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Chapter One - Microbiomes of soils, plants and animals: an introduction

Published online by Cambridge University Press:  07 March 2020

By
Rachael E. Antwis ,
Xavier A. Harrison ,
Michael J. Cox ,
Sophia Carryl ,
Meagan Dewar ,
James Doonan ,
Ellen L. Fry ,
Jack A. Gilbert ,
Bethan Greenwood  and
Reid N. Harris
...Show all authors
Edited by
Rachael E. Antwis ,
Xavier A. Harrison  and
Michael J. Cox
Rachael E. Antwis
Affiliation:
University of Salford
Xavier A. Harrison
Affiliation:
University of Exeter
Michael J. Cox
Affiliation:
University of Birmingham
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Summary

A classic example of microbiome function is its role in nutrient assimilation in both plants and animals, but other less obvious roles are becoming more apparent, particularly in terms of driving infectious and non-infectious disease outcomes and influencing host behaviour. However, numerous biotic and abiotic factors influence the composition of these communities, and host microbiomes can be susceptible to environmental change. How microbial communities will be altered by, and mitigate, the rapid environmental change we can expect in the next few decades remain to be seen. That said, given the enormous range of functional diversity conferred by microbes, there is currently something of a revolution in microbial bioengineering and biotechnology in order to address real-world problems including human and wildlife disease and crop and biofuel production. All of these concepts are explored in further detail throughout the book.

Keywords

microbial communitiesmicrobiomeholobionthologenomesymbiosis
Type
Chapter
Information
Microbiomes of Soils, Plants and Animals
An Integrated Approach
 , pp. 1 - 7
Publisher: Cambridge University Press
Print publication year: 2020

