A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists

Daniel Loos; Ailton Pereira da Costa Filho; Bas E. Dutilh; Amelia E. Barber; Gianni Panagiotou

doi:10.1016/j.celrep.2024.114046

A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists

Daniel Loos, Ailton Pereira da Costa Filho, Bas E. Dutilh, Amelia E. Barber^*, Gianni Panagiotou^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.

Original language	English
Article number	114046
Number of pages	20
Journal	Cell Reports
Volume	43
Issue number	4
DOIs	https://doi.org/10.1016/j.celrep.2024.114046
Publication status	Published - 23 Apr 2024

Bibliographical note

Publisher Copyright:
© 2024 The Authors

Funding

This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy \u2013 EXC 20151 \u2013 Project-ID 390813860. B.E.D. is supported by the European Research Council Consolidator grant 865694 and the Alexander von Humboldt Foundation in the context of an Alexander von Humboldt-Professorship. Conceptualization, A.E.B. and G.P.; methodology/validation, D.L. A.E.B. G.P. and B.E.D.; visualization, D.L. and A.P.d.C.F.; project administration/supervision, A.E.B. and G.P.; funding acquisition, A.E.B. and G.P.; writing \u2013 original draft, D.L. A.P.d.C.F. A.E.B. and G.P.; writing \u2013 review & editing, all authors. The authors declare no competing interests.

Funders	Funder number
Alexander von Humboldt-Stiftung
Deutsche Forschungsgemeinschaft	EXC 20151, 390813860
Deutsche Forschungsgemeinschaft
European Research Council	865694
European Research Council

Keywords

bacterial-fungal interactions
CP: Microbiology
environmental adaptation
generalism
microbial ecology
microbiome

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.celrep.2024.114046Licence: CC BY-NC-ND

1-s2.0-S2211124724003747-mainFinal published version, 4.12 MBLicence: CC BY-NC-ND

Cite this

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abstract = "Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.",

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A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists

Abstract

Bibliographical note

Funding

Keywords

UN SDGs

Access to Document

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