DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Divergent Responses of Forest Soil Microbial Communities under Elevated CO2 in Different Depths of Upper Soil Layers

Abstract

ABSTRACT Numerous studies have shown that the continuous increase of atmosphere CO2concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO2(eCO2) at different soil depth profiles in forest ecosystems. Here, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO2exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO2significantly shifted the compositions, including phylogenetic and functional gene structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO2at both soil depths, although the stimulation effect of eCO2on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO3-N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO2in forest soil microbial communities, which may provide new insight for a further understanding ofmore » forest ecosystem responses to global CO2increases. IMPORTANCEThe concentration of atmospheric carbon dioxide (CO2) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO2(eCO2) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO2on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO2at both soil depths. More functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO2at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm.« less

Authors:
 [1];  [2];  [3];  [4];  [2];  [2];  [5];  [6];  [7];  [8];  [9]
  1. Chinese Academy of Sciences (CAS), Beijing (China). CAS Key Lab. of Environmental Biotechnology. Research Center for Eco-Environmental Sciences; Liaoning Technical Univ., Fuxin (China). College of Environmental Science and Engineering
  2. Univ. of Oklahoma, Norman, OK (United States). Dept. of Microbiology and Plant Biology. Inst. for Environmental Genomics
  3. Chinese Academy of Sciences (CAS), Beijing (China). CAS Key Lab. of Environmental Biotechnology. Research Center for Eco-Environmental Sciences; Harbin Inst. of Technology (China). State Key Lab. of Urban Water Resource and Environment
  4. Central South Univ., Changsha (China). School of Minerals Processing and Bioengineering
  5. Chinese Academy of Sciences (CAS), Beijing (China). CAS Key Lab. of Environmental Biotechnology. Research Center for Eco-Environmental Sciences
  6. Liaoning Technical Univ., Fuxin (China). College of Environmental Science and Engineering
  7. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
  8. Univ. of Oklahoma, Norman, OK (United States). Dept. of Microbiology and Plant Biology. Inst. for Environmental Genomics; Tsinghua Univ., Beijing (China). State Key Joint Lab. of Environment Simulation and Pollution Control. School of Environment
  9. Chinese Academy of Sciences (CAS), Beijing (China). CAS Key Lab. of Environmental Biotechnology. Research Center for Eco-Environmental Sciences; Univ. of Oklahoma, Norman, OK (United States). Dept. of Microbiology and Plant Biology. Inst. for Environmental Genomics; Univ. of Chinese Academy of Sciences, Beijing (China). College of Resources and Environment
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Chinese Academy of Sciences (CAS), Beijing (China); Liaoning Technical Univ., Fuxin (China); Univ. of Oklahoma, Norman, OK (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE; Chinese Academy of Sciences (CAS); National Natural Science Foundation of China (NSFC); National Key Research and Development Program (China); China Postdoctoral Science Foundation; Natural Science Foundation of Liaoning Province of China
OSTI Identifier:
1423015
Alternate Identifier(s):
OSTI ID: 1479364
Grant/Contract Number:  
AC05-00OR22725; XDB15010302; 31540071; 2016YFC0500702; 2016M601145; 201602361
Resource Type:
Accepted Manuscript
Journal Name:
Applied and Environmental Microbiology
Additional Journal Information:
Journal Volume: 84; Journal Issue: 1; Journal ID: ISSN 0099-2240
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; microbial responses; elevated carbon dioxide; soil microbial community; free-air CO2 enrichment; functional genes; forest ecosystem

