1
|
Ning D, Wang Y, Fan Y, Wang J, Van Nostrand JD, Wu L, Zhang P, Curtis DJ, Tian R, Lui L, Hazen TC, Alm EJ, Fields MW, Poole F, Adams MWW, Chakraborty R, Stahl DA, Adams PD, Arkin AP, He Z, Zhou J. Environmental stress mediates groundwater microbial community assembly. Nat Microbiol 2024; 9:490-501. [PMID: 38212658 DOI: 10.1038/s41564-023-01573-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024]
Abstract
Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.
Collapse
Affiliation(s)
- Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Yajiao Wang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Yupeng Fan
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Jianjun Wang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Ping Zhang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Daniel J Curtis
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Renmao Tian
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Lauren Lui
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Terry C Hazen
- Department of Earth and Planetary Sciences, Bredesen Center, Department of Civil and Environmental Sciences, Center for Environmental Biotechnology, and Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Eric J Alm
- Department of Biological Engineering, Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew W Fields
- Center for Biofilm Engineering and Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Farris Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Paul D Adams
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Adam P Arkin
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
| |
Collapse
|
2
|
Park H, Joachimiak MP, Jungbluth SP, Yang Z, Riehl WJ, Canon RS, Arkin AP, Dehal PS. A bacterial sensor taxonomy across earth ecosystems for machine learning applications. mSystems 2024; 9:e0002623. [PMID: 38078749 PMCID: PMC10804942 DOI: 10.1128/msystems.00026-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 10/23/2023] [Indexed: 01/24/2024] Open
Abstract
Microbial communities have evolved to colonize all ecosystems of the planet, from the deep sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate environmental cues. This process is driven by signal transduction proteins such as histidine kinases, which use their sensing domains to bind or otherwise detect environmental cues and "transduce" signals to adjust internal processes. We hypothesized that an ecosystem's unique stimuli leave a sensor "fingerprint," able to identify and shed insight on ecosystem conditions. To test this, we collected 20,712 publicly available metagenomes from Host-associated, Environmental, and Engineered ecosystems across the globe. We extracted and clustered the collection's nearly 18M unique sensory domains into 113,712 similar groupings with MMseqs2. We built gradient-boosted decision tree machine learning models and found we could classify the ecosystem type (accuracy: 87%) and predict the levels of different physical parameters (R2 score: 83%) using the sensor cluster abundance as features. Feature importance enables identification of the most predictive sensors to differentiate between ecosystems which can lead to mechanistic interpretations if the sensor domains are well annotated. To demonstrate this, a machine learning model was trained to predict patient's disease state and used to identify domains related to oxygen sensing present in a healthy gut but missing in patients with abnormal conditions. Moreover, since 98.7% of identified sensor domains are uncharacterized, importance ranking can be used to prioritize sensors to determine what ecosystem function they may be sensing. Furthermore, these new predictive sensors can function as targets for novel sensor engineering with applications in biotechnology, ecosystem maintenance, and medicine.IMPORTANCEMicrobes infect, colonize, and proliferate due to their ability to sense and respond quickly to their surroundings. In this research, we extract the sensory proteins from a diverse range of environmental, engineered, and host-associated metagenomes. We trained machine learning classifiers using sensors as features such that it is possible to predict the ecosystem for a metagenome from its sensor profile. We use the optimized model's feature importance to identify the most impactful and predictive sensors in different environments. We next use the sensor profile from human gut metagenomes to classify their disease states and explore which sensors can explain differences between diseases. The sensors most predictive of environmental labels here, most of which correspond to uncharacterized proteins, are a useful starting point for the discovery of important environment signals and the development of possible diagnostic interventions.
Collapse
Affiliation(s)
- Helen Park
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- EPSRC/BBSRC Future Biomanufacturing Research Hub, EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marcin P. Joachimiak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sean P. Jungbluth
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ziming Yang
- Computational Science Initiative, Brookhaven National Laboratory, Upton, New York, USA
| | - William J. Riehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - R. Shane Canon
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Paramvir S. Dehal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| |
Collapse
|
3
|
Wu Q, Yu C, Liu Y, Xing P, Li H, Li B, Wan S, Wu QL. Microcystis blooms caused the decreasing richness of and interactions between free-living microbial functional genes in Lake Taihu, China. FEMS Microbiol Ecol 2024; 100:fiad166. [PMID: 38148131 PMCID: PMC10795575 DOI: 10.1093/femsec/fiad166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/17/2023] [Accepted: 12/23/2023] [Indexed: 12/28/2023] Open
Abstract
Microcystis blooms have a marked effect on microbial taxonomical diversity in eutrophic lakes, but their influence on the composition of microbial functional genes is still unclear. In this study, the free-living microbial functional genes (FMFG) composition was investigated in the period before Microcystis blooms (March) and during Microcystis blooms (July) using a comprehensive functional gene array (GeoChip 5.0). The composition and richness of FMFG in the water column was significantly different between these two periods. The FMFG in March was enriched in the functional categories of nitrogen, sulfur, and phosphorus cycling, whereas the FMFG in July was enriched in carbon cycling, organic remediation, and metal homeostasis. Molecular ecological network analysis further demonstrated fewer functional gene interactions and reduced complexity in July than in March. Module hubs of the March network were mediated by functional genes associated with carbon, nitrogen, sulfur, and phosphorus, whereas those in July by a metal homeostasis functional gene. We also observed stronger deterministic processes in the FMFG assembly in July than in March. Collectively, this study demonstrated that Microcystis blooms induced significant changes in FMFG composition and metabolic potential, and abundance-information, which can support the understanding and management of biogeochemical cycling in eutrophic lake ecosystems.
Collapse
Affiliation(s)
- Qiong Wu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chunyan Yu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yanru Liu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Huabing Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- The Fuxianhu Station of Deep Lake Research, Chinese Academy of Sciences, Chengjiang 652500, China
| | - Biao Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shiqiang Wan
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sino Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
4
|
Wang D, Li P, Mu D, Liu W, Chen Y, Fida M. Unveiling the biogeochemical mechanism of nitrate in the vadose zone-groundwater system: Insights from integrated microbiology, isotope techniques, and hydrogeochemistry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167481. [PMID: 37788773 DOI: 10.1016/j.scitotenv.2023.167481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/09/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023]
Abstract
Clarifying the biogeochemical mechanism of nitrate (NO3-) in the vadose zone-groundwater system, particularly in agricultural contexts, is crucial for mitigating groundwater NO3- pollution. However, comprehensive studies on the impacts of changes in chemical indicators and microbial communities on NO3- are still lacking. This paper aims to address this gap by employing hydrogeochemistry, stable isotopes, and microbial techniques to assess the NO3- biogeochemical processes in the vadose zone-groundwater system. The findings suggested that NO3- in upper soil layers was primarily influenced by plant root absorption, assimilation, and nitrification processes. The oxygen contents gradually decreased with the nitrification process, resulting in the occurrence of the denitrification. However, denitrification predominantly occurred in the 60-80 cm soil layer in the study area. The limited thickness of the denitrification layer results in less NO3- consumption, leading to increased NO3- leaching into groundwater. Hydrochemical and isotopic characteristics further indicated that groundwater NO3- concentrations were mainly controlled by nitrification, followed by denitrification and mixing processes. The 16S rRNA sequencing analysis revealed great influences of soil sampling depths and groundwater NO3- concentrations on the microbial community structure. Additionally, the PICRUSt2-based prediction results demonstrated a stronger potential for dissimilatory reduction of NO3- to ammonium (DNRA) in both soil and groundwater compared to the other processes, potentially due to the widespread presence of the nrfH functional genes. However, the chemical indicators and isotopes used in this study did not support the occurrence of DNRA process in the vadose zone-groundwater system. This finding highlights the importance of an integrated approach combining microbiological, isotopic, and hydrogeochemical data to comprehensive understanding biogeochemical processes. The study developed a conceptual model elucidating the NO3- biogeochemical processes in the vadose zone-groundwater system within an agricultural area, contributing to enhanced comprehension and advancement of sustainable management practices for groundwater nitrogen.
