Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials

Sihang Yang, Qiaoshu Zheng, Mengting Yuan, Zhou Shi, Nona R. Chiariello, Kathryn M. Docherty, Shikui Dong, Christopher B. Field, Yunfu Gu, Jessica L Gutknecht, Bruce A. Hungate, Xavier Le Roux, Xingyu Ma, Audrey Niboyet, Tong Yuan, Jizhong Zhou, Yunfeng Yang

Research output: Contribution to journalArticle

Abstract

The continuously increasing concentration of atmospheric CO2 has considerably altered ecosystem functioning. However, few studies have examined the long-term (i.e. over a decade) effect of elevated CO2 on soil microbial communities. Using 16S rRNA gene amplicons and a GeoChip microarray, we investigated soil microbial communities from a Californian annual grassland after 14 years of experimentally elevated CO2 (275 ppm higher than ambient). Both taxonomic and functional gene compositions of the soil microbial community were modified by elevated CO2. There was decrease in relative abundance for taxa with higher ribosomal RNA operon (rrn) copy number under elevated CO2, which is a functional trait that responds positively to resource availability in culture. In contrast, taxa with lower rrn copy number were increased by elevated CO2. As a consequence, the abundance-weighted average rrn copy number of significantly changed OTUs declined from 2.27 at ambient CO2 to 2.01 at elevated CO2. The nitrogen (N) fixation gene nifH and the ammonium-oxidizing gene amoA significantly decreased under elevated CO2 by 12.6% and 6.1%, respectively. Concomitantly, nitrifying enzyme activity decreased by 48.3% under elevated CO2, albeit this change was not significant. There was also a substantial but insignificant decrease in available soil N, with both nitrate (NO3 ) (−27.4%) and ammonium (NH4 +) (−15.4%) declining. Further, a large number of microbial genes related to carbon (C) degradation were also affected by elevated CO2, whereas those related to C fixation remained largely unchanged. The overall changes in microbial communities and soil N pools induced by long-term elevated CO2 suggest constrained microbial N decomposition, thereby slowing the potential maximum growth rate of the microbial community.

LanguageEnglish (US)
Pages1474-1481
Number of pages8
JournalScience of the Total Environment
Volume652
DOIs
StatePublished - Feb 20 2019

Fingerprint

microbial community
Genes
grassland
Ribosomal RNA
Soils
gene
RNA
Chemical analysis
Ammonium Compounds
soil
fixation
ammonium
Nitrogen fixation
Enzyme activity
resource availability
Microarrays
Nitrates
Ecosystems
enzyme activity
relative abundance

Keywords

  • Annual grassland
  • Elevated CO
  • GeoChip
  • MiSeq sequencing
  • Microbial communities

Cite this

Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials. / Yang, Sihang; Zheng, Qiaoshu; Yuan, Mengting; Shi, Zhou; Chiariello, Nona R.; Docherty, Kathryn M.; Dong, Shikui; Field, Christopher B.; Gu, Yunfu; Gutknecht, Jessica L; Hungate, Bruce A.; Le Roux, Xavier; Ma, Xingyu; Niboyet, Audrey; Yuan, Tong; Zhou, Jizhong; Yang, Yunfeng.

In: Science of the Total Environment, Vol. 652, 20.02.2019, p. 1474-1481.

Research output: Contribution to journalArticle

Yang, S, Zheng, Q, Yuan, M, Shi, Z, Chiariello, NR, Docherty, KM, Dong, S, Field, CB, Gu, Y, Gutknecht, JL, Hungate, BA, Le Roux, X, Ma, X, Niboyet, A, Yuan, T, Zhou, J & Yang, Y 2019, 'Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials' Science of the Total Environment, vol. 652, pp. 1474-1481. https://doi.org/10.1016/j.scitotenv.2018.10.353
Yang, Sihang ; Zheng, Qiaoshu ; Yuan, Mengting ; Shi, Zhou ; Chiariello, Nona R. ; Docherty, Kathryn M. ; Dong, Shikui ; Field, Christopher B. ; Gu, Yunfu ; Gutknecht, Jessica L ; Hungate, Bruce A. ; Le Roux, Xavier ; Ma, Xingyu ; Niboyet, Audrey ; Yuan, Tong ; Zhou, Jizhong ; Yang, Yunfeng. / Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials. In: Science of the Total Environment. 2019 ; Vol. 652. pp. 1474-1481.
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AU - Zheng, Qiaoshu

AU - Yuan, Mengting

AU - Shi, Zhou

AU - Chiariello, Nona R.

AU - Docherty, Kathryn M.

AU - Dong, Shikui

AU - Field, Christopher B.

AU - Gu, Yunfu

AU - Gutknecht, Jessica L

AU - Hungate, Bruce A.

AU - Le Roux, Xavier

AU - Ma, Xingyu

AU - Niboyet, Audrey

AU - Yuan, Tong

AU - Zhou, Jizhong

AU - Yang, Yunfeng

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N2 - The continuously increasing concentration of atmospheric CO2 has considerably altered ecosystem functioning. However, few studies have examined the long-term (i.e. over a decade) effect of elevated CO2 on soil microbial communities. Using 16S rRNA gene amplicons and a GeoChip microarray, we investigated soil microbial communities from a Californian annual grassland after 14 years of experimentally elevated CO2 (275 ppm higher than ambient). Both taxonomic and functional gene compositions of the soil microbial community were modified by elevated CO2. There was decrease in relative abundance for taxa with higher ribosomal RNA operon (rrn) copy number under elevated CO2, which is a functional trait that responds positively to resource availability in culture. In contrast, taxa with lower rrn copy number were increased by elevated CO2. As a consequence, the abundance-weighted average rrn copy number of significantly changed OTUs declined from 2.27 at ambient CO2 to 2.01 at elevated CO2. The nitrogen (N) fixation gene nifH and the ammonium-oxidizing gene amoA significantly decreased under elevated CO2 by 12.6% and 6.1%, respectively. Concomitantly, nitrifying enzyme activity decreased by 48.3% under elevated CO2, albeit this change was not significant. There was also a substantial but insignificant decrease in available soil N, with both nitrate (NO3 −) (−27.4%) and ammonium (NH4 +) (−15.4%) declining. Further, a large number of microbial genes related to carbon (C) degradation were also affected by elevated CO2, whereas those related to C fixation remained largely unchanged. The overall changes in microbial communities and soil N pools induced by long-term elevated CO2 suggest constrained microbial N decomposition, thereby slowing the potential maximum growth rate of the microbial community.

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