Citation Formats

Yu, Hao, He, Zhili, Wang, Aijie, Xie, Jianping, Wu, Liyou, Van Nostrand, Joy D., Jin, Decai, Shao, Zhimin, Schadt, Christopher W., Zhou, Jizhong, and Deng, Ye. Divergent Responses of Forest Soil Microbial Communities under Elevated CO2 in Different Depths of Upper Soil Layers. United States: N. p., 2017. Web. doi:10.1128/AEM.01694-17.
Yu, Hao, He, Zhili, Wang, Aijie, Xie, Jianping, Wu, Liyou, Van Nostrand, Joy D., Jin, Decai, Shao, Zhimin, Schadt, Christopher W., Zhou, Jizhong, & Deng, Ye. Divergent Responses of Forest Soil Microbial Communities under Elevated CO2 in Different Depths of Upper Soil Layers. United States. https://doi.org/10.1128/AEM.01694-17
Yu, Hao, He, Zhili, Wang, Aijie, Xie, Jianping, Wu, Liyou, Van Nostrand, Joy D., Jin, Decai, Shao, Zhimin, Schadt, Christopher W., Zhou, Jizhong, and Deng, Ye. Fri . "Divergent Responses of Forest Soil Microbial Communities under Elevated CO2 in Different Depths of Upper Soil Layers". United States. https://doi.org/10.1128/AEM.01694-17. https://www.osti.gov/servlets/purl/1423015.
@article{osti_1423015,
title = {Divergent Responses of Forest Soil Microbial Communities under Elevated CO2 in Different Depths of Upper Soil Layers},
author = {Yu, Hao and He, Zhili and Wang, Aijie and Xie, Jianping and Wu, Liyou and Van Nostrand, Joy D. and Jin, Decai and Shao, Zhimin and Schadt, Christopher W. and Zhou, Jizhong and Deng, Ye},
abstractNote = {ABSTRACT Numerous studies have shown that the continuous increase of atmosphere CO2concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO2(eCO2) at different soil depth profiles in forest ecosystems. Here, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO2exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO2significantly shifted the compositions, including phylogenetic and functional gene structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO2at both soil depths, although the stimulation effect of eCO2on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO3-N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO2in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO2increases. IMPORTANCEThe concentration of atmospheric carbon dioxide (CO2) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO2(eCO2) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO2on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO2at both soil depths. More functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO2at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm.},
doi = {10.1128/AEM.01694-17},
journal = {Applied and Environmental Microbiology},
number = 1,
volume = 84,
place = {United States},
year = {Fri Oct 27 00:00:00 EDT 2017},
month = {Fri Oct 27 00:00:00 EDT 2017}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 18 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

GeoChip-Based Analysis of Microbial Functional Gene Diversity in a Landfill Leachate-Contaminated Aquifer
journal, May 2012

  • Lu, Zhenmei; He, Zhili; Parisi, Victoria A.
  • Environmental Science & Technology, Vol. 46, Issue 11
  • DOI: 10.1021/es300478j

PROGRESSIVE NITROGEN LIMITATION OF ECOSYSTEM PROCESSES UNDER ELEVATED CO 2 IN A WARM-TEMPERATE FOREST
journal, January 2006

  • Finzi, Adrien C.; Moore, David J. P.; DeLucia, Evan H.
  • Ecology, Vol. 87, Issue 1
  • DOI: 10.1890/04-1748

Plant species richness, elevated CO 2 , and atmospheric nitrogen deposition alter soil microbial community composition and function
journal, May 2007


Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities
journal, October 2015

  • Deng, Ye; He, Zhili; Xiong, Jinbo
  • Global Change Biology, Vol. 22, Issue 2
  • DOI: 10.1111/gcb.13098

Carbon Flux and Growth in Mature Deciduous Forest Trees Exposed to Elevated CO2
journal, August 2005


Soil carbon and nitrogen cycling and storage throughout the soil profile in a sweetgum plantation after 11 years of CO2-enrichment
journal, March 2012


Simulated geologic carbon storage leak reduces bacterial richness and alters bacterial community composition in surface soil
journal, September 2014


Altered soil microbial community at elevated CO2 leads to loss of soil carbon
journal, March 2007

  • Carney, K. M.; Hungate, B. A.; Drake, B. G.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 12
  • DOI: 10.1073/pnas.0610045104

Elevated Carbon Dioxide Alters the Structure of Soil Microbial Communities
journal, February 2012