Collapse
Affiliation(s)
- Dan Wang
- School of Water and Environment, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China; Key Laboratory of Eco-hydrology and Water Security in Arid and Semi-arid Regions of the Ministry of Water Resources, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China
| | - Peiyue Li
- School of Water and Environment, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China; Key Laboratory of Eco-hydrology and Water Security in Arid and Semi-arid Regions of the Ministry of Water Resources, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China.
| | - Dawei Mu
- School of Water and Environment, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China; Key Laboratory of Eco-hydrology and Water Security in Arid and Semi-arid Regions of the Ministry of Water Resources, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China
| | - Weichao Liu
- School of Water and Environment, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China; Key Laboratory of Eco-hydrology and Water Security in Arid and Semi-arid Regions of the Ministry of Water Resources, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China
| | - Yinfu Chen
- School of Water and Environment, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China; Key Laboratory of Eco-hydrology and Water Security in Arid and Semi-arid Regions of the Ministry of Water Resources, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China
| | - Misbah Fida
- School of Water and Environment, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China; Key Laboratory of Eco-hydrology and Water Security in Arid and Semi-arid Regions of the Ministry of Water Resources, Chang'an University, No. 126 Yanta Road, Xi'an 710054, Shaanxi, China
| |
Collapse
|
5
|
Xiong R, Li Y, Gao X, Li N, Lou R, Saeed L, Huang J. Effects of a long-term operation wetland for wastewater treatment on the spatial pattern and function of microbial communities in groundwater. ENVIRONMENTAL RESEARCH 2023; 228:115929. [PMID: 37072080 DOI: 10.1016/j.envres.2023.115929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 05/16/2023]
Abstract
Constructed wetlands have been used globally for wastewater treatment owing to low energy inputs and operating costs. However, the impact of their long-term operation on groundwater microbial communities is still unclear. This study aims to investigate the effects and further reveal the linkage between a large-scale surface flow constructed wetland (in operation for 14 years) and groundwater. Changes in the characteristics of groundwater microbial communities and their potential influencing factors were studied based on hydrochemical analysis, Illumina MiSeq sequencing, and multivariate statistical analysis methods. Results show that the long-term operation wetland significantly elevated groundwater nutrient levels and increased the risk of ammonia nitrogen pollution compared to background values. An apparent heterogeneity of microbial communities exhibited in the vertical direction and a similarity in the horizontal direction. Wetland operations substantially altered the structure of microbial communities at 3, 5, and 12 m depths, particularly a reduced abundance of denitrifying and chemoheterotrophic functional genera. The formation and evolution of groundwater microbial community structure mainly subjected to the contributions of dissolved oxygen (33.70%), total nitrogen (21.40%), dissolved organic carbon (11.09%), and pH (10.60%) variations resulted from the wetland operation and largely differed in depths. A combined effect of these factors on the groundwater should be concerned for such a long-term running wetland system. This study provides a new insight into the responses of groundwater microbial community structure driving by wetland operation and a better understanding of corresponding variation of microbial-based geochemical processes.
Collapse
Affiliation(s)
- Rongwei Xiong
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yong Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China; National Engineering Research Center of Water Resources Efficient Utilization and Engineering Safety, Hohai University, Nanjing, 210098, PR China.
| | - Xiufang Gao
- College of Resources and Environment, Yangtze University, Wuhan, 430100, PR China; Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou, 434025, PR China
| | - Na Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Ruitao Lou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Laraib Saeed
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Jinquan Huang
- Department of Soil and Water Conservation, Yangtze River Scientific Research Institute, Wuhan, 430010, PR China
| |
Collapse
|
6
|
Zhang LZ, He W, Huang FY, He W, Zhou P, Chen C, Rensing C, Brandt KK, He J, Liu F, Zhao Y, Guo H. Response of microbial taxonomic and nitrogen functional attributes to elevated nitrate in suburban groundwater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 874:162524. [PMID: 36868285 DOI: 10.1016/j.scitotenv.2023.162524] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/05/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Anthropogenic nitrogen (N) input has led to elevated levels of nitrate nitrogen (NO3--N) in the groundwater. However, insights into the responses of the microbial community and its N metabolic functionality to elevated NO3--N in suburban groundwater are still limited. Here, we explored the microbial taxonomy, N metabolic attributes, and their responses to NO3--N pollution in groundwaters from Chaobai River catchment (CR) and Huai River catchment (HR) in Beijing, China. Results showed that average NO3--N and NH4+-N concentrations in CR groundwater were 1.7 and 3.0 folds of those in HR. NO3--N was the dominant nitrogen specie both in HR and CR groundwater (over 80 %). Significantly different structures and compositions of the microbial communities and N cycling gene profiles were found between CR groundwater and HR groundwater (p < 0.05), with CR groundwater harboring significantly lower microbial richness and abundance of N metabolic genes. However, denitrification was the dominant microbial N cycling process in both CR and HR groundwater. Strong associations among NO3--N, NH4+-N, microbial taxonomic, and N functional attributes were found (p < 0.05), suggesting denitrifiers and Candidatus_Brocadia might serve as potential featured biomarkers for the elevated NO3--N and NH4+-N concentration in groundwater. Path analysis further revealed the significant effect of NO3--N on the overall microbial N functionality and microbial denitrification (p < 0.05). Collectively, our results provide field evidence that elevated levels of NO3--N and NH4+-N under different hydrogeologic conditions had a significant effect on the microbial taxonomic and N functional attributes in groundwater, with potential implications for improving sustainable N management and risk assessment of groundwater.
Collapse
Affiliation(s)
- Ling-Zhi Zhang
- School of Water Resources and Environment & Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences (Beijing), Beijing 100083, China
| | - Wei He
- Beijing Municipal Research Institute of Eco-Environmental Protection, Beijing 100037, China
| | - Fu-Yi Huang
- Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Wei He
- School of Water Resources and Environment & Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences (Beijing), Beijing 100083, China
| | - Pengpeng Zhou
- School of Water Resources and Environment & Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences (Beijing), Beijing 100083, China
| | - Cuibai Chen
- School of Water Resources and Environment & Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences (Beijing), Beijing 100083, China
| | - Christopher Rensing
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kristian Koefoed Brandt
- Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Frederiksberg 1871, Denmark; Sino-Danish Center for Education and Research, Beijing, China
| | - Jiangtao He
- School of Water Resources and Environment & Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences (Beijing), Beijing 100083, China
| | - Fei Liu
- School of Water Resources and Environment & Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences (Beijing), Beijing 100083, China
| | - Yi Zhao
- School of Water Resources and Environment & Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences (Beijing), Beijing 100083, China.
| | - Huaming Guo
- School of Water Resources and Environment & Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences (Beijing), Beijing 100083, China.
