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Unzueta-Martínez A, Scanes E, Parker LM, Ross PM, O'Connor W, Bowen JL. Microbiomes of the Sydney Rock Oyster are acquired through both vertical and horizontal transmission. Anim Microbiome 2022; 4:32. [PMID: 35590396 PMCID: PMC9118846 DOI: 10.1186/s42523-022-00186-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/07/2022] [Indexed: 11/10/2022] Open
Abstract
Background The term holobiont is widely accepted to describe animal hosts and their associated microorganisms. The genomes of all that the holobiont encompasses, are termed the hologenome and it has been proposed as a unit of selection in evolution. To demonstrate that natural selection acts on the hologenome, a significant portion of the associated microbial genomes should be transferred between generations. Using the Sydney Rock Oyster (Saccostrea glomerata) as a model, we tested if the microbes of this broadcast spawning species could be passed down to the next generation by conducting single parent crosses and tracking the microbiome from parent to offspring and throughout early larval stages using 16S rRNA gene amplicon sequencing. From each cross, we sampled adult tissues (mantle, gill, stomach, gonad, eggs or sperm), larvae (D-veliger, umbo, eyed pediveliger, and spat), and the surrounding environment (water and algae feed) for microbial community analysis. Results We found that each larval stage has a distinct microbiome that is partially influenced by their parental microbiome, particularly the maternal egg microbiome. We also demonstrate the presence of core microbes that are consistent across all families, persist throughout early life stages (from eggs to spat), and are not detected in the microbiomes of the surrounding environment. In addition to the core microbiomes that span all life cycle stages, there is also evidence of environmentally acquired microbial communities, with earlier larval stages (D-veliger and umbo), more influenced by seawater microbiomes, and later larval stages (eyed pediveliger and spat) dominated by microbial members that are specific to oysters and not detected in the surrounding environment. Conclusion Our study characterized the succession of oyster larvae microbiomes from gametes to spat and tracked selected members that persisted across multiple life stages. Overall our findings suggest that both horizontal and vertical transmission routes are possible for the complex microbial communities associated with a broadcast spawning marine invertebrate. We demonstrate that not all members of oyster-associated microbiomes are governed by the same ecological dynamics, which is critical for determining what constitutes a hologenome. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00186-9.
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Affiliation(s)
- Andrea Unzueta-Martínez
- Department of Marine and Environmental Science, Northeastern University, Nahant, MA, 01908, USA. .,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Elliot Scanes
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Laura M Parker
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Kensington, NSW, 2052, Australia
| | - Pauline M Ross
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Wayne O'Connor
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Taylors Beach, NSW, 2316, Australia
| | - Jennifer L Bowen
- Department of Marine and Environmental Science, Northeastern University, Nahant, MA, 01908, USA
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Busck MM, Lund MB, Bird TL, Bechsgaard JS, Bilde T, Schramm A. Temporal and spatial microbiome dynamics across natural populations of the social spider Stegodyphus dumicola. FEMS Microbiol Ecol 2022; 98:6526868. [PMID: 35147190 DOI: 10.1093/femsec/fiac015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/07/2022] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Host symbiont interactions may form obligatory or facultative associations that are context dependent. Long-term studies on microbiome composition from wild populations should assess the temporal and spatial dynamics of host-microbe associations. We characterized the temporal and spatial variation in the bacterial microbiome composition in six populations of the social spider Stegodyphus dumicola for 2.5 years, using 16S rRNA gene amplicon sequencing of whole spiders. Individuals within a nest exhibit highly similar microbiomes, which remain stable over several generations and are not predictably affected by seasonal variation in temperature or humidity. This stability in nest microbiome is likely due to social transmission, whereas drift-like processes during new nest foundations explain variation in host microbiomes between nests. This is supported by the lack of obligate symbionts (i.e. no symbionts are present in all spider individuals). Quantitative PCR analyses showed that the bacterial load of individual spiders is stable in healthy nests but can increase dramatically in perishing nests. These increases are not driven by specific bacterial taxa but likely caused by loss of host immune control under deteriorating conditions. Spider nests show an annual survival rate of approximately 45%, but nest death is not correlated to microbiome composition, and the bacteria found in S. dumicola are not considered to be high virulence pathogens.