  • Deng, Ye; He, Zhili; Xu, Meiying
  • Applied and Environmental Microbiology, Vol. 78, Issue 8
  • DOI: 10.1128/AEM.06924-11

Stable-carbon isotopes and soil organic carbon in wheat under CO2 enrichment
journal, May 2001


ATMOSPHERIC CO 2 AND THE COMPOSITION AND FUNCTION OF SOIL MICROBIAL COMMUNITIES
journal, February 2000


Forest response to elevated CO2 is conserved across a broad range of productivity
journal, December 2005

  • Norby, R. J.; DeLucia, E. H.; Gielen, B.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 50
  • DOI: 10.1073/pnas.0509478102

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem
journal, March 2015

  • Xiong, Jinbo; He, Zhili; Shi, Shengjing
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep09316

Bacterial community structure and function change in association with colonizer plants during early primary succession in a glacier forefield
journal, March 2012


Empirical Evaluation of a New Method for Calculating Signal-to-Noise Ratio for Microarray Data Analysis
journal, March 2008

  • He, Z.; Zhou, J.
  • Applied and Environmental Microbiology, Vol. 74, Issue 10
  • DOI: 10.1128/AEM.02536-07

Elevated atmospheric carbon dioxide increases soil carbon
journal, December 2005


Ecological Lessons from Free-Air CO 2 Enrichment (FACE) Experiments
journal, December 2011


Effects of free-air CO2 enrichment (FACE) on CH4 emission from a rice paddy field
journal, October 2003


The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide
journal, July 2011


Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide: Soil bacterial response in six ecosystems
journal, January 2012


Microbial community functional structure in response to micro-aerobic conditions in sulfate-reducing sulfur-producing bioreactor
journal, May 2014


GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity
journal, April 2010


High Concentrations of the Antibiotic Spiramycin in Wastewater Lead to High Abundance of Ammonia-Oxidizing Archaea in Nitrifying Populations
journal, July 2015

  • Zhang, Yu; Tian, Zhe; Liu, Miaomiao
  • Environmental Science & Technology, Vol. 49, Issue 15
  • DOI: 10.1021/acs.est.5b01293

Changes in Fungal Community Composition in Response to Elevated Atmospheric CO2 and Nitrogen Fertilization Varies with Soil Horizon
journal, January 2013


Crude oil as a microbial seed bank with unexpected functional potentials
journal, November 2015

  • Cai, Man; Nie, Yong; Chi, Chang-Qiao
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep16057

Soil organisms and global climate change: Soil organisms and global climate change
journal, January 2011


Root turnover as determinant of the cycling of C, N, and P in a dry heathland ecosystem
journal, January 1992

  • Aerts, R.; Bakker, C.; De Caluwe, H.
  • Biogeochemistry, Vol. 15, Issue 3
  • DOI: 10.1007/BF00002935

NET PRIMARY PRODUCTIVITY OF A CO 2 -ENRICHED DECIDUOUS FOREST AND THE IMPLICATIONS FOR CARBON STORAGE
journal, October 2002


Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria
journal, February 2015


Digging deeper: fine-root responses to rising atmospheric CO2 concentration in forested ecosystems
journal, December 2009


Soil microbial activity in a Liquidambar plantation unresponsive to CO2-driven increases in primary production
journal, November 2003


Allometric determination of tree growth in a CO2-enriched sweetgum stand
journal, May 2001


Fine root dynamics in a loblolly pine forest are influenced by free-air-CO 2 -enrichment: a six-year-minirhizotron study
journal, March 2008


ELEVATED CO 2 STIMULATES NET ACCUMULATIONS OF CARBON AND NITROGEN IN LAND ECOSYSTEMS: A META-ANALYSIS
journal, January 2006

  • Luo, Yiqi; Hui, Dafeng; Zhang, Deqiang
  • Ecology, Vol. 87, Issue 1
  • DOI: 10.1890/04-1724

Fine root branch orders respond differentially to carbon source-sink manipulations in a longleaf pine forest
journal, June 2004


