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

Zhili He; Yvette Piceno; Ye Deng; Meiying Xu; Zhenmei Lu; Todd Desantis; Gary Andersen; Sarah E Hobbie; Peter B Reich; Jizhong Zhou

doi:10.1038/ismej.2011.99

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

Zhili He, Yvette Piceno, Ye Deng, Meiying Xu, Zhenmei Lu, Todd Desantis, Gary Andersen, Sarah E Hobbie, Peter B Reich, Jizhong Zhou

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Abstract

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO ₂. Although the stimulating effects of elevated CO ₂ (eCO ₂) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO ₂ conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO ₂. PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO ₂, and such significant effects of eCO ₂ on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO ₂. Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO ₂. Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO ₂ and environmental factors shaping the microbial community structure.

Original language	English (US)
Pages (from-to)	259-272
Number of pages	14
Journal	ISME Journal
Volume	6
Issue number	2
DOIs	https://doi.org/10.1038/ismej.2011.99
State	Published - Feb 2012

Bibliographical note

Funding Information:
This work was supported by the United States Department of Agriculture (Project 2007-35319-18305) through the NSF-USDA Microbial Observatories Program; the National Science Foundation under DEB-0716587, DEB-0620652, DEB-0322057, DEB-0080382, DEB-0218039, DEB-0219104, DEB-0217631, DEB-0716587, LTREB DEB-0716587 and LTER DEB-9411972 projects; the DOE Program for Ecosystem Research; the Minnesota Environment and Natural Resources Trust Fund (DE-FG96ER2291) and the DOE under contract DE-AC02-05CH11231 through the University of California and Lawrence Berkeley National Laboratory; and by NIH Grant U01-HG004866.

Keywords

PhyloChip
elevated CO
microbial community structure
microbial composition
soil microbial community

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10.1038/ismej.2011.99

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title = "The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide",

abstract = "One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO 2. Although the stimulating effects of elevated CO 2 (eCO 2) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO 2 conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO 2. PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO 2, and such significant effects of eCO 2 on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO 2. Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO 2. Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO 2 and environmental factors shaping the microbial community structure.",

keywords = "PhyloChip, elevated CO, microbial community structure, microbial composition, soil microbial community",

author = "Zhili He and Yvette Piceno and Ye Deng and Meiying Xu and Zhenmei Lu and Todd Desantis and Gary Andersen and Hobbie, {Sarah E} and Reich, {Peter B} and Jizhong Zhou",

note = "Funding Information: This work was supported by the United States Department of Agriculture (Project 2007-35319-18305) through the NSF-USDA Microbial Observatories Program; the National Science Foundation under DEB-0716587, DEB-0620652, DEB-0322057, DEB-0080382, DEB-0218039, DEB-0219104, DEB-0217631, DEB-0716587, LTREB DEB-0716587 and LTER DEB-9411972 projects; the DOE Program for Ecosystem Research; the Minnesota Environment and Natural Resources Trust Fund (DE-FG96ER2291) and the DOE under contract DE-AC02-05CH11231 through the University of California and Lawrence Berkeley National Laboratory; and by NIH Grant U01-HG004866.",

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doi = "10.1038/ismej.2011.99",

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T1 - The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide

AU - He, Zhili

AU - Piceno, Yvette

AU - Deng, Ye

AU - Xu, Meiying

AU - Lu, Zhenmei

AU - Desantis, Todd

AU - Andersen, Gary

AU - Hobbie, Sarah E

AU - Reich, Peter B

AU - Zhou, Jizhong

N1 - Funding Information: This work was supported by the United States Department of Agriculture (Project 2007-35319-18305) through the NSF-USDA Microbial Observatories Program; the National Science Foundation under DEB-0716587, DEB-0620652, DEB-0322057, DEB-0080382, DEB-0218039, DEB-0219104, DEB-0217631, DEB-0716587, LTREB DEB-0716587 and LTER DEB-9411972 projects; the DOE Program for Ecosystem Research; the Minnesota Environment and Natural Resources Trust Fund (DE-FG96ER2291) and the DOE under contract DE-AC02-05CH11231 through the University of California and Lawrence Berkeley National Laboratory; and by NIH Grant U01-HG004866.

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N2 - One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO 2. Although the stimulating effects of elevated CO 2 (eCO 2) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO 2 conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO 2. PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO 2, and such significant effects of eCO 2 on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO 2. Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO 2. Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO 2 and environmental factors shaping the microbial community structure.

AB - One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO 2. Although the stimulating effects of elevated CO 2 (eCO 2) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO 2 conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO 2. PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO 2, and such significant effects of eCO 2 on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO 2. Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO 2. Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO 2 and environmental factors shaping the microbial community structure.

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

Abstract

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