| |
Collapse
|
7
|
Zhang B, Li ZL, Bai CH, Liu JL, Nan J, Cao D, Li LW. Characteristics of groundwater microbial communities' structure under the impact of elevated nitrate concentrations in north China plain. ENVIRONMENTAL RESEARCH 2023; 218:115003. [PMID: 36495969 DOI: 10.1016/j.envres.2022.115003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/23/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
In groundwater environments, the interaction between microbial communities and the hydrogeochemical parameters have been investigated extensively in the past years. However, little is known whether the maximum contamination level (MCL) is a threshold value that dictates the microbial composition. In this study, we analyzed 10 groundwater samples for their nitrate, nitrite, COD and sulfate concentrations, and characterized their microbial compositions using 16 S rRNA based high-throughput sequencing methods. All the 10 samples had oxygen demands higher than the corresponding MCL of China (10 mg L-1); moreover, 4 out of 10 samples also had nitrate concentrations higher than the corresponding MCL, which indicated that the groundwater quality was negatively impacted by anthropogenic activities. Comparing the microbial composition of groundwater that had higher-than-MCL nitrate concentrations to those that had lower-than-MCL nitrate concentrations, no significant differences were detected in communities' richness and diversity. However, the non-metric multi-dimensional analysis suggested that the 4 groundwater samples whose nitrate concentration exceed MCL are distinctly different from those of the rest 6 samples, indicating that MCL does have a significant impact on microbial structures. Pearson's correlation analysis suggested that none of the four analyzed hydrochemical parameters had significant impact on microbial communities' richness and diversity; however, at the genus level, the correlation results suggested that JG30-KM-CM45, Sphingomonas and Rhodococcus are closely correlated with nitrate concentration. The findings of this study deepened our understanding with respect to the relationships between the environmental quality indices and the microbial compositions of groundwater.
Collapse
Affiliation(s)
- Bo Zhang
- Key Lab of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, No. 18 Shuangqing Road, Haidian District, Beijing, 10086, China.
| | - Zhi-Ling Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Cai-Hua Bai
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Jing-Lan Liu
- Tianjin Geological Research and Marine Geology Center, Tianjin, 300381, China
| | - Jun Nan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Di Cao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Li-Wei Li
- Tianjin Geological Research and Marine Geology Center, Tianjin, 300381, China.
| |
Collapse
|
8
|
Bärenstrauch M, Vanhove AS, Allégra S, Peuble S, Gallice F, Paran F, Lavastre V, Girardot F. Microbial diversity and geochemistry of groundwater impacted by steel slag leachates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:156987. [PMID: 35772557 DOI: 10.1016/j.scitotenv.2022.156987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
To understand long-term impacts of steel slag material on aquifer geochemistry and microbial communities, we conducted four sampling campaigns in the Gier alluvial groundwater (Loire, France). In its northern part, the aquifer flows under a 200,000 m3 steel slag exhibiting high levels of chromium and molybdenum. Geochemical analyses of the water table revealed the existence of water masses with different chemical signatures. They allowed us to identify an area particularly contaminated by leachates from the slag heap, whatever the sampling period. Water samples from this area were compared to non-contaminated samples, with geochemical characteristics similar to the river samples. To follow changes in microbial communities, the V3-V4 region of 16 s rRNA gene was sequenced. Overall, we observed lower diversity indices in contaminated areas, with higher relative abundances of Verrucomicrobiota and Myxococcota phyla, while several Proteobacteria orders exhibited lower relative abundances. In particular, one single genus among the Verrucomicrobiota, Candidatus Omnitrophus, represented up to 36 % of total taxon abundance in areas affected by steel slag leachates. A large proportion of taxa identified in groundwater were also detected in the upstream river, indicating strong river-groundwater interactions. Our findings pave the way for future research work on C. Omnitrophus remediation capacities.
Collapse
Affiliation(s)
- Margot Bärenstrauch
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France
| | - Audrey S Vanhove
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France
| | - Séverine Allégra
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France
| | - Steve Peuble
- Mines Saint-Étienne, Centre "Sciences des Processus Industriels et Naturels" (SPIN), Département "Procédés pour l'Environnement et les Géo-ressources" (PEG), UMR 5600 EVS, UMR 5307 LGF, F-42023 Saint-Etienne, France
| | - Frédéric Gallice
- Mines Saint-Étienne, Centre "Sciences des Processus Industriels et Naturels" (SPIN), Département "Procédés pour l'Environnement et les Géo-ressources" (PEG), UMR 5600 EVS, UMR 5307 LGF, F-42023 Saint-Etienne, France
| | - Frédéric Paran
- Mines Saint-Étienne, Centre "Sciences des Processus Industriels et Naturels" (SPIN), Département "Procédés pour l'Environnement et les Géo-ressources" (PEG), UMR 5600 EVS, UMR 5307 LGF, F-42023 Saint-Etienne, France
| | - Véronique Lavastre
- Université de Lyon, Université Jean Monnet Saint-Etienne, Laboratoire de Géologie de Lyon - Terre Planètes Environnement LGL-TPE, CNRS -UMR 5276, F-42023 Saint-Etienne, France
| | - Françoise Girardot
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France.
| |
Collapse
|
9
|
Hassan S, Sabreena, Khurshid Z, Bhat SA, Kumar V, Ameen F, Ganai BA. Marine Bacteria and Omic Approaches: A Novel and Potential Repository for Bioremediation Assessment. J Appl Microbiol 2022; 133:2299-2313. [PMID: 35818751 DOI: 10.1111/jam.15711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/15/2022] [Accepted: 07/01/2022] [Indexed: 10/17/2022]
Abstract
Marine environments accommodating diverse assortments of life constitute a great pool of differentiated natural resources. The cumulative need to remedy unpropitious effects of anthropogenic activities on estuaries, and coastal marine ecosystems has propelled the development of effective bioremediation strategies. Marine bacteria producing biosurfactants are promising agents for bio-remediating oil pollution in marine environments, making them prospective candidates for enhancing oil recovery. Molecular omics technologies are considered an emerging field of research in ecological and diversity assessment owing to their utility in environmental surveillance and bioremediation of polluted sites. A thorough literature review was undertaken to understand the applicability of different omic techniques employed for bioremediation assessment using marine bacteria. This review further establishes that for bioremediation of environmental pollutants (i.e., heavy metals, hydrocarbons, xenobiotic and numerous recalcitrant compounds), organisms isolated from marine environments can be better utilized for their removal. The literature survey shows that omics approaches can provide exemplary knowledge about microbial communities and their role in the bioremediation of environmental pollutants. This review centres on applications of marine bacteria in enhanced bioremediation, utilizing the omics approaches that can be a vital biological contrivance in environmental monitoring to tackle environmental degradation. The paper aims to identify the gaps in investigations involving marine bacteria to help researchers, ecologists, and decision-makers to develop a holistic understanding regarding their utility in bioremediation assessment.
Collapse
Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, India
| | - Sabreena
- Department of Environmental Science, University of Kashmir, India
| | | | | | - Vineet Kumar
- Department of Botany, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, Chhattisgarh-495009, India
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | |
Collapse
|
10
|
Aldas-Vargas A, Hauptfeld E, Hermes GDA, Atashgahi S, Smidt H, Rijnaarts HHM, Sutton NB. Selective pressure on microbial communities in a drinking water aquifer - Geochemical parameters vs. micropollutants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 299:118807. [PMID: 35007672 DOI: 10.1016/j.envpol.2022.118807] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/26/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Groundwater quality is crucial for drinking water production, but groundwater resources are increasingly threatened by contamination with pesticides. As pesticides often occur at micropollutant concentrations, they are unattractive carbon sources for microorganisms and typically remain recalcitrant. Exploring microbial communities in aquifers used for drinking water production is an essential first step towards understanding the fate of micropollutants in groundwater. In this study, we investigated the interaction between groundwater geochemistry, pesticide presence, and microbial communities in an aquifer used for drinking water production. Two groundwater monitoring wells in The Netherlands were sampled in 2014, 2015, and 2016. In both wells, water was sampled from five discrete depths ranging from 13 to 54 m and was analyzed for geochemical parameters, pesticide concentrations and microbial community composition using 16S rRNA gene sequencing and qPCR. Groundwater geochemistry was stable throughout the study period and pesticides were heterogeneously distributed at low concentrations (μg L-1 range). Microbial community composition was also stable throughout the sampling period. Integration of a unique dataset of chemical and microbial data showed that geochemical parameters and to a lesser extent pesticides exerted selective pressure on microbial communities. Microbial communities in both wells showed similar composition in the deeper aquifer, where pumping results in horizontal flow. This study provides insight into groundwater parameters that shape microbial community composition. This information can contribute to the future implementation of remediation technologies to guarantee safe drinking water production.
