotas clustered according to host identity, demonstrating a dominant contribution of environmental diversity, but also a significant contribution of host genetics. The dominance of environmental contributions hindered identification of host-associated microbial taxa from 16S data. Characterization of gut isolates from C. elegans and C. briggsae, focusing on the core family Enterobacteriaceae, were also unable to expose phylogenetic distinctions between microbiotas of the two species. However, functional evaluation of the isolates revealed host-specific contributions, wherein gut commensals protected their own host from infection, but not a non-host. Identification of commensal host-specificity at the functional level, otherwise overlooked in standard sequence-based analyses, suggests that the contribution of host genetics to shaping of gut microbiotas may be greater than previously realized.
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Affiliation(s)
- Maureen Berg
- Department of Integrative Biology, University of California, Berkeley Berkeley, CA, USA
| | - Xiao Ying Zhou
- Department of Integrative Biology, University of California, Berkeley Berkeley, CA, USA
| | - Michael Shapira
- Department of Integrative Biology, University of California, BerkeleyBerkeley, CA, USA; Graduate Group in Microbiology, University of California, BerkeleyBerkeley, CA, USA
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75
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Dittmer J, van Opstal EJ, Shropshire JD, Bordenstein SR, Hurst GDD, Brucker RM. Disentangling a Holobiont - Recent Advances and Perspectives in Nasonia Wasps. Front Microbiol 2016; 7:1478. [PMID: 27721807 PMCID: PMC5033955 DOI: 10.3389/fmicb.2016.01478] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/05/2016] [Indexed: 12/18/2022] Open
Abstract
The parasitoid wasp genus Nasonia (Hymenoptera: Chalcidoidea) is a well-established model organism for insect development, evolutionary genetics, speciation, and symbiosis. The host-microbiota assemblage which constitutes the Nasonia holobiont (a host together with all of its associated microbes) consists of viruses, two heritable bacterial symbionts and a bacterial community dominated in abundance by a few taxa in the gut. In the wild, all four Nasonia species are systematically infected with the obligate intracellular bacterium Wolbachia and can additionally be co-infected with Arsenophonus nasoniae. These two reproductive parasites have different transmission modes and host manipulations (cytoplasmic incompatibility vs. male-killing, respectively). Pioneering studies on Wolbachia in Nasonia demonstrated that closely related Nasonia species harbor multiple and mutually incompatible Wolbachia strains, resulting in strong symbiont-mediated reproductive barriers that evolved early in the speciation process. Moreover, research on host-symbiont interactions and speciation has recently broadened from its historical focus on heritable symbionts to the entire microbial community. In this context, each Nasonia species hosts a distinguishable community of gut bacteria that experiences a temporal succession during host development and members of this bacterial community cause strong hybrid lethality during larval development. In this review, we present the Nasonia species complex as a model system to experimentally investigate questions regarding: (i) the impact of different microbes, including (but not limited to) heritable endosymbionts, on the extended phenotype of the holobiont, (ii) the establishment and regulation of a species-specific microbiota, (iii) the role of the microbiota in speciation, and (iv) the resilience and adaptability of the microbiota in wild populations subjected to different environmental pressures. We discuss the potential for easy microbiota manipulations in Nasonia as a promising experimental approach to address these fundamental aspects.
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Affiliation(s)
- Jessica Dittmer
- Rowland Institute at Harvard, Harvard University, Cambridge MA, USA
| | | | - J Dylan Shropshire
- Department of Biological Sciences, Vanderbilt University, Nashville TN, USA
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, NashvilleTN, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University, NashvilleTN, USA
| | - Gregory D D Hurst
- Institute of Integrative Biology, University of Liverpool Liverpool, UK
| | - Robert M Brucker
- Rowland Institute at Harvard, Harvard University, Cambridge MA, USA
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76
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Bili M, Cortesero AM, Mougel C, Gauthier JP, Ermel G, Simon JC, Outreman Y, Terrat S, Mahéo F, Poinsot D. Bacterial Community Diversity Harboured by Interacting Species. PLoS One 2016; 11:e0155392. [PMID: 27258532 PMCID: PMC4892616 DOI: 10.1371/journal.pone.0155392] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/06/2016] [Indexed: 02/07/2023] Open
Abstract
All animals are infected by microbial partners that can be passengers or residents and influence many biological traits of their hosts. Even if important factors that structure the composition and abundance of microbial communities within and among host individuals have been recently described, such as diet, developmental stage or phylogeny, few studies have conducted cross-taxonomic comparisons, especially on host species related by trophic relationships. Here, we describe and compare the microbial communities associated with the cabbage root fly Delia radicum and its three major parasitoids: the two staphylinid beetles Aleochara bilineata and A. bipustulata and the hymenopteran parasitoid Trybliographa rapae. For each species, two populations from Western France were sampled and microbial communities were described through culture independent methods (454 pyrosequencing). Each sample harbored at least 59 to 261 different bacterial phylotypes but was strongly dominated by one or two. Microbial communities differed markedly in terms of composition and abundance, being mainly influenced by phylogenetic proximity but also geography to a minor extent. Surprisingly, despite their strong trophic interaction, parasitoids shared a very low proportion of microbial partners with their insect host. Three vertically transmitted symbionts from the genus Wolbachia, Rickettsia, and Spiroplasma were found in this study. Among them, Wolbachia and Spiroplasma were found in both the cabbage fly and at least one of its parasitoids, which could result from horizontal transfers through trophic interactions. Phylogenetic analysis showed that this hypothesis may explain some but not all cases. More work is needed to understand the dynamics of symbiotic associations within trophic network and the effect of these bacterial communities on the fitness of their hosts.
