Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

Christopher Penton, Derek St. Louis, Amanda Pham, James R. Cole, Liyou Wu, Yiqi Luo, E. A G Schuur, Jizhong Zhou, James M. Tiedje

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming is under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.

Original languageEnglish (US)
Article number746
JournalFrontiers in Microbiology
Volume6
Issue numberJUL
DOIs
StatePublished - 2015

Fingerprint

Soil
Climate
Ecosystem
Amino Acid Sequence
Nitrogen
Databases
Temperature
Grassland
Permafrost
Population
Genes

Keywords

  • Climate change
  • Denitrification
  • nifH
  • nirK
  • nirS
  • nosZ
  • Permafrost
  • Warming

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

Cite this

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils. / Penton, Christopher; St. Louis, Derek; Pham, Amanda; Cole, James R.; Wu, Liyou; Luo, Yiqi; Schuur, E. A G; Zhou, Jizhong; Tiedje, James M.

In: Frontiers in Microbiology, Vol. 6, No. JUL, 746, 2015.

Research output: Contribution to journalArticle

Penton, Christopher ; St. Louis, Derek ; Pham, Amanda ; Cole, James R. ; Wu, Liyou ; Luo, Yiqi ; Schuur, E. A G ; Zhou, Jizhong ; Tiedje, James M. / Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils. In: Frontiers in Microbiology. 2015 ; Vol. 6, No. JUL.
@article{4d3f23d9b6294e328098fe62e443e408,
title = "Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils",
abstract = "Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming is under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.",
keywords = "Climate change, Denitrification, nifH, nirK, nirS, nosZ, Permafrost, Warming",
author = "Christopher Penton and {St. Louis}, Derek and Amanda Pham and Cole, {James R.} and Liyou Wu and Yiqi Luo and Schuur, {E. A G} and Jizhong Zhou and Tiedje, {James M.}",
year = "2015",
doi = "10.3389/fmicb.2015.00746",
language = "English (US)",
volume = "6",
journal = "Frontiers in Microbiology",
issn = "1664-302X",
publisher = "Frontiers Media S. A.",
number = "JUL",

}

TY - JOUR

T1 - Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

AU - Penton, Christopher

AU - St. Louis, Derek

AU - Pham, Amanda

AU - Cole, James R.

AU - Wu, Liyou

AU - Luo, Yiqi

AU - Schuur, E. A G

AU - Zhou, Jizhong

AU - Tiedje, James M.

PY - 2015

Y1 - 2015

N2 - Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming is under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.

AB - Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming is under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.

KW - Climate change

KW - Denitrification

KW - nifH

KW - nirK

KW - nirS

KW - nosZ

KW - Permafrost

KW - Warming

UR - http://www.scopus.com/inward/record.url?scp=84938838176&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84938838176&partnerID=8YFLogxK

U2 - 10.3389/fmicb.2015.00746

DO - 10.3389/fmicb.2015.00746

M3 - Article

VL - 6

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

IS - JUL

M1 - 746

ER -