University of Oulu

Gravuer K and Eskelinen A (2017) Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities. Front. Microbiol. 8:1271. doi: 10.3389/fmicb.2017.01271

Nutrient and rainfall additions shift phylogenetically estimated traits of soil microbial communities

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Author: Gravuer, Kelly1,2; Eskelinen, Anu3,4,5,6
Organizations: 1raduate Group in Ecology, Department of Plant Sciences, University of California, Davis, Davis, CA, United States
2Present Address: Kelly Gravuer, Center for Biodiversity Outcomes, Arizona State University, Tempe, AZ, United States; The Nature Conservancy, Arlington, VA, United States
3Department of Physiological Diversity, Helmholtz Center for Environmental Research–UFZ, Leipzig, Germany
4German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
5Department of Ecology, University of Oulu, Oulu, Finland
6Department of Environmental Science and Policy, University of California, Davis, Davis, CA, United States
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1.5 MB)
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Language: English
Published: Frontiers Media, 2017
Publish Date: 2017-08-24


Microbial traits related to ecological responses and functions could provide a common currency facilitating synthesis and prediction; however, such traits are difficult to measure directly for all taxa in environmental samples. Past efforts to estimate trait values based on phylogenetic relationships have not always distinguished between traits with high and low phylogenetic conservatism, limiting reliability, especially in poorly known environments, such as soil. Using updated reference trees and phylogenetic relationships, we estimated two phylogenetically conserved traits hypothesized to be ecologically important from DNA sequences of the 16S rRNA gene from soil bacterial and archaeal communities. We sampled these communities from an environmental change experiment in California grassland applying factorial addition of late-season precipitation and soil nutrients to multiple soil types for 3 years prior to sampling. Estimated traits were rRNA gene copy number, which contributes to how rapidly a microbe can respond to an increase in resources and may be related to its maximum growth rate, and genome size, which suggests the breadth of environmental and substrate conditions in which a microbe can thrive. Nutrient addition increased community-weighted mean estimated rRNA gene copy number and marginally increased estimated genome size, whereas precipitation addition decreased these community means for both estimated traits. The effects of both treatments on both traits were associated with soil properties, such as ammonium, available phosphorus, and pH. Estimated trait responses within several phyla were opposite to the community mean response, indicating that microbial responses, although largely consistent among soil types, were not uniform across the tree of life. Our results show that phylogenetic estimation of microbial traits can provide insight into how microbial ecological strategies interact with environmental changes. The method could easily be applied to any of the thousands of existing 16S rRNA sequence data sets and offers potential to improve our understanding of how microbial communities mediate ecosystem function responses to global changes.

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Series: Frontiers in microbiology
ISSN: 1664-302X
ISSN-E: 1664-302X
ISSN-L: 1664-302X
Volume: 8
Article number: 1271
DOI: 10.3389/fmicb.2017.01271
Type of Publication: A1 Journal article – refereed
Field of Science: 1183 Plant biology, microbiology, virology
1181 Ecology, evolutionary biology
Funding: The study was supported by a Mildred E. Mathias Graduate Student Research Grant from the University of California Natural Reserve System, a UC Davis Natural Reserve System Grant, an EPA STAR Graduate Research Fellowship (FP-91770601), an ARCS Foundation of Northern California Scholarship, and a Theodore and Angela Foin Fellowship to KG, and the Academy of Finland (projects 253385 and 297191) and Wihuri Foundation to AE.
Academy of Finland Grant Number: 253385
Detailed Information: 253385 (Academy of Finland Funding decision)
297191 (Academy of Finland Funding decision)
Copyright information: Copyright © 2017 Gravuer and Eskelinen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.