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Affiliation(s)
- Mikaël Bili
- Université Rennes 1, UMR1349 IGEPP, F-35000, Rennes, France
- Université Européenne de Bretagne, Rennes, France
| | - Anne Marie Cortesero
- Université Rennes 1, UMR1349 IGEPP, F-35000, Rennes, France
- Université Européenne de Bretagne, Rennes, France
| | | | | | - Gwennola Ermel
- UMR CNRS 6026 Interactions Cellulaires et Moléculaires, Université de Rennes, Rennes, France
| | | | | | | | | | - Denis Poinsot
- Université Rennes 1, UMR1349 IGEPP, F-35000, Rennes, France
- Université Européenne de Bretagne, Rennes, France
- * E-mail:
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77
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Shapira M. Gut Microbiotas and Host Evolution: Scaling Up Symbiosis. Trends Ecol Evol 2016; 31:539-549. [PMID: 27039196 DOI: 10.1016/j.tree.2016.03.006] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/18/2016] [Accepted: 03/05/2016] [Indexed: 02/07/2023]
Abstract
Our understanding of species evolution is undergoing restructuring. It is well accepted that host-symbiont coevolution is responsible for fundamental aspects of biology. However, the emerging importance of plant- and animal-associated microbiotas to their hosts suggests a scale of coevolutionary interactions many-fold greater than previously considered. This review builds on current understanding of symbionts and their contributions to host evolution to evaluate recent data demonstrating similar contributions of gut microbiotas. It further considers a multilayered model for microbiota to account for emerging themes in host-microbiota interactions. Drawing on the structure of bacterial genomes, this model distinguishes between a host-adapted core microbiota, and a flexible, environmentally modulated microbial pool, differing in constraints on their maintenance and in their contributions to host adaptation.
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Affiliation(s)
- Michael Shapira
- University of California, Berkeley, department of Integrative Biology and Graduate Group in Microbiology. Valley Life Sciences Building, room 5155, Berkeley, CA 94720, USA.
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78
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Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes. mSystems 2016; 1:mSystems00028-16. [PMID: 27822520 PMCID: PMC5069740 DOI: 10.1128/msystems.00028-16] [Citation(s) in RCA: 280] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization—what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization—what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.
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79
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Rebollar EA, Antwis RE, Becker MH, Belden LK, Bletz MC, Brucker RM, Harrison XA, Hughey MC, Kueneman JG, Loudon AH, McKenzie V, Medina D, Minbiole KPC, Rollins-Smith LA, Walke JB, Weiss S, Woodhams DC, Harris RN. Using "Omics" and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases. Front Microbiol 2016; 7:68. [PMID: 26870025 PMCID: PMC4735675 DOI: 10.3389/fmicb.2016.00068] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 01/14/2016] [Indexed: 12/20/2022] Open
Abstract
Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called "omics," are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools and in silico models that link bacterial community structure with bacterial defensive function can allow the identification of species involved in pathogen inhibition. We recommend using 16S rRNA gene amplicon sequencing and methods such as indicator species analysis, the Kolmogorov-Smirnov Measure, and co-occurrence networks to identify bacteria that are associated with pathogen resistance in field surveys and experimental trials. In addition to 16S amplicon sequencing, we recommend approaches that give insight into symbiont function such as shotgun metagenomics, metatranscriptomics, or metabolomics to maximize the probability of finding effective probiotic candidates, which can then be isolated in culture and tested in persistence and clinical trials. An effective mitigation strategy to ameliorate chytridiomycosis and other emerging infectious diseases is necessary; the advancement of omic methods and the integration of multiple omic data provide a promising avenue toward conservation of imperiled species.
