Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome

Nelson, William C.; Graham, Emily B.; Crump, Alex R.; Fansler, Sarah J.; Arntzen, Evan V.; Kennedy, David W.; Stegen, James C.

doi:10.1371/journal.pone.0228165

Title: Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome

Journal Article · 27 January 2020 · PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0228165 · OSTI ID:1595181

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^[1]; Fansler, Sarah J. ^[1];

^[1]; Kennedy, David W. ^[1];

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Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Biodiversity is thought to prevent decline in community function in response to changing environmental conditions through replacement of organisms with similar functional capacity but different optimal growth characteristics. We examined how this concept translates to the within-gene level by exploring seasonal dynamics of within-gene diversity for genes involved in nitrogen cycling in hyporheic zone communities. Nitrification genes displayed low richness—defined as the number of unique within-gene phylotypes—across seasons. Conversely, denitrification genes varied in both richness and the degree to which phylotypes were recruited or lost. These results demonstrate that there is not a universal mechanism for maintaining community functional potential for nitrogen cycling activities, even across seasonal environmental shifts to which communities would be expected to be well adapted. As such, extreme environmental changes could have very different effects on the stability of the different nitrogen cycle activities. These outcomes suggest a need to modify existing conceptual models that link biodiversity to microbiome function to incorporate within-gene diversity. Specifically, we suggest an expanded conceptualization that 1) recognizes component steps (genes) with low diversity as potential bottlenecks influencing pathway-level function, and 2) includes variation in both the number of entities (e.g. species, phylotypes) that can contribute to a given process and the turnover of those entities in response to shifting conditions. In conclusion, building these concepts into process-based ecosystem models represents an exciting opportunity to connect within-gene-scale ecological dynamics to ecosystem-scale services.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-76RL01830; AC06-76RLO 1830

OSTI ID:: 1595181

Alternate ID(s):: OSTI ID: 1597652

Report Number(s):: PNNL-SA-125632

Journal Information:: PLoS ONE, Vol. 15, Issue 1; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 7 works

Citation information provided by
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59 BASIC BIOLOGICAL SCIENCES
microbial ecology
hyporheic zone
nitrification
denitrification
metagenomics

Title: Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome

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