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References

Autenrieth, IB. (2017) The microbiome in health and disease: A new role of microbes in molecular medicine. Journal of Molecular Medicine, 95, 1–3.CrossRefGoogle ScholarPubMed
Baldo, L, Pretus, JL, Riera, JL, et al. (2017) Convergence of gut microbiotas in the adaptive radiations of African cichlid fishes. The ISME Journal, 11, 1975–1987.CrossRefGoogle ScholarPubMed
Berg, G, Rybakova, D, Grube, M, et al. (2016) The plant microbiome explored: Implications for experimental botany. Journal of Experimental Botany, 67, 995–1002.Google Scholar
Blaser, MJ, Cardon, ZG, Cho, MK, et al. (2016) Toward a predictive understanding of Earth’s microbiomes to address 21st century challenges. mBio, 7, e00714–16.CrossRefGoogle Scholar
Bordenstein, SR, Theis, KR. (2015) Host biology in light of the microbiome: Ten principles of holobionts and hologenomes. PLoS Biology, 13, 1–23.Google Scholar
Bosch, TCG, McFall-Ngai, MJ. (2011) Metaorganisms as the new frontier. Zoology, 114, 185–190.CrossRefGoogle ScholarPubMed
Chen, BS, Teh, BS, Sun, C, et al. (2016) Biodiversity and activity of the gut microbiota across the life history of the insect herbivore Spodoptera littoralis. Scientific Reports, 6, 14.Google Scholar
Chisholm, ST, Coaker, G, Day, B, et al. (2006) Host–microbe interactions: Shaping the evolution of the plant immune response. Cell, 124, 803–814.Google Scholar
Davenport, ER, Sanders, JG, Song, SJ, et al. (2017) The human microbiome in evolution. BMC Biology, 15, 1–12.Google Scholar
Douglas, AE. (2015) Multiorganismal insects: Diversity and function of resident microorganisms. Annual Review of Entomology, 60, 17–34.Google Scholar
Douglas, AE, Werren, JH. (2016) Holes in the hologeome: Why host–microbe symbioses are not holobionts. mBio, 7, e02099–15.Google Scholar
Esposti, MD, Romero, EM. (2017) The functional microbiome of arthropods. PLoS ONE, 12, 26.Google Scholar
Fierer, N. (2017) Embracing the unknown: Disentangling the complexities of the soil microbiome. Nature Reviews Microbiology, 15, 579–590.Google Scholar
Fisher, MC, Gow, NAR, Gurr, SJ. (2016) Tackling emerging fungal threats to animal health, food security and ecosystem resilience. Philosophical Transactions of the Royal Society B: Biological Sciences, 371, 20160332.CrossRefGoogle ScholarPubMed
Flint, HJ, Bayer, EA, Rincon, MT, et al. (2008) Polysaccharide utilisation by gut bacteria: Potential for new insights from genomic analysis. Nature Reviews Microbiology, 6, 121–131.Google Scholar
Gilbert, SF, Sapp, J, Tauber, AI. (2012) A symbiotic view of life: We have never been individuals. Quarterly Review of Biology, 87, 325–341.CrossRefGoogle ScholarPubMed
Gilbert, JA, Blaser, MJ, Caporaso, JG, et al. (2018) Current understanding of the human microbiome. Nature Medicine, 24, 392–400.Google Scholar
Gopal, M, Gupta, A. (2016) Microbiome selection could spur next-generation plant breeding strategies. Frontiers in Microbiology, 7, 1–10.Google Scholar
Grice, EA, Segre, JA. (2012) The human microbiome: Our second genome. Annual Review of Genomics and Human Genetics, 13, 151–170.Google Scholar
Hammer, TJ, Bowers, MD. (2015) Gut microbes may facilitate insect herbivory of chemically defended plants. Oecologia, 179, 1–14.Google Scholar
Human Microbiome Consortium. (2012) Structure, function and diversity of the healthy human microbiome. Nature, 486, 207–214.Google Scholar
Ley, R, Hamady, M, Lozupone, C. (2008) Evolution of mammals and their gut microbes. Science, 320, 1647–1651.Google Scholar
Lynch, SV, Pedersen, O. (2016) The human intestinal microbiome in health and disease. New England Journal of Medicine, 375, 2369–2379.Google Scholar
Macke, E, Tasiemski, A, Massol, F, et al. (2017) Life history and eco-evolutionary dynamics in light of the gut microbiota. Oikos, 126, 508–531.Google Scholar
McFall-Ngai, M, Hadfield, MG, Bosch, TCG, et al. (2013) Animals in a bacterial world, a new imperative for the life sciences. Proceedings of the National Academy of Sciences, 110, 3229–3236.Google Scholar
Oliver, KM, Degnan, PH, Burke, GR, Moran, NA. (2010) Facultative symbionts in aphids and the horizontal transfer of ecologically important traits. Annual Review of Entomology, 55, 247–266.Google Scholar
Osborne, OG, De-Kayne, R, Bidartondo, MI, et al. (2018) Arbuscular mycorrhizal fungi promote coexistence and niche divergence of sympatric palm species on a remote oceanic island. New Phytologist, 217, 1254–1266.Google Scholar
Pii, Y, Mimmo, T, Tomasi, N, et al. (2015) Microbial interactions in the rhizosphere: Beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process: A review. Biology and Fertility of Soils, 51, 403–415.Google Scholar
Rohwer, F, Seguritan, V, Azam, F, Knowlton, N. (2002) Diversity and distribution of coral-associated bacteria. Marine Ecology Progress Series, 243, 1–10.Google Scholar
Rosenberg, E, Zilber-Rosenberg, I. (2016) Microbes drive evolution of animals and plants: The hologenome concept. mBio, 7, e01395-15.Google Scholar
Rosenberg, E, Zilber-Rosenberg, I. (2018) The hologenome concept of evolution after 10 years. Microbiome, 6, 78.Google Scholar
Sender, R, Fuchs, S, Milo, R. (2016) Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell, 164, 337–340.Google Scholar
Thakuria, D, Schmidt, O, Finan, D, et al. (2010) Gut wall bacteria of earthworms: A natural selection process. The ISME Journal, 4, 357–366.Google Scholar
Thompson, JR, Rivera, HE, Closek, CJ, Medina, M. (2015) Microbes in the coral holobiont: Partners through evolution, development, and ecological interactions. Frontiers in Cellular and Infection Microbiology, 4, 20.Google Scholar
Tompkins, DM, Carver, S, Jones, ME, et al. (2015) Emerging infectious diseases of wildlife: A critical perspective. Trends in Parasitology, 31, 149–159.Google Scholar
Turner, TR, James, EK, Poole, PS. (2013) The plant microbiome. Genome Biology, 14, 1–10.Google Scholar
Yatsunenko, T, Rey, FE, Manary, MJ, et al. (2012) Human gut microbiome viewed across age and geography. Nature, 486, 222–227.Google Scholar
Young, VB. (2017) The role of the microbiome in human health and disease: An introduction for clinicians. BMJ, 356, j831.Google Scholar
Youngblut, ND, Reischer, GH, Walters, W, et al. (2019). Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nature Communications, 10, 2200.CrossRefGoogle ScholarPubMed

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