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Affiliation(s)
- Eria A. Rebollar
- Department of Biology, James Madison UniversityHarrisonburg, VA, USA
| | - Rachael E. Antwis
- Unit for Environmental Sciences and Management, North-West UniversityPotchefstroom, South Africa
- Institute of Zoology, Zoological Society of LondonLondon, UK
- School of Environment and Life Sciences, University of SalfordSalford, UK
| | - Matthew H. Becker
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological ParkWashington, DC, USA
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Molly C. Bletz
- Zoological Institute, Technische Universität BraunschweigBraunschweig, Germany
| | | | | | - Myra C. Hughey
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Jordan G. Kueneman
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Andrew H. Loudon
- Department of Zoology, Biodiversity Research Centre, University of British ColumbiaVancouver, BC, Canada
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | | | - Louise A. Rollins-Smith
- Department of Pathology, Microbiology and Immunology and Department of Pediatrics, Vanderbilt University School of Medicine, Department of Biological Sciences, Vanderbilt UniversityNashville, TN, USA
| | - Jenifer B. Walke
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Sophie Weiss
- Department of Chemical and Biological Engineering, University of Colorado at BoulderBoulder, CO, USA
| | | | - Reid N. Harris
- Department of Biology, James Madison UniversityHarrisonburg, VA, USA
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Abstract
With the increasing appreciation for the crucial roles that microbial symbionts play in the development and fitness of plant and animal hosts, there has been a recent push to interpret evolution through the lens of the "hologenome"--the collective genomic content of a host and its microbiome. But how symbionts evolve and, particularly, whether they undergo natural selection to benefit hosts are complex issues that are associated with several misconceptions about evolutionary processes in host-associated microbial communities. Microorganisms can have intimate, ancient, and/or mutualistic associations with hosts without having undergone natural selection to benefit hosts. Likewise, observing host-specific microbial community composition or greater community similarity among more closely related hosts does not imply that symbionts have coevolved with hosts, let alone that they have evolved for the benefit of the host. Although selection at the level of the symbiotic community, or hologenome, occurs in some cases, it should not be accepted as the null hypothesis for explaining features of host-symbiont associations.
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81
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Johnston PR, Rolff J. Host and Symbiont Jointly Control Gut Microbiota during Complete Metamorphosis. PLoS Pathog 2015; 11:e1005246. [PMID: 26544881 PMCID: PMC4636265 DOI: 10.1371/journal.ppat.1005246] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 10/02/2015] [Indexed: 01/08/2023] Open
Abstract
Holometabolous insects undergo a radical anatomical re-organisation during metamorphosis. This poses a developmental challenge: the host must replace the larval gut but at the same time retain symbiotic gut microbes and avoid infection by opportunistic pathogens. By manipulating host immunity and bacterial competitive ability, we study how the host Galleria mellonella and the symbiotic bacterium Enterococcus mundtii interact to manage the composition of the microbiota during metamorphosis. Disenabling one or both symbiotic partners alters the composition of the gut microbiota, which incurs fitness costs: adult hosts with a gut microbiota dominated by pathogens such as Serratia and Staphylococcus die early. Our results reveal an interaction that guarantees the safe passage of the symbiont through metamorphosis and benefits the resulting adult host. Host-symbiont "conspiracies" as described here are almost certainly widespread in holometobolous insects including many disease vectors.
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Affiliation(s)
| | - Jens Rolff
- Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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82
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Ushida K, Tsuchida S, Ogura Y, Toyoda A, Maruyama F. Domestication and cereal feeding developed domestic pig-type intestinal microbiota in animals of suidae. Anim Sci J 2015; 87:835-41. [DOI: 10.1111/asj.12492] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 06/05/2015] [Accepted: 06/18/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Kazunari Ushida
- Graduate School of Life and Environmental Sciences; Kyoto Prefectural University, Shimogamo
| | - Sayaka Tsuchida
- Graduate School of Life and Environmental Sciences; Kyoto Prefectural University, Shimogamo
| | - Yoshitoshi Ogura
- Division of Bioenvironmental Science, Frontier Science Research Center; University of Miyazaki; Miyazaki
| | - Atsushi Toyoda
- Comparative Genomics Laboratory; National Institute of Genetics; Mishima
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine; Kyoto University; Kyoto Japan
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83
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Interactions between Cooccurring Lactic Acid Bacteria in Honey Bee Hives. Appl Environ Microbiol 2015; 81:7261-70. [PMID: 26253685 DOI: 10.1128/aem.01259-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/01/2015] [Indexed: 11/20/2022] Open
Abstract
In contrast to the honey bee gut, which is colonized by a few characteristic bacterial clades, the hive of the honey bee is home to a diverse array of microbes, including many lactic acid bacteria (LAB). In this study, we used culture, combined with sequencing, to sample the LAB communities found across hive environments. Specifically, we sought to use network analysis to identify microbial hubs sharing nearly identical operational taxonomic units, evidence which may indicate cooccurrence of bacteria between environments. In the process, we identified interactions between noncore bacterial members (Fructobacillus and Lactobacillaceae) and honey bee-specific "core" members. Both Fructobacillus and Lactobacillaceae colonize brood cells, bee bread, and nectar and may serve the role of pioneering species, establishing an environment conducive to the inoculation by honey bee core bacteria. Coculture assays showed that these noncore bacterial members promote the growth of honey bee-specific bacterial species. Specifically, Fructobacillus by-products in spent medium supported the growth of the Firm-5 honey bee-specific clade in vitro. Metabolic characterization of Fructobacillus using carbohydrate utilization assays revealed that this strain is capable of utilizing the simple sugars fructose and glucose, as well as the complex plant carbohydrate lignin. We tested Fructobacillus for antibiotic sensitivity and found that this bacterium, which may be important for establishment of the microbiome, is sensitive to the commonly used antibiotic tetracycline. Our results point to the possible significance of "noncore" and environmental microbial community members in the modulation of honey bee microbiome dynamics and suggest that tetracycline use by beekeepers should be limited.
