Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

Fierer, Noah; Lauber, Christian L.; Ramirez, Kelly S.; Zaneveld, Jesse; Bradford, Mark A.; Knight, Rob

doi:10.1038/ismej.2011.159

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

Journal Article · Thu Dec 01 00:00:00 EST 2011 · The ISME Journal

DOI:https://doi.org/10.1038/ismej.2011.159· OSTI ID:1623755

Fierer, Noah ^[1]; Lauber, Christian L. ^[2]; Ramirez, Kelly S. ^[3]; Zaneveld, Jesse ^[4]; Bradford, Mark A. ^[5]; Knight, Rob ^[6]

Univ. of Colorado, Boulder, CO (United States). Cooperative Inst. for Research in Environmental Sciences; Univ. of Colorado, Boulder, CO (United States). Dept. of Ecology and Evolutionary Biology; DOE/OSTI
Univ. of Colorado, Boulder, CO (United States). Cooperative Inst. for Research in Environmental Sciences
Univ. of Colorado, Boulder, CO (United States). Dept. of Ecology and Evolutionary Biology
Univ. of Colorado, Boulder, CO (United States). Dept. of Molecular, Cellular and Developmental Biology
Yale Univ., New Haven, CT (United States). School of Forestry and Environmental Studies
Univ. of Colorado, Boulder, CO (United States). Dept. of Chemistry and Biochemistry; Howard Hughes Medical Inst., Chevy Chase, MD (United States)

Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencingbased analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Colorado, Boulder, CO (United States); Yale Univ., New Haven, CT (United States)

Sponsoring Organization:: Andrew W Mellon Foundation; Howard Hughes Medical Institute; National Science Foundation (NSF); National Institutes of Health (NIH); USDA; USDOE

OSTI ID:: 1623755

Journal Information:: The ISME Journal, Journal Name: The ISME Journal Journal Issue: 5 Vol. 6; ISSN 1751-7362

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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TiO ₂ nanoparticles affect the bacterial community structure and Eisenia fetida (Savigny, 1826) in an arable soil Sánchez-López, Katia Berenice; De los Santos-Ramos, Francisco J.; Gómez-Acata, Elizabeth Selene PeerJ, Vol. 7 https://doi.org/10.7717/peerj.6939	journal	January 2019
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Anthropogenic nitrogen enrichment enhances soil carbon accumulation by impacting saprotrophs rather than ectomycorrhizal fungal activity Maaroufi, Nadia I.; Nordin, Annika; Palmqvist, Kristin Wiley https://doi.org/10.7892/boris.132568	text	January 2019

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