Collapse
Affiliation(s)
- Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700, EV Wageningen, the Netherlands
| | - Ernestina Hauptfeld
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700, EV Wageningen, the Netherlands; Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700, EH Wageningen, the Netherlands
| | - Gerben D A Hermes
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700, EH Wageningen, the Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700, EH Wageningen, the Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700, EH Wageningen, the Netherlands
| | - Huub H M Rijnaarts
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700, EV Wageningen, the Netherlands
| | - Nora B Sutton
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700, EV Wageningen, the Netherlands.
| |
Collapse
|
11
|
Miri S, Davoodi SM, Robert T, Brar SK, Martel R, Rouissi T. Enzymatic biodegradation of highly p-xylene contaminated soil using cold-active enzymes: A soil column study. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127099. [PMID: 34523486 DOI: 10.1016/j.jhazmat.2021.127099] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
Enzymatic bioremediation is a sustainable and environment-friendly method for the clean-up of contaminated soil and water. In the present study, enzymatic bioremediation was designed using cold-active enzymes (psychrozymes) which catalyze oxidation steps of p-xylene biodegradation in highly contaminated soil (initial concentration of 13,000 mg/kg). The enzymes were obtained via co-culture of two psychrophilic Pseudomonas strains and characterized by kinetic studies and tandem LC-MS/MS. To mimic in situ application of enzyme mixture, bioremediation of p-xylene contaminated soil was carried out in soil column (140 mL) tests with the injection (3 pore volume) of different concentrations of enzyme cocktails (X, X/5, and X/10). Enzyme cocktail in X concentration contained about 10 U/mL of xylene monooxygenase (XMO) and 20 U/mL of catechol 2, 3 dioxygenases (C2,3D). X/5 and X/10 correspond to 5x and 10x dilution of enzyme cocktail respectively. The results showed that around 92-94% p-xylene removal was achieved in the treated soil column with enzyme concentration X, X/5 after second enzyme injection. While the p-xylene removal rate obtained by X/10 concentration of enzyme was less than 30% and near to untreated soil column (22.2%). The analysis of microbial diversity and biotoxicity assay (root elongation and seed germination) confirmed the advantage of using enzymes as a green and environmentally friendly approach for decontamination of pollutants with minimal or even positive effects on microbial community and also enrichment of soil after treatment.
Collapse
Affiliation(s)
- Saba Miri
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Ontario M3J 1P3, Canada; INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec G1K 9A9, Canada.
| | - Seyyed Mohammadreza Davoodi
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Ontario M3J 1P3, Canada; INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec G1K 9A9, Canada.
| | - Thomas Robert
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec G1K 9A9, Canada.
| | - Satinder Kaur Brar
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Ontario M3J 1P3, Canada; INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec G1K 9A9, Canada.
| | - Richard Martel
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec G1K 9A9, Canada.
| | - Tarek Rouissi
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec G1K 9A9, Canada.
| |
Collapse
|
12
|
Chandler L, Harford AJ, Hose GC, Humphrey CL, Chariton A, Greenfield P, Davis J. Saline mine-water alters the structure and function of prokaryote communities in shallow groundwater below a tropical stream. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 284:117318. [PMID: 34052601 DOI: 10.1016/j.envpol.2021.117318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Bacteria and archaea (prokaryotes) are vital components for maintaining healthy function of groundwater ecosystems. The prokaryotic community composition and associated putative functional processes were examined in a shallow sandy aquifer in a wet-dry tropical environment. The aquifer had a contaminated gradient of saline mine-water, which primarily consisted of elevated magnesium (Mg2+) and sulfate (SO42-), although other major ions and trace metals were also present. Groundwaters were sampled from piezometers, approximately 2 m in depth, located in the creek channel upstream and downstream of the mine-water influence. Sampling occurred during the dry-season when only subsurface water flow was present. Next generation sequencing was used to analyse the prokaryote assemblages using 16S rDNA and metabolic functions were predicted with FAPROTAX. Significant changes in community composition and functional processes were observed with exposure to mine-waters. Communities in the exposed sites had significantly lower relative abundance of methanotrophs such as Methylococcaceae and methanogens (Methanobacteriaceae), but higher abundance in Nitrososphaeraceae, associated with nitrification, indicating potentially important changes in the biogeochemistry of the exposed sites. The changes were most strongly correlated with concentrations of SO42-, Mg2+ and Na+. This knowledge allows an assessment of the risk of mine-water contamination to groundwater ecosystem function and aids mine-water management.
Collapse
Affiliation(s)
- Lisa Chandler
- Research Institute for the Environment and Livelihoods, College of Engineering, IT & Environment, Charles Darwin University, Darwin, Northern Territory, Australia; Supervising Scientist Branch, Department of Agriculture, Water and the Environment, Darwin, Northern Territory, Australia.
| | - Andrew J Harford
- Supervising Scientist Branch, Department of Agriculture, Water and the Environment, Darwin, Northern Territory, Australia
| | - Grant C Hose
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Chris L Humphrey
- Supervising Scientist Branch, Department of Agriculture, Water and the Environment, Darwin, Northern Territory, Australia
| | - Anthony Chariton
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Paul Greenfield
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Jenny Davis
- Research Institute for the Environment and Livelihoods, College of Engineering, IT & Environment, Charles Darwin University, Darwin, Northern Territory, Australia
| |
Collapse
|
13
|
Dong Y, Sanford RA, Connor L, Chee-Sanford J, Wimmer BT, Iranmanesh A, Shi L, Krapac IG, Locke RA, Shao H. Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL. WATER RESEARCH 2021; 202:117431. [PMID: 34320445 DOI: 10.1016/j.watres.2021.117431] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput FluidigmTM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N2 fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. This research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.
Collapse
Affiliation(s)
- Yiran Dong
- School of Environmental Studies, China University of Geosciences, Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Robert A Sanford
- Department of Geology, University of Illinois Urbana-Champaign, USA
| | | | | | | | | | - Liang Shi
- School of Environmental Studies, China University of Geosciences, Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | | | | | | |
Collapse
|
14
|
Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
Collapse
Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
| |
Collapse
|
15
|
Lui LM, Majumder ELW, Smith HJ, Carlson HK, von Netzer F, Fields MW, Stahl DA, Zhou J, Hazen TC, Baliga NS, Adams PD, Arkin AP. Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. Front Microbiol 2021; 12:642422. [PMID: 33841364 PMCID: PMC8024649 DOI: 10.3389/fmicb.2021.642422] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.