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84
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Abstract
Groundbreaking research on the universality and diversity of microorganisms is now challenging the life sciences to upgrade fundamental theories that once seemed untouchable. To fully appreciate the change that the field is now undergoing, one has to place the epochs and foundational principles of Darwin, Mendel, and the modern synthesis in light of the current advances that are enabling a new vision for the central importance of microbiology. Animals and plants are no longer heralded as autonomous entities but rather as biomolecular networks composed of the host plus its associated microbes, i.e., "holobionts." As such, their collective genomes forge a "hologenome," and models of animal and plant biology that do not account for these intergenomic associations are incomplete. Here, we integrate these concepts into historical and contemporary visions of biology and summarize a predictive and refutable framework for their evaluation. Specifically, we present ten principles that clarify and append what these concepts are and are not, explain how they both support and extend existing theory in the life sciences, and discuss their potential ramifications for the multifaceted approaches of zoology and botany. We anticipate that the conceptual and evidence-based foundation provided in this essay will serve as a roadmap for hypothesis-driven, experimentally validated research on holobionts and their hologenomes, thereby catalyzing the continued fusion of biology's subdisciplines. At a time when symbiotic microbes are recognized as fundamental to all aspects of animal and plant biology, the holobiont and hologenome concepts afford a holistic view of biological complexity that is consistent with the generally reductionist approaches of biology.
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Affiliation(s)
- Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kevin R. Theis
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
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85
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Rynkiewicz EC, Hemmerich C, Rusch DB, Fuqua C, Clay K. Concordance of bacterial communities of two tick species and blood of their shared rodent host. Mol Ecol 2015; 24:2566-79. [DOI: 10.1111/mec.13187] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/10/2015] [Accepted: 03/20/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Evelyn C. Rynkiewicz
- Institute of Evolutionary Biology & Centre for Immunity; Infection and Evolution; University of Edinburgh; Edinburgh EH9 3JT UK
- Department of Biology; Indiana University; 1001 E 3rd St Bloomington IN 47405 USA
| | - Chris Hemmerich
- Center for Genomics and Bioinformatics; Indiana University; 1001 E 3rd St Bloomington IN 47405 USA
| | - Douglas B. Rusch
- Center for Genomics and Bioinformatics; Indiana University; 1001 E 3rd St Bloomington IN 47405 USA
| | - Clay Fuqua
- Department of Biology; Indiana University; 1001 E 3rd St Bloomington IN 47405 USA
| | - Keith Clay
- Department of Biology; Indiana University; 1001 E 3rd St Bloomington IN 47405 USA
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86
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Guo J, Wu J, Chen Y, Evans JD, Dai R, Luo W, Li J. Characterization of gut bacteria at different developmental stages of Asian honey bees, Apis cerana. J Invertebr Pathol 2015; 127:110-4. [PMID: 25805518 DOI: 10.1016/j.jip.2015.03.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 03/15/2015] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
Abstract
Previous surveys have shown that adult workers of the Asian honey bee Apis cerana harbor four major gut microbes (Bifidobacterium, Snodgrassella alvi, Gilliamella apicola, and Lactobacillus). Using quantitative PCR we characterized gut bacterial communities across the life cycle of A. cerana from larvae to workers. Our results indicate that the presence and quantity of these four bacteria were low on day 1, increased rapidly after day 5, and then peaked during days 10-20. They stabilized from days 20-25 or days 25-30, then dropped to a low level at day 30. In addition, the larvae infected by Sacbrood virus or European foulbrood had significantly lower copies of 16S rRNA genes than healthy individuals.
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Affiliation(s)
- Jun Guo
- Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing 100093, China; Institute of Economic Animals, Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Jie Wu
- Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing 100093, China.
| | - Yanping Chen
- USDA-ARS, Bee Research Laboratory, Beltsville, MD 20705, USA
| | - Jay D Evans
- USDA-ARS, Bee Research Laboratory, Beltsville, MD 20705, USA
| | - Rongguo Dai
- Institute of Economic Animals, Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Wenhua Luo
- Institute of Economic Animals, Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Jilian Li
- Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing 100093, China.
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87
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Abstract
All insects are colonized by microorganisms on the insect exoskeleton, in the gut and hemocoel, and within insect cells. The insect microbiota is generally different from microorganisms in the external environment, including ingested food. Specifically, certain microbial taxa are favored by the conditions and resources in the insect habitat, by their tolerance of insect immunity, and by specific mechanisms for their transmission. The resident microorganisms can promote insect fitness by contributing to nutrition, especially by providing essential amino acids, B vitamins, and, for fungal partners, sterols. Some microorganisms protect their insect hosts against pathogens, parasitoids, and other parasites by synthesizing specific toxins or modifying the insect immune system. Priorities for future research include elucidation of microbial contributions to detoxification, especially of plant allelochemicals in phytophagous insects, and resistance to pathogens; as well as their role in among-insect communication; and the potential value of manipulation of the microbiota to control insect pests.