Nitrogen fertilization strategies in a short-rotation sycamore plantation
journal, March 1994

  • van Miegroet, Helga; Norby, Richard J.; Tschaplinski, Tim J.
  • Forest Ecology and Management, Vol. 64, Issue 1
  • DOI: 10.1016/0378-1127(94)90123-6

A possible plant-mediated feedback between elevated CO2, denitrification and the enhanced greenhouse effect
journal, January 1998


Microbial contributions to climate change through carbon cycle feedbacks
journal, July 2008

  • Bardgett, Richard D.; Freeman, Chris; Ostle, Nicholas J.
  • The ISME Journal, Vol. 2, Issue 8
  • DOI: 10.1038/ismej.2008.58

Assessment of 10 years of CO2 fumigation on soil microbial communities and function in a sweetgum plantation
journal, March 2009


GeoChip-based analysis of the microbial community functional structures in simultaneous desulfurization and denitrification process
journal, July 2014


Using landscape and depth gradients to decouple the impact of correlated environmental variables on soil microbial community composition
journal, February 2007


The shifts of sediment microbial community phylogenetic and functional structures during chromium (VI) reduction
journal, September 2016


Can a wheat cultivar with high transpiration efficiency maintain its yield advantage over a near-isogenic cultivar under elevated CO2?
journal, July 2012


Influence of depth and sampling time on bacterial community structure in an upland grassland soil
journal, February 2003


Plant species and functional group effects on abiotic and microbial soil properties and plant-soil feedback responses in two grasslands
journal, September 2006


Nitrogen limitation constrains sustainability of ecosystem response to CO2
journal, April 2006

  • Reich, Peter B.; Hobbie, Sarah E.; Lee, Tali
  • Nature, Vol. 440, Issue 7086
  • DOI: 10.1038/nature04486

CO2 enhancement of forest productivity constrained by limited nitrogen availability
journal, October 2010

  • Norby, R. J.; Warren, J. M.; Iversen, C. M.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 45
  • DOI: 10.1073/pnas.1006463107

Variation of Microbial Communities in Soil, Rhizosphere, and Rhizoplane in Response to Crop Species, Soil Type, and Crop Development
journal, December 2001


Bioenergy to save the world: Producing novel energy plants for growth on abandoned land
journal, May 2008

  • Schröder, Peter; Herzig, Rolf; Bojinov, Bojin
  • Environmental Science and Pollution Research, Vol. 15, Issue 3
  • DOI: 10.1065/espr2008.03.481

Soil Microbial Community Responses to Multiple Experimental Climate Change Drivers
journal, December 2009

  • Castro, H. F.; Classen, A. T.; Austin, E. E.
  • Applied and Environmental Microbiology, Vol. 76, Issue 4
  • DOI: 10.1128/AEM.02874-09

Elevated CO2 influences microbial carbon and nitrogen cycling
journal, January 2013


Abundance and composition response of wheat field soil bacterial and fungal communities to elevated CO2 and increased air temperature
journal, November 2016


Microbial diversity drives multifunctionality in terrestrial ecosystems
journal, January 2016

  • Delgado-Baquerizo, Manuel; Maestre, Fernando T.; Reich, Peter B.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms10541

Challenges in elevated CO2 experiments on forests
journal, January 2010


Assessing the Microbial Community and Functional Genes in a Vertical Soil Profile with Long-Term Arsenic Contamination
journal, November 2012


Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification
journal, July 2006

  • Wu, L.; Liu, X.; Schadt, C. W.
  • Applied and Environmental Microbiology, Vol. 72, Issue 7
  • DOI: 10.1128/AEM.02738-05

CO 2 enrichment increases carbon and nitrogen input from fine roots in a deciduous forest
journal, August 2008


Nitrous oxide emissions from grass swards during the eighth year of elevated atmospheric pCO2 (Swiss FACE)
journal, August 2003


The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems
journal, March 2008


Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystem
journal, October 2013