Collapse
Affiliation(s)
- Lauren M. Lui
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Erica L.-W. Majumder
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Heidi J. Smith
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Hans K. Carlson
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Frederick von Netzer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Matthew W. Fields
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology & Plant Biology, School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, United States
| | - Terry C. Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Paul D. Adams
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Adam P. Arkin
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| |
Collapse
|
16
|
Gao J, Liu M, Shi S, Liu Y, Duan Y, Lv X, Bohu T, Li Y, Hu Y, Wang N, Wang Q, Zhuang G, Zhuang X. Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions. Microorganisms 2021; 9:microorganisms9020211. [PMID: 33498486 PMCID: PMC7909544 DOI: 10.3390/microorganisms9020211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 12/31/2020] [Accepted: 01/14/2021] [Indexed: 11/16/2022] Open
Abstract
In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China-the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.
Collapse
Affiliation(s)
- Jie Gao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Y.L.); (N.W.); (Q.W.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Miao Liu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (M.L.); (Y.L.); (Y.H.)
| | - Sixue Shi
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China;
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (M.L.); (Y.L.); (Y.H.)
| | - Ying Liu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Y.L.); (N.W.); (Q.W.)
| | - Yu Duan
- Beijing Business Department, Beijing Enterprises Water Group Limited, Beijing 100124, China;
| | - Xianguo Lv
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China;
| | - Tsing Bohu
- CSIRO Mineral Resources, 26 Dick Perry Avenue, Kensington, WA 6151, Australia;
| | - Yuehui Li
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (M.L.); (Y.L.); (Y.H.)
| | - Yuanman Hu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (M.L.); (Y.L.); (Y.H.)
| | - Na Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Y.L.); (N.W.); (Q.W.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Qiuying Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Y.L.); (N.W.); (Q.W.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Guoqiang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Y.L.); (N.W.); (Q.W.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China;
- Correspondence: (G.Z.); (X.Z.); Tel.: +86-10-62849613 (G.Z.); +86-10-62849193 (X.Z.)
| | - Xuliang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Y.L.); (N.W.); (Q.W.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China;
- Correspondence: (G.Z.); (X.Z.); Tel.: +86-10-62849613 (G.Z.); +86-10-62849193 (X.Z.)
| |
Collapse
|
17
|
Testing Different Membrane Filters for 16S rRNA Gene-Based Metabarcoding in Karstic Springs. WATER 2020. [DOI: 10.3390/w12123400] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Introduction: Karstic springs are used worldwide by rural communities as sources of fresh water for humans and livestock. In Romania, one-third of the population has no direct access to a public water supply. The present study is part of a country-wide project to develop simple, quick and cheap methods for seasonal environmental and microbiological monitoring of karstic springs used as drinking water by rural populations. Critical steps for monitoring workflow consist of evaluating water quality and selecting suitable membrane filters to efficiently capture environmental DNA for further microbial diversity estimation using 16S rRNA gene-based metabarcoding. Methods: Several commercial membrane filters of different compositions and pore sizes were tested on the water sampled from three karstic springs in Romania, followed by water chemistry and whole community 16S rRNA gene-based metabarcoding analysis. Results: We found that different types of applied membrane filters provide varying recovery in diversity and abundance of both overall and pathogenic bacteria. Conclusions: The result of the experiment with different filters shows that mixed cellulose ester, cellulose acetate, and nitrate membranes of 0.20 and 0.22 µm are the best for amplicon-based metabarcoding monitoring of karst springs.
Collapse
|
18
|
He Z, Deng Y, Xu M, Li J, Liang J, Xiong J, Yu H, Wu B, Wu L, Xue K, Shi S, Carrillo Y, Van Nostrand JD, Hobbie SE, Reich PB, Schadt CW, Kent AD, Pendall E, Wallenstein M, Luo Y, Yan Q, Zhou J. Microbial functional genes commonly respond to elevated carbon dioxide. ENVIRONMENT INTERNATIONAL 2020; 144:106068. [PMID: 32871382 DOI: 10.1016/j.envint.2020.106068] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Atmospheric CO2 concentration is increasing, largely due to anthropogenic activities. Previous studies of individual free-air CO2 enrichment (FACE) experimental sites have shown significant impacts of elevated CO2 (eCO2) on soil microbial communities; however, no common microbial response patterns have yet emerged, challenging our ability to predict ecosystem functioning and sustainability in the future eCO2 environment. Here we analyzed 66 soil microbial communities from five FACE sites, and showed common microbial response patterns to eCO2, especially for key functional genes involved in carbon and nitrogen fixation (e.g., pcc/acc for carbon fixation, nifH for nitrogen fixation), carbon decomposition (e.g., amyA and pulA for labile carbon decomposition, mnp and lcc for recalcitrant carbon decomposition), and greenhouse gas emissions (e.g., mcrA for methane production, norB for nitrous oxide production) across five FACE sites. Also, the relative abundance of those key genes was generally increased and directionally associated with increased biomass, soil carbon decomposition, and soil moisture. In addition, a further literature survey of more disparate FACE experimental sites indicated increased biomass, soil carbon decay, nitrogen fixation, methane and nitrous oxide emissions, plant and soil carbon and nitrogen under eCO2. A conceptual framework was developed to link commonly responsive functional genes with ecosystem processes, such as pcc/acc vs. soil carbon storage, amyA/pulA/mnp/lcc vs. soil carbon decomposition, and nifH vs. nitrogen availability, suggesting that such common responses of microbial functional genes may have the potential to predict ecosystem functioning and sustainability in the future eCO2 environment.
Collapse
Affiliation(s)
- Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States; College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
| | - Ye Deng
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Meiying Xu
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Juan Li
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Junyi Liang
- Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Jinbo Xiong
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Hao Yu
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Harbin Institute of Technology, Harbin 150001, China; School of Environmental Science and Engineering, Liaoning Technical University, Fuxin 123000, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Liyou Wu
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Kai Xue
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Shengjing Shi
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, United States
| | - Yolima Carrillo
- Hawkesbury Institute for the Environment, University of Western Sydney, Sydney 2751, Australia; University of Wyoming, Laramie, WY 82071, United States
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Sarah E Hobbie
- The University of Minnesota, St. Paul, MN 55108, United States
| | - Peter B Reich
- Hawkesbury Institute for the Environment, University of Western Sydney, Sydney 2751, Australia; The University of Minnesota, St. Paul, MN 55108, United States
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Angela D Kent
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Elise Pendall
- Hawkesbury Institute for the Environment, University of Western Sydney, Sydney 2751, Australia; University of Wyoming, Laramie, WY 82071, United States
| | - Matthew Wallenstein
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO 80523, United States
| | - Yiqi Luo
- Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States.
| | - Jizhong Zhou
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
19
|
In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations. PLoS One 2020; 15:e0232437. [PMID: 32986713 PMCID: PMC7521895 DOI: 10.1371/journal.pone.0232437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/09/2020] [Indexed: 11/19/2022] Open
Abstract
Subsurface microbial communities mediate the transformation and fate of redox sensitive materials including organic matter, metals and radionuclides. Few studies have explored how changing geochemical conditions influence the composition of groundwater microbial communities over time. We temporally monitored alterations in abiotic forces on microbial community structure using 1L in-field bioreactors receiving background and contaminated groundwater at the Oak Ridge Reservation, TN. Planktonic and biofilm microbial communities were initialized with background water for 4 days to establish communities in triplicate control reactors and triplicate test reactors and then fed filtered water for 14 days. On day 18, three reactors were switched to receive filtered groundwater from a contaminated well, enriched in total dissolved solids relative to the background site, particularly chloride, nitrate, uranium, and sulfate. Biological and geochemical data were collected throughout the experiment, including planktonic and biofilm DNA for 16S rRNA amplicon sequencing, cell counts, total protein, anions, cations, trace metals, organic acids, bicarbonate, pH, Eh, DO, and conductivity. We observed significant shifts in both planktonic and biofilm microbial communities receiving contaminated water. This included a loss of rare taxa, especially amongst members of the Bacteroidetes, Acidobacteria, Chloroflexi, and Betaproteobacteria, but enrichment in the Fe- and nitrate- reducing Ferribacterium and parasitic Bdellovibrio. These shifted communities were more similar to the contaminated well community, suggesting that geochemical forces substantially influence microbial community diversity and structure. These influences can only be captured through such comprehensive temporal studies, which also enable more robust and accurate predictive models to be developed.