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88
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O'Connor TK, Humphrey PT, Lapoint RT, Whiteman NK, O'Grady PM. Microbial interactions and the ecology and evolution of Hawaiian Drosophilidae. Front Microbiol 2014; 5:616. [PMID: 25566196 PMCID: PMC4270190 DOI: 10.3389/fmicb.2014.00616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 10/29/2014] [Indexed: 02/06/2023] Open
Abstract
Adaptive radiations are characterized by an increased rate of speciation and expanded range of habitats and ecological niches exploited by those species. The Hawaiian Drosophilidae is a classic adaptive radiation; a single ancestral species colonized Hawaii approximately 25 million years ago and gave rise to two monophyletic lineages, the Hawaiian Drosophila and the genus Scaptomyza. The Hawaiian Drosophila are largely saprophagous and rely on approximately 40 endemic plant families and their associated microbes to complete development. Scaptomyza are even more diverse in host breadth. While many species of Scaptomyza utilize decomposing plant substrates, some species have evolved to become herbivores, parasites on spider egg masses, and exploit microbes on living plant tissue. Understanding the origin of the ecological diversity encompassed by these nearly 700 described species has been a challenge. The central role of microbes in drosophilid ecology suggests bacterial and fungal associates may have played a role in the diversification of the Hawaiian Drosophilidae. Here we synthesize recent ecological and microbial community data from the Hawaiian Drosophilidae to examine the forces that may have led to this adaptive radiation. We propose that the evolutionary success of the Hawaiian Drosophilidae is due to a combination of factors, including adaptation to novel ecological niches facilitated by microbes.
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Affiliation(s)
| | - Parris T Humphrey
- Ecology and Evolutionary Biology, University of Arizona Tucson, AZ, USA
| | - Richard T Lapoint
- Ecology and Evolutionary Biology, University of Arizona Tucson, AZ, USA
| | - Noah K Whiteman
- Ecology and Evolutionary Biology, University of Arizona Tucson, AZ, USA
| | - Patrick M O'Grady
- Environmental Science, Policy and Management, University of California Berkeley Berkeley, CA, USA
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89
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Stilling RM, Bordenstein SR, Dinan TG, Cryan JF. Friends with social benefits: host-microbe interactions as a driver of brain evolution and development? Front Cell Infect Microbiol 2014; 4:147. [PMID: 25401092 PMCID: PMC4212686 DOI: 10.3389/fcimb.2014.00147] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/03/2014] [Indexed: 12/21/2022] Open
Abstract
The tight association of the human body with trillions of colonizing microbes that we observe today is the result of a long evolutionary history. Only very recently have we started to understand how this symbiosis also affects brain function and behavior. In this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. In particular, we explore the integration of human brain development with evolution, symbiosis, and RNA biology, which together represent a “social triangle” that drives human social behavior and cognition. We argue that, in order to understand how inter-kingdom communication can affect brain adaptation and plasticity, it is inevitable to consider epigenetic mechanisms as important mediators of genome-microbiome interactions on an individual as well as a transgenerational time scale. Finally, we unite these interpretations with the hologenome theory of evolution. Taken together, we propose a tighter integration of neuroscience fields with host-associated microbiology by taking an evolutionary perspective.
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Affiliation(s)
- Roman M Stilling
- Alimentary Pharmabiotic Centre, University College Cork Cork, Ireland ; Department Anatomy and Neuroscience, University College Cork Cork, Ireland
| | - Seth R Bordenstein
- Departments of Biological Sciences and Pathology, Microbiology, and Immunology, Vanderbilt University Nashville, TN, USA
| | - Timothy G Dinan
- Alimentary Pharmabiotic Centre, University College Cork Cork, Ireland ; Department of Psychiatry, University College Cork Cork, Ireland
| | - John F Cryan
- Alimentary Pharmabiotic Centre, University College Cork Cork, Ireland ; Department Anatomy and Neuroscience, University College Cork Cork, Ireland
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90
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Vavre F, Kremer N. Microbial impacts on insect evolutionary diversification: from patterns to mechanisms. CURRENT OPINION IN INSECT SCIENCE 2014; 4:29-34. [PMID: 28043405 DOI: 10.1016/j.cois.2014.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 08/04/2014] [Accepted: 08/05/2014] [Indexed: 06/06/2023]
Abstract
Symbiosis can favor rapid shifts in host phenotypic traits, particularly through the contribution of symbionts to the host's physiology. In addition, variations in the microbiota composition between individuals can be associated with pre-zygotic and post-zygotic barriers. All together, these phenomena may contribute to insect diversification and speciation. Recent advances have also shown that the host-microbiota molecular dialog, mediated notably by host immune and developmental pathways, is critical for the acquisition and control of the microbiota, and could also contribute to reproductive isolation. While still a controversial hypothesis, adaptation through symbiosis could thus trigger host-symbiont coevolution and accelerate differentiation.
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Affiliation(s)
- Fabrice Vavre
- Université de Lyon, F-69000, Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne F-69622, France.
| | - Natacha Kremer
- Université de Lyon, F-69000, Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne F-69622, France
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91
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Chandler JA, Turelli M. Comment on "The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia". Science 2014; 345:1011. [PMID: 25170144 DOI: 10.1126/science.1251997] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Brucker and Bordenstein (Reports, 9 August 2013, p. 667) claim that adaptive codivergence of gut bacteria with hosts contributes to hybrid lethality. Yet, they provide no evidence for coadaptation of bacteria and Nasonia hosts. Their data on hybrid viability suggest that bacteria contribute to inviability only because intrinsic hybrid dysfunction increases susceptibility to free-living bacteria. Hologenomic speciation remains testable speculation without experimental support.
