Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome

Harrison, XA; McDevitt, A; Dunn, J; Grifftihs, S; Benvenuto, C; Birtles, RJ; Boubli, JP; Bown, K; Bridson, C; Brooks, DR; Browett, SS; Carden, R; Clever, F; Coscia, I; Edwards, KL; Ferry, N; Goodhead, IB; Highlands, A; Hopper, J; Jackson, J; Jehle, R; Kaizer, M; King, T; Lea, J; Lenka, JL; McCubbin, A; McKenzie, J; Moraes, B; O’Meara, D; Pescod, P; Preziosi, RF; Rowntree, JK; Shultz, S; Silk, M; Stockdale, JE; Symondson, WOC; de la Pena, M; Walker, S; Wood, M; Meade, E; Antwis, RE

Abstract

Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate marked variation across host taxonomy in patterns of covariation between bacterial and fungal abundances. Host phylogeny drives differences in overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in the mammalian gut microbiome.
Sample type, tissue storage and DNA extraction method also affected bacterial and fungal community composition, and future studies would benefit from standardised approaches to sample processing.
Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.

Citation

Harrison, X., McDevitt, A., Dunn, J., Grifftihs, S., Benvenuto, C., Birtles, R., …Antwis, R. (2021). Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome. Proceedings of the Royal Society B: Biological Sciences, 288(1957), 20210552. https://doi.org/10.1098/rspb.2021.0552

• Journal Article Type: Article
• Acceptance Date: Jul 14, 2021
• Publication Date: Aug 18, 2021
• Deposit Date: Jul 15, 2021
• Publicly Available Date: Jul 15, 2021
• Journal: Proceedings of the Royal Society B: Biological Sciences
• Print ISSN: 0962-8452
• Electronic ISSN: 1471-2954
• Publisher: The Royal Society
• Volume: 288
• Issue: 1957
• Pages: 20210552
• DOI: https://doi.org/10.1098/rspb.2021.0552
• Publisher URL: https://doi.org/10.1098/rspb.2021.0552
• Related Public URLs: http://rspb.royalsocietypublishing.org/
• Additional Information: Funders : Natural Environment Research Council (NERC);Radioactive Waste Management Ltd;Environment Agency and the Genetics Society;Coordenação de Aperfeicoamento de Pessoal de Nível Superior (CAPES), Brazil;Natural Environment Research Council; Projects : TRansfer - Exposure – Effects (TREE);NE/L000318/1; Grant Number: NE/L000318/1