Collapse
|
20
|
Wang B, Zheng X, Zhang H, Xiao F, He Z, Yan Q. Keystone taxa of water microbiome respond to environmental quality and predict water contamination. ENVIRONMENTAL RESEARCH 2020; 187:109666. [PMID: 32445949 DOI: 10.1016/j.envres.2020.109666] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/24/2020] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
Abstract
The human activity introduces strong environmental stresses, and results in great spatiotemporal heterogeneity for the environment. Although the effects of environmental factors on the microbial diversity and succession have been widely studied, knowledge about how keystone taxa respond to environmental stresses remains poorly understood. We examined bacterial and archaeal communities from 45 wetland ponds covering a wide range of waters in Hangzhou. We found that shifts in bacterial and archaeal communities were strongly correlated with water pollution as indicated by the comprehensive water quality identification (CWQI). The SEGMENTED analysis suggested that there were non-linear responses of microbial communities and keystone taxa to the water pollution gradient. Moreover, these significant tipping points (e.g., CWQI > 4.0) would afford a warning line for urban wetland management. Notably, keystone taxa of bacterial communities could be used to successfully (~88.9% accuracy) predict water contamination levels. This study provides new insights into the potential for keystone bacterial taxa to predict water contamination.
Collapse
Affiliation(s)
- Binhao Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Hangjun Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
| |
Collapse
|
21
|
Yan Z, Song N, Wang C, Jiang H. Functional potential and assembly of microbes from sediments in a lake bay and adjoining river ecosystem for polycyclic aromatic hydrocarbon biodegradation. Environ Microbiol 2020; 23:628-640. [PMID: 32468666 DOI: 10.1111/1462-2920.15104] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/23/2020] [Accepted: 05/25/2020] [Indexed: 11/26/2022]
Abstract
Lake and adjoining river ecosystems are ecologically and economically valuable and are heavily threatened by anthropogenic activities. Determining the inherent capacity of ecosystems for polycyclic aromatic hydrocarbon (PAH) biodegradation can help quantify environmental impacts on the functioning of ecosystems, especially on that of the microbial community. Here, PAH biodegradation potential was compared between sediments collected from a lake bay (LS) and an adjoining river (RS) ecosystem. Microbial community composition, function, and their co-occurrence patterns were also explored. In the RS, the biodegradation rates (KD ) of pyrene or PAH were almost two orders of magnitude higher than those in the LS. Sediment functional community structure and network interactions were dramatically different between the LS and RS. Although PAH degradation genes (p450aro, quinoline, and qorl) were detected in the LS, the community activity of these genes needed to be biostimulated for accelerated bioremediation. In contrast, functional communities in the RS were capable of spontaneous natural attenuation of PAH. The degradation of PAH in the RS also required coordinated response of the complex functional community. Taken together, elucidating functions and network interactions in sediment microbial communities and their responses to environmental changes are very important for the bioremediation of anthropogenic toxic contaminants.
Collapse
Affiliation(s)
- Zaisheng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Na Song
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Changhui Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| |
Collapse
|
22
|
Zeng T, Mo G, Hu Q, Wang G, Liao W, Xie S. Microbial characteristic and bacterial community assessment of sediment sludge upon uranium exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 261:114176. [PMID: 32088436 DOI: 10.1016/j.envpol.2020.114176] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/29/2020] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
The microbial characteristics and bacterial communities of sediment sludge upon different concentrations of exposure to uranium were investigated by high solution transmission electron microscopy (HRTEM), energy dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS) and high-throughput sequencing. After exposure to initial uranium concentrations of 10-50 μM for 24 h in synthetic wastewater, the removal efficiencies of uranium reached 80.7%-96.5%. The spherical and short rod bacteria were dominant in the sludge exposed to uranium. HRTEM-EDS and XPS analyses indicated that reduction and adsorption were the main mechanisms for uranium removal. Short-term exposure to low concentrations of uranium resulted in a decrease in bacterial richness but an increase in diversity. A dramatic change in the composition and abundances of the bacterial community were present in the sediment sludge exposed to uranium. The highest removal efficiency was identified in the sediment sludge exposed to 30 μM uranium, and the dominant bacteria included Acinetobacter (44.9%), Klebsiella (20.0%), Proteiniclasticum (6.7%), Enterobacteriaceae (6.6%), Desulfovibrio (4.4%), Porphyromonadaceae (4.1%), Comamonas (2.4%) and Sedimentibacter (2.3%). By comparison to the inoculum sediment sludge, exposure to uranium caused a substantial difference in the majority of bacterial abundance.
Collapse
Affiliation(s)
- Taotao Zeng
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China.
| | - Guanhai Mo
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China
| | - Qing Hu
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China
| | - Guohua Wang
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China
| | - Wei Liao
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China
| | - Shuibo Xie
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China; Key Discipline Laboratory for National Defence for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, China
| |
Collapse
|
23
|
Bagwell CE, Gillispie EC, Lawter AR, Qafoku NP. Evaluation of gaseous substrates for microbial immobilization of contaminant mixtures in unsaturated subsurface sediments. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2020; 214-215:106183. [PMID: 32063288 DOI: 10.1016/j.jenvrad.2020.106183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/24/2020] [Accepted: 01/25/2020] [Indexed: 06/10/2023]
Abstract
Extensive vadose zone metals and organic contamination remains at many former industrial and defense manufacturing sites, and effective remedial solutions are needed to slow or prevent its migration to groundwater. In this study, the application of gaseous substrates to stimulate microbial respiratory reduction of comingled radioisotopes and nitrate under unsaturated conditions was examined for possible application at the Hanford Site, a former nuclear production facility in southeastern WA, USA. First, screening studies were performed to qualitatively measure the sediment respiratory response to 14 gaseous or volatile organic substrates at two moisture contents, 4% and 8%. Volatile substrates produced the strongest respiratory response, among them were butyrate, pentane, butyl acetate. Ethane and butane were the most effective gaseous substrates but only at 8% water content. Hanford sediment from two waste sites with distinctive chemistries were wetted to 7% moisture content, packed into columns, and treated with ethane or butane. After 4 weeks, columns were then leached to quantify retardation in the mobility of aqueous contaminant concentrations compared to no gas control columns. Treatment with both gases resulted in >80% removal of Cr from the aqueous phase. However, NO3 concentration and a waste sites exposure history to NO3 had a major effect on U and Tc reduction. Incomplete nitrate reduction outcompeted U and Tc in waste site sediments having limited prior exposure to NO3. Conversely, waste site sediments co-contaminated with NO3 were able to achieve highly reduced conditions resulting in complete denitrification of NO3, and delayed leaching of U and Tc. This implied effective reduction of both contaminants to less mobile species. This study demonstrates that unsaturated vadose sediments at Hanford waste sites have the capacity for a sustained respiratory response to gaseous substrate injection, which could potentially be deployed as part of an overall strategy to reduce the flux of long-lived radionuclides to groundwater at Hanford and other legacy waste sites.