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Affiliation(s)
- James Angus Chandler
- Department of Microbiology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Michael Turelli
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA.
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92
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Brucker RM, Bordenstein SR. Response to Comment on "The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia". Science 2014; 345:1011. [PMID: 25170145 DOI: 10.1126/science.1256708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chandler and Turelli postulate that intrinsic hybrid dysfunction underscores hybrid lethality in Nasonia. Although it is a suitable conception for examining hybrid incompatibilities, their account of the evidence is factually inaccurate and leaves out the evolutionary process for why lethality became conditional on nuclear-microbe interactions. Hybrid incompatibilities in the context of phylosymbiosis are resolved by hologenomic principles and exemplify this emerging postmodern synthesis.
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Affiliation(s)
- Robert M Brucker
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA. Rowland Institute at Harvard University, Cambridge, MA 02142, USA.
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA. Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN 37232, USA.
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93
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Paulson AR, von Aderkas P, Perlman SJ. Bacterial associates of seed-parasitic wasps (Hymenoptera: Megastigmus). BMC Microbiol 2014; 14:224. [PMID: 25286971 PMCID: PMC4197294 DOI: 10.1186/s12866-014-0224-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 08/18/2014] [Indexed: 12/21/2022] Open
Abstract
Background The success of herbivorous insects has been shaped largely by their association with microbes. Seed parasitism is an insect feeding strategy involving intimate contact and manipulation of a plant host. Little is known about the microbial associates of seed-parasitic insects. We characterized the bacterial symbionts of Megastigmus (Hymenoptera: Torymidae), a lineage of seed-parasitic chalcid wasps, with the goal of identifying microbes that might play an important role in aiding development within seeds, including supplementing insect nutrition or manipulating host trees. We screened multiple populations of seven species for common facultative inherited symbionts. We also performed culture independent surveys of larvae, pupae, and adults of M. spermotrophus using 454 pyrosequencing. This major pest of Douglas-fir is the best-studied Megastigmus, and was previously shown to manipulate its tree host into redirecting resources towards unfertilized ovules. Douglas-fir ovules and the parasitoid Eurytoma sp. were also surveyed using pyrosequencing to help elucidate possible transmission mechanisms of the microbial associates of M. spermotrophus. Results Three wasp species harboured Rickettsia; two of these also harboured Wolbachia. Males and females were infected at similar frequencies, suggesting that these bacteria do not distort sex ratios. The M. spermotrophus microbiome is dominated by five bacterial OTUs, including lineages commonly found in other insect microbiomes and in environmental samples. The bacterial community associated with M. spermotrophus remained constant throughout wasp development and was dominated by a single OTU – a strain of Ralstonia, in the Betaproteobacteria, comprising over 55% of all bacterial OTUs from Megastigmus samples. This strain was also present in unparasitized ovules. Conclusions This is the first report of Ralstonia being an abundant and potentially important member of an insect microbiome, although other closely-related Betaproteobacteria, such as Burkholderia, are important insect symbionts. We speculate that Ralstonia might play a role in nutrient recycling, perhaps by redirecting nitrogen. The developing wasp larva feeds on megagametophyte tissue, which contains the seed storage reserves and is especially rich in nitrogen. Future studies using Ralstonia-specific markers will determine its distribution in other Megastigmus species, its mode of transmission, and its role in wasp nutrition. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0224-4) contains supplementary material, which is available to authorized users.
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Otani S, Mikaelyan A, Nobre T, Hansen LH, Koné NA, Sørensen SJ, Aanen DK, Boomsma JJ, Brune A, Poulsen M. Identifying the core microbial community in the gut of fungus-growing termites. Mol Ecol 2014; 23:4631-44. [DOI: 10.1111/mec.12874] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 07/08/2014] [Accepted: 07/11/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Saria Otani
- Section for Ecology and Evolution; Department of Biology; Centre for Social Evolution; University of Copenhagen; Copenhagen Denmark
| | - Aram Mikaelyan
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
| | - Tânia Nobre
- Laboratory of Genetics; Wageningen University; Wageningen The Netherlands
| | - Lars H. Hansen
- Section for Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - N'Golo A. Koné
- UFR des-Sciences de la Nature; Station d’Écologie de LAMTO; Université Nangui Abrogoua; BP 28 N'Douci Ivory Coast
| | - Søren J. Sørensen
- Section for Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Duur K. Aanen
- Laboratory of Genetics; Wageningen University; Wageningen The Netherlands
| | - Jacobus J. Boomsma
- Section for Ecology and Evolution; Department of Biology; Centre for Social Evolution; University of Copenhagen; Copenhagen Denmark
| | - Andreas Brune
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
| | - Michael Poulsen
- Section for Ecology and Evolution; Department of Biology; Centre for Social Evolution; University of Copenhagen; Copenhagen Denmark
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95
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Mason CJ, Raffa KF. Acquisition and structuring of midgut bacterial communities in gypsy moth (Lepidoptera: Erebidae) larvae. ENVIRONMENTAL ENTOMOLOGY 2014; 43:595-604. [PMID: 24780292 DOI: 10.1603/en14031] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Insects are associated with a diversity of bacteria that colonize their midguts. The extent to which these communities reflect maternal transmission, environmental acquisition, and subsequent structuring by the extreme conditions within the insect gut are poorly understood in many species. We used gypsy moth (Lymantria dispar L.) as a model to investigate interactions between egg mass and environmental sources of bacteria on larval midgut communities. Egg masses were collected from several wild and laboratory populations, and the effects of diet, initial egg mass community, and internal host environment were evaluated using 454 16S-rRNA gene pyrosequencing. Wild populations were highly diverse, while laboratory-maintained egg masses were associated with few operational taxonomic units. As larvae developed, their midgut bacterial communities became more similar to each other and the consumed diet despite initial differences in egg mass-associated bacteria. Subsequent experiments revealed that while midgut membership was more similar to bacteria associated with diet than with egg mass-associated bacteria, we were unable to detect distinct, persistent differences attributable to specific host plants. The differences between foliar communities and midgut communities of larvae that ingested them were owing to relative changes in populations of several bacteria phylotypes. We conclude that gypsy moth has a relatively characteristic midgut bacterial community that is reflective of, but ultimately distinct from, its foliar diet. This work demonstrates that environmental acquisition of diverse microbes can lead to similar midgut bacterial assemblages, underscoring the importance of host physiological environment in structuring bacterial communities.