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Affiliation(s)
- Mette M Busck
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Marie B Lund
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Tharina L Bird
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology (BIUST), Botswana.,Section for Genetics, Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark.,General Entomology, Ditsong National Museum of Natural History, Pretoria, South Africa.,Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Jesper S Bechsgaard
- Section for Genetics, Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Trine Bilde
- Section for Genetics, Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
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3
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Goodrich-Blair H. Interactions of host-associated multispecies bacterial communities. Periodontol 2000 2021; 86:14-31. [PMID: 33690897 DOI: 10.1111/prd.12360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The oral microbiome comprises microbial communities colonizing biotic (epithelia, mucosa) and abiotic (enamel) surfaces. Different communities are associated with health (eg, immune development, pathogen resistance) and disease (eg, tooth loss and periodontal disease). Like any other host-associated microbiome, colonization and persistence of both beneficial and dysbiotic oral microbiomes are dictated by successful utilization of available nutrients and defense against host and competitor assaults. This chapter will explore these general features of microbe-host interactions through the lens of symbiotic (mutualistic and antagonistic/pathogenic) associations with nonmammalian animals. Investigations in such systems across a broad taxonomic range have revealed conserved mechanisms and processes that underlie the complex associations among microbes and between microbes and hosts.
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Affiliation(s)
- Heidi Goodrich-Blair
- Department of Microbiology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
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4
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Russell SL. Transmission mode is associated with environment type and taxa across bacteria-eukaryote symbioses: a systematic review and meta-analysis. FEMS Microbiol Lett 2019; 366:5289862. [DOI: 10.1093/femsle/fnz013] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 01/15/2019] [Indexed: 12/22/2022] Open
Affiliation(s)
- Shelbi L Russell
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95060; USA
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5
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Aira M, Pérez-Losada M, Domínguez J. Diversity, structure and sources of bacterial communities in earthworm cocoons. Sci Rep 2018; 8:6632. [PMID: 29700426 PMCID: PMC5919978 DOI: 10.1038/s41598-018-25081-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/05/2018] [Indexed: 01/09/2023] Open
Abstract
Animals start interactions with the bacteria that will constitute their microbiomes at embryonic stage. After mating, earthworms produce cocoons externally which will be colonized with bacteria from their parents and the environment. Due to the key role bacterial symbionts play on earthworm fitness, it is important to study bacterial colonization during cocoon formation. Here we describe the cocoon microbiome of the earthworms Eisenia andrei and E. fetida, which included 275 and 176 bacterial species, respectively. They were dominated by three vertically-transmitted symbionts, Microbacteriaceae, Verminephrobacter and Ca. Nephrothrix, which accounted for 88% and 66% of the sequences respectively. Verminephrobacter and Ca. Nephrothrix showed a high rate of sequence variation, suggesting that they could be biparentally acquired during mating. The other bacterial species inhabiting the cocoons came from the bedding, where they accounted for a small fraction of the diversity (27% and 7% of bacterial species for E. andrei and E. fetida bedding). Hence, earthworm cocoon microbiome includes a large fraction of the vertically-transmitted symbionts and a minor fraction, but more diverse, horizontally and non-randomly acquired from the environment. These data suggest that horizontally-transmitted bacteria to cocoons may play an important role in the adaptation of earthworms to new environments or diets.
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Affiliation(s)
- Manuel Aira
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Vigo, E-36310, Spain.
| | - Marcos Pérez-Losada
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA, 20147, USA
| | - Jorge Domínguez
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Vigo, E-36310, Spain
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Fisher RM, Henry LM, Cornwallis CK, Kiers ET, West SA. The evolution of host-symbiont dependence. Nat Commun 2017; 8:15973. [PMID: 28675159 PMCID: PMC5500886 DOI: 10.1038/ncomms15973] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/15/2017] [Indexed: 11/09/2022] Open
Abstract
Organisms across the tree of life form symbiotic partnerships with microbes for metabolism, protection and resources. While some hosts evolve extreme dependence on their symbionts, others maintain facultative associations. Explaining this variation is fundamental to understanding when symbiosis can lead to new higher-level individuals, such as during the evolution of the eukaryotic cell. Here we perform phylogenetic comparative analyses on 106 unique host-bacterial symbioses to test for correlations between symbiont function, transmission mode, genome size and host dependence. We find that both transmission mode and symbiont function are correlated with host dependence, with reductions in host fitness being greatest when nutrient-provisioning, vertically transmitted symbionts are removed. We also find a negative correlation between host dependence and symbiont genome size in vertically, but not horizontally, transmitted symbionts. These results suggest that both function and population structure are important in driving irreversible dependence between hosts and symbionts.
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Affiliation(s)
- Roberta M Fisher
- Department of Ecological Science, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085-1087, 1081 HV Amsterdam, The Netherlands.,Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Lee M Henry
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | | | - E Toby Kiers
- Department of Ecological Science, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085-1087, 1081 HV Amsterdam, The Netherlands
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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