Collapse
Affiliation(s)
- Christopher E Bagwell
- Pacific Northwest National Laboratory, Earth Systems Science Division, Richland, WA, USA.
| | - Elizabeth C Gillispie
- Pacific Northwest National Laboratory, Earth Systems Science Division, Richland, WA, USA
| | - Amanda R Lawter
- Pacific Northwest National Laboratory, Earth Systems Science Division, Richland, WA, USA
| | - Nikolla P Qafoku
- Pacific Northwest National Laboratory, Earth Systems Science Division, Richland, WA, USA
| |
Collapse
|
24
|
Gao Q, Dong Q, Wu L, Yang Y, Hale L, Qin Z, Xie C, Zhang Q, Van Nostrand JD, Zhou J. Environmental antibiotics drives the genetic functions of resistome dynamics. ENVIRONMENT INTERNATIONAL 2020; 135:105398. [PMID: 31862641 DOI: 10.1016/j.envint.2019.105398] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
The increasing prevalence of antibiotic-resistant microorganisms imposes a global threat to public health. The over reliant use of antibiotics in the food industry has contributed considerably to the dissemination of antibiotics into various environments, yet the mechanisms by which antibiotic dissemination influences the assembly of the microbial community continues to remain obscure. Here, we examine bacterial and fungal community assemblies in swine manure, compost, compost amended, and unamended agricultural soil in five suburban areas of Beijing, China. Total antibiotic concentration decreased by factors of 10-1000 from manure and compost to soils. The bacterial α-diversity was found to be low in manure and compost samples, while the fungal α-diversity was similar across all samples. We detected significantly (p < 0.05) higher relative abundances of well recognized pathogenic microbial taxa, virulence associated genes, and antibiotic resistance genes (ARGs) in manure and compost than those in agricultural soils, revealing the higher microbial capacity of pathogenicity, virulence and antibiotic resistance. Unexpectedly, the relative abundances of both bacterial and fungal taxa did not predict the antibiotic concentration. A possible explanation was that bacterial and fungal communities were mainly shaped by random assemblies. Rather, antibiotic concentration could be well predicted by relative abundances of antibiotic resistance, stress and virulence associated genes. Despite the weak interconnection between ARGs and the microbiome, we demonstrate that microbial genes should be the focal point in tracking the ecological effects of antibiotic dissemination by revealing microbial community patterns along the dissemination chain of antibiotics.
Collapse
Affiliation(s)
- Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Qiang Dong
- Institute of Chemical Defense, Beijing 102205, China
| | - Linwei Wu
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA.
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Lauren Hale
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA; Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, USDA, Parlier, CA 93648-9757, USA
| | - Ziyan Qin
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Changyi Xie
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Qiuting Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| |
Collapse
|
25
|
Janßen R, Zabel J, von Lukas U, Labrenz M. An artificial neural network and Random Forest identify glyphosate-impacted brackish communities based on 16S rRNA amplicon MiSeq read counts. MARINE POLLUTION BULLETIN 2019; 149:110530. [PMID: 31454615 DOI: 10.1016/j.marpolbul.2019.110530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 08/16/2019] [Accepted: 08/17/2019] [Indexed: 06/10/2023]
Abstract
Machine learning algorithms can be trained on complex data sets to detect, predict, or model specific aspects. Aim of this study was to train an artificial neural network in comparison to a Random Forest model to detect induced changes in microbial communities, in order to support environmental monitoring efforts of contamination events. Models were trained on taxon count tables obtained via next-generation amplicon sequencing of water column samples originating from a lab microcosm incubation experiment conducted over 140 days to determine the effects of glyphosate on succession within brackish-water microbial communities. Glyphosate-treated assemblages were classified correctly; a subsetting approach identified the taxa primarily responsible for this, permitting the reduction of input features. This study demonstrates the potential of artificial neural networks to predict indicator species for glyphosate contamination. The results could empower the development of environmental monitoring strategies with applications limited to neither glyphosate nor amplicon sequence data.
Collapse
Affiliation(s)
- René Janßen
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Mecklenburg-Western Pomerania, Germany
| | - Jakob Zabel
- Maritime Graphics, Fraunhofer Institute for Computer Graphics Research, Rostock, Mecklenburg-Western Pomerania, Germany
| | - Uwe von Lukas
- Maritime Graphics, Fraunhofer Institute for Computer Graphics Research, Rostock, Mecklenburg-Western Pomerania, Germany
| | - Matthias Labrenz
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Mecklenburg-Western Pomerania, Germany.
| |
Collapse
|
26
|
The Spatial Distribution of the Microbial Community in a Contaminated Aquitard below an Industrial Zone. WATER 2019. [DOI: 10.3390/w11102128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The industrial complex Neot Hovav, in Israel, is situated above an anaerobic fractured chalk aquitard, which is polluted by a wide variety of hazardous organic compounds. These include volatile and non-volatile, halogenated, organic compounds. In this study, we characterized the indigenous bacterial population in 17 boreholes of the groundwater environment, while observing the spatial variations in the population and structure as a function of distance from the polluting source. In addition, the de-halogenating potential of the microbial groundwater population was tested through a series of lab microcosm experiments, thus exemplifying the potential and limitations for bioremediation of the site. In all samples, the dominant phylum was Proteobacteria. In the production plant area, the non-obligatory organo-halide respiring bacteria (OHRB) Firmicutes Phylum was also detected in the polluted water, in abundancies of up to 16 %. Non-metric multidimensional scaling (NMDS) analysis of the microbial community structure in the groundwater exhibited clusters of distinct populations following the location in the industrial complex and distance from the polluting source. Dehalogenation of halogenated ethylene was demonstrated in contrast to the persistence of brominated alcohols. Persistence is likely due to the chemical characteristics of brominated alcohols, and not because of the absence of active de-halogenating bacteria.
Collapse
|
27
|
Ning D, Deng Y, Tiedje JM, Zhou J. A general framework for quantitatively assessing ecological stochasticity. Proc Natl Acad Sci U S A 2019; 116:16892-16898. [PMID: 31391302 PMCID: PMC6708315 DOI: 10.1073/pnas.1904623116] [Citation(s) in RCA: 389] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it is generally accepted that both deterministic and stochastic processes play important roles in community assembly, quantifying their relative importance is challenging. Here we propose a general mathematical framework to quantify ecological stochasticity under different situations in which deterministic factors drive the communities more similar or dissimilar than null expectation. An index, normalized stochasticity ratio (NST), was developed with 50% as the boundary point between more deterministic (<50%) and more stochastic (>50%) assembly. NST was tested with simulated communities by considering abiotic filtering, competition, environmental noise, and spatial scales. All tested approaches showed limited performance at large spatial scales or under very high environmental noise. However, in all of the other simulated scenarios, NST showed high accuracy (0.90 to 1.00) and precision (0.91 to 0.99), with averages of 0.37 higher accuracy (0.1 to 0.7) and 0.33 higher precision (0.0 to 1.8) than previous approaches. NST was also applied to estimate stochasticity in the succession of a groundwater microbial community in response to organic carbon (vegetable oil) injection. Our results showed that community assembly was shifted from more deterministic (NST = 21%) to more stochastic (NST = 70%) right after organic carbon input. As the vegetable oil was consumed, the community gradually returned to be more deterministic (NST = 27%). In addition, our results demonstrated that null model algorithms and community similarity metrics had strong effects on quantifying ecological stochasticity.