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Affiliation(s)
- Charles J Mason
- Department of Entomology, 345 Russell Laboratories, 1630 Linden Drive, University of Wisconsin-Madison, Madison, WI 53706, USA
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96
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Woodhams DC, Brucker RM. Disease defence through generations: leaf-cutter ants and their symbiotic bacteria. Mol Ecol 2014; 22:4141-4143. [PMID: 23927408 DOI: 10.1111/mec.12431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 06/18/2013] [Accepted: 06/28/2013] [Indexed: 11/30/2022]
Abstract
Microbial ecology of animals is taking on significance in the modern dialogue for the biology of species. Similar to a nuclear genome, the entire bacterial assemblage maintains an ancestral signal of the host's evolution leading to cophylogeny between the host and the microbes they harbour (Brucker & Bordenstein 2012b). The stability of such associations is of great interest as they provide a means for species to acquire new traits and genetic diversity that their own genomes lack (McFall-Ngai et al. 2013). The role of gut microbiota, for example, in host health and nutrition is widely recognized and a shared characteristic among animals. The role of bacteria colonizing the outside surfaces of animals is less well understood, but rather than random colonization, these microbes on skin, cuticles, scales and feathers in many cases provide benefits to the host. The symbiosis of leaf-cutter ants, their fungus gardens and their microbiota is a fascinating and complex system. Whether culture-independent bacterial diversity on the cuticle of leaf-cutter ants is high or highly constrained by subcuticular gland secretions is one prominent question. In this issue of Molecular Ecology, Andersen et al. (2013) show that leaf-cutting ants, Acromyrmex echinatior, maintain a dominant and colony-specific bacterium called Pseudonocardia on their cuticles (the laterocervical plates in particular). This bacterium is involved in protecting the ants and their fungal gardens from disease. Other fungus-gardening attine species as well as soil and vegetation can harbour Pseudonocardia. However, it was previously unknown how stable the bacterial strain-ant colony association was through the lifetime of the colony.
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Affiliation(s)
- Douglas C Woodhams
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302-0334, USA.,Smithsonian Tropical Research Institute, 9100 Panama City PL, Washington, DC 20521-9100, USA
| | - Robert M Brucker
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
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97
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Hammer TJ, McMillan WO, Fierer N. Metamorphosis of a butterfly-associated bacterial community. PLoS One 2014; 9:e86995. [PMID: 24466308 PMCID: PMC3900687 DOI: 10.1371/journal.pone.0086995] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 12/17/2013] [Indexed: 02/07/2023] Open
Abstract
Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.
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Affiliation(s)
- Tobin J. Hammer
- Department of Ecology and Evolutionary Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, Colorado, United States of America
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - W. Owen McMillan
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, Colorado, United States of America
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98
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Bottos EM, Woo AC, Zawar-Reza P, Pointing SB, Cary SC. Airborne bacterial populations above desert soils of the McMurdo Dry Valleys, Antarctica. MICROBIAL ECOLOGY 2014; 67:120-8. [PMID: 24121801 PMCID: PMC3907674 DOI: 10.1007/s00248-013-0296-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 09/17/2013] [Indexed: 05/15/2023]
Abstract
Bacteria are assumed to disperse widely via aerosolized transport due to their small size and resilience. The question of microbial endemicity in isolated populations is directly related to the level of airborne exogenous inputs, yet this has proven hard to identify. The ice-free terrestrial ecosystem of Antarctica, a geographically and climatically isolated continent, was used to interrogate microbial bio-aerosols in relation to the surrounding ecology and climate. High-throughput sequencing of bacterial ribosomal RNA (rRNA) genes was combined with analyses of climate patterns during an austral summer. In general terms, the aerosols were dominated by Firmicutes, whereas surrounding soils supported Actinobacteria-dominated communities. The most abundant taxa were also common to aerosols from other continents, suggesting that a distinct bio-aerosol community is widely dispersed. No evidence for significant marine input to bioaerosols was found at this maritime valley site, instead local influence was largely from nearby volcanic sources. Back trajectory analysis revealed transport of incoming regional air masses across the Antarctic Plateau, and this is envisaged as a strong selective force. It is postulated that local soil microbial dispersal occurs largely via stochastic mobilization of mineral soil particulates.
