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Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes

With knowledge on microbial composition and diversity, investigation of within-community interactions is a further step to elucidate microbial ecological functions, such as the biodegradation of hazardous contaminants. In this work, microbial functional molecular ecological networks were studied in...

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Autores principales: Liang, Yuting, Zhao, Huihui, Deng, Ye, Zhou, Jizhong, Li, Guanghe, Sun, Bo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737900/
https://www.ncbi.nlm.nih.gov/pubmed/26870020
http://dx.doi.org/10.3389/fmicb.2016.00060
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author Liang, Yuting
Zhao, Huihui
Deng, Ye
Zhou, Jizhong
Li, Guanghe
Sun, Bo
author_facet Liang, Yuting
Zhao, Huihui
Deng, Ye
Zhou, Jizhong
Li, Guanghe
Sun, Bo
author_sort Liang, Yuting
collection PubMed
description With knowledge on microbial composition and diversity, investigation of within-community interactions is a further step to elucidate microbial ecological functions, such as the biodegradation of hazardous contaminants. In this work, microbial functional molecular ecological networks were studied in both contaminated and uncontaminated soils to determine the possible influences of oil contamination on microbial interactions and potential functions. Soil samples were obtained from an oil-exploring site located in South China, and the microbial functional genes were analyzed with GeoChip, a high-throughput functional microarray. By building random networks based on null model, we demonstrated that overall network structures and properties were significantly different between contaminated and uncontaminated soils (P < 0.001). Network connectivity, module numbers, and modularity were all reduced with contamination. Moreover, the topological roles of the genes (module hub and connectors) were altered with oil contamination. Subnetworks of genes involved in alkane and polycyclic aromatic hydrocarbon degradation were also constructed. Negative co-occurrence patterns prevailed among functional genes, thereby indicating probable competition relationships. The potential “keystone” genes, defined as either “hubs” or genes with highest connectivities in the network, were further identified. The network constructed in this study predicted the potential effects of anthropogenic contamination on microbial community co-occurrence interactions.
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spelling pubmed-47379002016-02-11 Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes Liang, Yuting Zhao, Huihui Deng, Ye Zhou, Jizhong Li, Guanghe Sun, Bo Front Microbiol Microbiology With knowledge on microbial composition and diversity, investigation of within-community interactions is a further step to elucidate microbial ecological functions, such as the biodegradation of hazardous contaminants. In this work, microbial functional molecular ecological networks were studied in both contaminated and uncontaminated soils to determine the possible influences of oil contamination on microbial interactions and potential functions. Soil samples were obtained from an oil-exploring site located in South China, and the microbial functional genes were analyzed with GeoChip, a high-throughput functional microarray. By building random networks based on null model, we demonstrated that overall network structures and properties were significantly different between contaminated and uncontaminated soils (P < 0.001). Network connectivity, module numbers, and modularity were all reduced with contamination. Moreover, the topological roles of the genes (module hub and connectors) were altered with oil contamination. Subnetworks of genes involved in alkane and polycyclic aromatic hydrocarbon degradation were also constructed. Negative co-occurrence patterns prevailed among functional genes, thereby indicating probable competition relationships. The potential “keystone” genes, defined as either “hubs” or genes with highest connectivities in the network, were further identified. The network constructed in this study predicted the potential effects of anthropogenic contamination on microbial community co-occurrence interactions. Frontiers Media S.A. 2016-02-03 /pmc/articles/PMC4737900/ /pubmed/26870020 http://dx.doi.org/10.3389/fmicb.2016.00060 Text en Copyright © 2016 Liang, Zhao, Deng, Zhou, Li and Sun. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Liang, Yuting
Zhao, Huihui
Deng, Ye
Zhou, Jizhong
Li, Guanghe
Sun, Bo
Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes
title Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes
title_full Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes
title_fullStr Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes
title_full_unstemmed Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes
title_short Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes
title_sort long-term oil contamination alters the molecular ecological networks of soil microbial functional genes
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737900/
https://www.ncbi.nlm.nih.gov/pubmed/26870020
http://dx.doi.org/10.3389/fmicb.2016.00060
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