Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning
ABSTRACT Contamination from anthropogenic activities has significantly impacted Earth’s biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gen...
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American Society for Microbiology
2018
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oai:doaj.org-article:bf0ea4a03320438aad6de2a8fd8d2ea42021-11-15T15:53:26ZMicrobial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning10.1128/mBio.02435-172150-7511https://doaj.org/article/bf0ea4a03320438aad6de2a8fd8d2ea42018-03-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02435-17https://doaj.org/toc/2150-7511ABSTRACT Contamination from anthropogenic activities has significantly impacted Earth’s biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning. IMPORTANCE Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as uranium or nitrate increased. These key microbial functional genes could be used to successfully predict environmental contamination and ecosystem functioning. This study represents a significant advance in using functional gene markers to predict the spatial distribution of environmental contaminants and ecosystem functioning toward predictive microbial ecology, which is an ultimate goal of microbial ecology.Zhili HePing ZhangLinwei WuAndrea M. RochaQichao TuZhou ShiBo WuYujia QinJianjun WangQingyun YanDaniel CurtisDaliang NingJoy D. Van NostrandLiyou WuYunfeng YangDwayne A. EliasDavid B. WatsonMichael W. W. AdamsMatthew W. FieldsEric J. AlmTerry C. HazenPaul D. AdamsAdam P. ArkinJizhong ZhouAmerican Society for Microbiologyarticlegroundwater microbiomerandom forestecosystem functioningenvironmental contaminationmetagenomicsmicrobial functional geneMicrobiologyQR1-502ENmBio, Vol 9, Iss 1 (2018) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
groundwater microbiome random forest ecosystem functioning environmental contamination metagenomics microbial functional gene Microbiology QR1-502 |
| spellingShingle |
groundwater microbiome random forest ecosystem functioning environmental contamination metagenomics microbial functional gene Microbiology QR1-502 Zhili He Ping Zhang Linwei Wu Andrea M. Rocha Qichao Tu Zhou Shi Bo Wu Yujia Qin Jianjun Wang Qingyun Yan Daniel Curtis Daliang Ning Joy D. Van Nostrand Liyou Wu Yunfeng Yang Dwayne A. Elias David B. Watson Michael W. W. Adams Matthew W. Fields Eric J. Alm Terry C. Hazen Paul D. Adams Adam P. Arkin Jizhong Zhou Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning |
| description |
ABSTRACT Contamination from anthropogenic activities has significantly impacted Earth’s biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning. IMPORTANCE Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as uranium or nitrate increased. These key microbial functional genes could be used to successfully predict environmental contamination and ecosystem functioning. This study represents a significant advance in using functional gene markers to predict the spatial distribution of environmental contaminants and ecosystem functioning toward predictive microbial ecology, which is an ultimate goal of microbial ecology. |
| format |
article |
| author |
Zhili He Ping Zhang Linwei Wu Andrea M. Rocha Qichao Tu Zhou Shi Bo Wu Yujia Qin Jianjun Wang Qingyun Yan Daniel Curtis Daliang Ning Joy D. Van Nostrand Liyou Wu Yunfeng Yang Dwayne A. Elias David B. Watson Michael W. W. Adams Matthew W. Fields Eric J. Alm Terry C. Hazen Paul D. Adams Adam P. Arkin Jizhong Zhou |
| author_facet |
Zhili He Ping Zhang Linwei Wu Andrea M. Rocha Qichao Tu Zhou Shi Bo Wu Yujia Qin Jianjun Wang Qingyun Yan Daniel Curtis Daliang Ning Joy D. Van Nostrand Liyou Wu Yunfeng Yang Dwayne A. Elias David B. Watson Michael W. W. Adams Matthew W. Fields Eric J. Alm Terry C. Hazen Paul D. Adams Adam P. Arkin Jizhong Zhou |
| author_sort |
Zhili He |
| title |
Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning |
| title_short |
Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning |
| title_full |
Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning |
| title_fullStr |
Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning |
| title_full_unstemmed |
Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning |
| title_sort |
microbial functional gene diversity predicts groundwater contamination and ecosystem functioning |
| publisher |
American Society for Microbiology |
| publishDate |
2018 |
| url |
https://doaj.org/article/bf0ea4a03320438aad6de2a8fd8d2ea4 |
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