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Affiliation(s)
- Eric M. Bottos
- />International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton, New Zealand
- />Department of Biological Sciences, The University of Waikato, Private Bag 3105, Hamilton, New Zealand
| | - Anthony C. Woo
- />Sorbonne Paris Cité, Faculté de Médecine, Université Paris Descartes, Paris Descartes, 24 rue du Faubourg Saint-Jacques, 75014 Paris, France
| | - Peyman Zawar-Reza
- />International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton, New Zealand
- />Department of Geography, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Stephen B. Pointing
- />International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton, New Zealand
- />Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142 New Zealand
| | - Stephen C. Cary
- />International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton, New Zealand
- />Department of Biological Sciences, The University of Waikato, Private Bag 3105, Hamilton, New Zealand
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99
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Stilling RM, Dinan TG, Cryan JF. Microbial genes, brain & behaviour - epigenetic regulation of the gut-brain axis. GENES BRAIN AND BEHAVIOR 2013; 13:69-86. [PMID: 24286462 DOI: 10.1111/gbb.12109] [Citation(s) in RCA: 406] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 11/13/2013] [Accepted: 11/25/2013] [Indexed: 12/12/2022]
Abstract
To date, there is rapidly increasing evidence for host-microbe interaction at virtually all levels of complexity, ranging from direct cell-to-cell communication to extensive systemic signalling, and involving various organs and organ systems, including the central nervous system. As such, the discovery that differential microbial composition is associated with alterations in behaviour and cognition has significantly contributed to establishing the microbiota-gut-brain axis as an extension of the well-accepted gut-brain axis concept. Many efforts have been focused on delineating a role for this axis in health and disease, ranging from stress-related disorders such as depression, anxiety and irritable bowel syndrome to neurodevelopmental disorders such as autism. There is also a growing appreciation of the role of epigenetic mechanisms in shaping brain and behaviour. However, the role of epigenetics in informing host-microbe interactions has received little attention to date. This is despite the fact that there are many plausible routes of interaction between epigenetic mechanisms and the host-microbiota dialogue. From this new perspective we put forward novel, yet testable, hypotheses. Firstly, we suggest that gut-microbial products can affect chromatin plasticity within their host's brain that in turn leads to changes in neuronal transcription and eventually alters host behaviour. Secondly, we argue that the microbiota is an important mediator of gene-environment interactions. Finally, we reason that the microbiota itself may be viewed as an epigenetic entity. In conclusion, the fields of (neuro)epigenetics and microbiology are converging at many levels and more interdisciplinary studies are necessary to unravel the full range of this interaction.
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100
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Microbial ecology of the hive and pollination landscape: bacterial associates from floral nectar, the alimentary tract and stored food of honey bees (Apis mellifera). PLoS One 2013; 8:e83125. [PMID: 24358254 PMCID: PMC3866269 DOI: 10.1371/journal.pone.0083125] [Citation(s) in RCA: 187] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 10/30/2013] [Indexed: 01/29/2023] Open
Abstract
Nearly all eukaryotes are host to beneficial or benign bacteria in their gut lumen, either vertically inherited, or acquired from the environment. While bacteria core to the honey bee gut are becoming evident, the influence of the hive and pollination environment on honey bee microbial health is largely unexplored. Here we compare bacteria from floral nectar in the immediate pollination environment, different segments of the honey bee (Apis mellifera) alimentary tract, and food stored in the hive (honey and packed pollen or “beebread”). We used cultivation and sequencing to explore bacterial communities in all sample types, coupled with culture-independent analysis of beebread. We compare our results from the alimentary tract with both culture-dependent and culture-independent analyses from previous studies. Culturing the foregut (crop), midgut and hindgut with standard media produced many identical or highly similar 16S rDNA sequences found with 16S rDNA clone libraries and next generation sequencing of 16S rDNA amplicons. Despite extensive culturing with identical media, our results do not support the core crop bacterial community hypothesized by recent studies. We cultured a wide variety of bacterial strains from 6 of 7 phylogenetic groups considered core to the honey bee hindgut. Our results reveal that many bacteria prevalent in beebread and the crop are also found in floral nectar, suggesting frequent horizontal transmission. From beebread we uncovered a variety of bacterial phylotypes, including many possible pathogens and food spoilage organisms, and potentially beneficial bacteria including Lactobacillus kunkeei, Acetobacteraceae and many different groups of Actinobacteria. Contributions of these bacteria to colony health may include general hygiene, fungal and pathogen inhibition and beebread preservation. Our results are important for understanding the contribution to pollinator health of both environmentally vectored and core microbiota, and the identification of factors that may affect bacterial detection and transmission, colony food storage and disease susceptibility.
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