skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Genetic correlation network prediction of forest soil microbial functional organization

Abstract

Soil ecological functions are largely determined by the activities of soil microorganisms, which, in turn, are regulated by relevant interactions between genes and their corresponding pathways. Therefore, the genetic network can theoretically elucidate the functional organization that supports complex microbial community functions, although this has not been previously attempted. We generated a genetic correlation network based on 5421 genes derived from metagenomes of forest soils, identifying 7191 positive and 123 negative correlation relationships. This network consisted of 27 clusters enriched with sets of genes within speci fi c functions, represented with corresponding cluster hubs. The clusters revealed a hierarchical architecture, re fl ecting the functional organization in the soil metagenomes. Positive correlations mapped functional associations, whereas negative correlations often mapped regulatory processes. The potential functions of uncharacterized genes were predicted based on the functions of located clusters. The global genetic correlation network highlights the functional organization in soil metagenomes and provides a resource for predicting gene functions. We anticipate that the genetic correlation network may be exploited to comprehensively decipher soil microbial commu

Authors:
 [1];  [1];  [1];  [1];  [1];  [2];  [1]; ORCiD logo [3];  [1]
  1. Zhejiang Univ., Hangzhou (China).; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou (China)
  2. Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Lemont, IL (United States)
  3. Katholieke Univ. Leuven, Heverlee (Belgium)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
National Natural Science Foundation of China (NNSFC); Fundamental Research Funds for the Central Universities; USDOE
OSTI Identifier:
1489668
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Volume: 12; Journal Issue: 10; Journal ID: ISSN 1751-7362
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES

Citation Formats

Ma, Bin, Zhao, Kankan, Lv, Xiaofei, Su, Weiqin, Dai, Zhongmin, Gilbert, Jack A., Brookes, Philip C., Faust, Karoline, and Xu, Jianming. Genetic correlation network prediction of forest soil microbial functional organization. United States: N. p., 2018. Web. doi:10.1038/s41396-018-0232-8.
Ma, Bin, Zhao, Kankan, Lv, Xiaofei, Su, Weiqin, Dai, Zhongmin, Gilbert, Jack A., Brookes, Philip C., Faust, Karoline, & Xu, Jianming. Genetic correlation network prediction of forest soil microbial functional organization. United States. doi:10.1038/s41396-018-0232-8.
Ma, Bin, Zhao, Kankan, Lv, Xiaofei, Su, Weiqin, Dai, Zhongmin, Gilbert, Jack A., Brookes, Philip C., Faust, Karoline, and Xu, Jianming. Wed . "Genetic correlation network prediction of forest soil microbial functional organization". United States. doi:10.1038/s41396-018-0232-8. https://www.osti.gov/servlets/purl/1489668.
@article{osti_1489668,
title = {Genetic correlation network prediction of forest soil microbial functional organization},
author = {Ma, Bin and Zhao, Kankan and Lv, Xiaofei and Su, Weiqin and Dai, Zhongmin and Gilbert, Jack A. and Brookes, Philip C. and Faust, Karoline and Xu, Jianming},
abstractNote = {Soil ecological functions are largely determined by the activities of soil microorganisms, which, in turn, are regulated by relevant interactions between genes and their corresponding pathways. Therefore, the genetic network can theoretically elucidate the functional organization that supports complex microbial community functions, although this has not been previously attempted. We generated a genetic correlation network based on 5421 genes derived from metagenomes of forest soils, identifying 7191 positive and 123 negative correlation relationships. This network consisted of 27 clusters enriched with sets of genes within speci fi c functions, represented with corresponding cluster hubs. The clusters revealed a hierarchical architecture, re fl ecting the functional organization in the soil metagenomes. Positive correlations mapped functional associations, whereas negative correlations often mapped regulatory processes. The potential functions of uncharacterized genes were predicted based on the functions of located clusters. The global genetic correlation network highlights the functional organization in soil metagenomes and provides a resource for predicting gene functions. We anticipate that the genetic correlation network may be exploited to comprehensively decipher soil microbial commu},
doi = {10.1038/s41396-018-0232-8},
journal = {The ISME Journal},
issn = {1751-7362},
number = 10,
volume = 12,
place = {United States},
year = {2018},
month = {7}
}

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

Save / Share:

Works referenced in this record:

Microbial diversity and function in soil: from genes to ecosystems
journal, June 2002