Collapse
Affiliation(s)
- Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK 73019
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084 Beijing, China
| | - Ye Deng
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK 73019
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China
- Institute for Marine Science and Technology, Shandong University, 266237 Qingdao, China
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824;
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019;
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK 73019
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084 Beijing, China
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| |
Collapse
|
28
|
Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities. mSystems 2019; 4:4/4/e00296-19. [PMID: 31213523 PMCID: PMC6581690 DOI: 10.1128/msystems.00296-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly developed GeoChip 5.0 is the most comprehensive microarray available to date for examining the functional capabilities of microbial communities important to biogeochemistry, ecology, environmental sciences, and human health. The GeoChip 5 is highly specific, sensitive, and quantitative based on both computational and experimental assays. Use of the array on a contaminated groundwater sample provided novel insights on the impacts of environmental contaminants on groundwater microbial communities. While functional gene arrays (FGAs) have greatly expanded our understanding of complex microbial systems, specificity, sensitivity, and quantitation challenges remain. We developed a new generation of FGA, GeoChip 5.0, using the Agilent platform. Two formats were created, a smaller format (GeoChip 5.0S), primarily covering carbon-, nitrogen-, sulfur-, and phosphorus-cycling genes and others providing ecological services, and a larger format (GeoChip 5.0M) containing the functional categories involved in biogeochemical cycling of C, N, S, and P and various metals, stress response, microbial defense, electron transport, plant growth promotion, virulence, gyrB, and fungus-, protozoan-, and virus-specific genes. GeoChip 5.0M contains 161,961 oligonucleotide probes covering >365,000 genes of 1,447 gene families from broad, functionally divergent taxonomic groups, including bacteria (2,721 genera), archaea (101 genera), fungi (297 genera), protists (219 genera), and viruses (167 genera), mainly phages. Computational and experimental evaluation indicated that designed probes were highly specific and could detect as little as 0.05 ng of pure culture DNAs within a background of 1 μg community DNA (equivalent to 0.005% of the population). Additionally, strong quantitative linear relationships were observed between signal intensity and amount of pure genomic (∼99% of probes detected; r > 0.9) or soil (∼97%; r > 0.9) DNAs. Application of the GeoChip to a contaminated groundwater microbial community indicated that environmental contaminants (primarily heavy metals) had significant impacts on the biodiversity of the communities. This is the most comprehensive FGA to date, capable of directly linking microbial genes/populations to ecosystem functions. IMPORTANCE The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly developed GeoChip 5.0 is the most comprehensive microarray available to date for examining the functional capabilities of microbial communities important to biogeochemistry, ecology, environmental sciences, and human health. The GeoChip 5 is highly specific, sensitive, and quantitative based on both computational and experimental assays. Use of the array on a contaminated groundwater sample provided novel insights on the impacts of environmental contaminants on groundwater microbial communities.
Collapse
|
29
|
Mosmeri H, Gholami F, Shavandi M, Dastgheib SMM, Alaie E. Bioremediation of benzene-contaminated groundwater by calcium peroxide (CaO 2) nanoparticles: Continuous-flow and biodiversity studies. JOURNAL OF HAZARDOUS MATERIALS 2019; 371:183-190. [PMID: 30851671 DOI: 10.1016/j.jhazmat.2019.02.071] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 01/25/2019] [Accepted: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Calcium peroxide (CaO2) nanoparticles have been extensively applied in treatment of contaminated groundwater through bioremediation or modified Fenton (MF) processes. In the present study utilization of CaO2 in bioremediation and MF (CaO2+FeSO4) reaction is investigated for benzene (50 mg/L) removal in continuous flow sand-packed columns. The results indicated that MF produced OH radicals markedly increased benzene remediation at first 30 days (up to 93%). But, OH generation rate was gradually declined when the pH was increased and finally 75% of initial benzene removed after 100d. In bioremediation column, because of supplying adequate oxygen by CaO2, the number of planktonic bacteria logarithmically increased to more than 5 × 106 CFU/mL (two orders of magnitude) and consequently 100% benzene removal was achieved by the end of experiment. Scanning electron microscopy analysis visualized the attached biofilm growth on sand surfaces in CaO2 injected columns indicating their key role in the remediation process. The impact of each process on the microbial biodiversity of groundwater was investigated by next generation sequencing (NGS) of the 16S rRNA gene. The alpha and beta analysis indicated that microbial diversity is decreased by CaO2 injection while benzene-degrading species such as Silanimonas, Arthrobacter and Pseudomonas spp. were dominated in remediation column.
Collapse
Affiliation(s)
- Hamid Mosmeri
- Ecology and Environmental Pollution Control Research Group, Research Institute of Petroleum Industry, Tehran, Iran
| | - Fatemeh Gholami
- Department of Microbiology, College of Science, University of Tehran, Tehran, Iran
| | - Mahmoud Shavandi
- Ecology and Environmental Pollution Control Research Group, Research Institute of Petroleum Industry, Tehran, Iran.
| | | | - Ebrahim Alaie
- Environment and Biotechnology Research Division, Research Institute of Petroleum Industry, Tehran, Iran
| |
Collapse
|
30
|
The Characterization of Microbial Communities Response to Shallow Groundwater Contamination in Typical Piedmont Region of Taihang Mountains in the North China Plain. WATER 2019. [DOI: 10.3390/w11040736] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Regional-scale nitrate and organic contaminants in the shallow groundwater were investigated in the Piedmont region of Taihang Mountains (PRTM), but the information of the microbial communities is limited. However, microorganisms provide a dominated contribution to indicate and degrade the contaminants in the aquifer. Therefore, this study investigates the microbial diversity and contamination microbial indicators of groundwater samples with different contaminated types to better understand the contamination in the PRTM. Seventy-six samples were collected between two rivers in the Tang-Dasha River Basin covering 4000 km2 in the PRTM. High-throughput sequencing was employed to determine the samples’ DNA sequences. The samples were divided into four groups: background (B), nitrate contamination (N), organic contamination (O) and organic-nitrate contamination (O_N) based on the cumulative probability distribution and the Chinese groundwater standard levels of NO3−, COD and DO concentrations. Then, the microbial diversity and contamination microbial indicators were studied in the four groups. The results showed that the O group exhibited lower diversity than other groups. Bacteria detected in these four groups covered 531 families, 987 genera, and 1881 species. Taxonomic assignment analysis indicated that Rhodobacter, Vogesella, Sphingobium dominated in the O_N group, N group, and O group, and accounted for 18.05%, 17.74%, 16.45% in each group at genus level, respectively. Furthermore, these three genera were identified as contamination microbial indicators to the three types of contamination, respectively. The results provide a potential molecular microbiological method to identity contamination in shallow groundwater, and established a strong foundation for further investigation and remediation in the PRTM.
Collapse
|
31
|
Zheng T, Deng Y, Wang Y, Jiang H, O'Loughlin EJ, Flynn TM, Gan Y, Ma T. Seasonal microbial variation accounts for arsenic dynamics in shallow alluvial aquifer systems. JOURNAL OF HAZARDOUS MATERIALS 2019; 367:109-119. [PMID: 30594709 DOI: 10.1016/j.jhazmat.2018.12.087] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/19/2018] [Accepted: 12/22/2018] [Indexed: 06/09/2023]
Abstract
Determining the temporal variation of microbial communities in groundwater systems is essential to improve our understanding of hydrochemical dynamics in aquifers, particularly as it relates to the fate of redox-sensitive contaminants like arsenic (As). Therefore, a high-resolution hydrobiogeochemical investigation was conducted in the As-affected alluvial aquifer systems of the Jianghan Plain. In two 25 m-deep monitoring wells, the seasonal variation in the composition of groundwater microbial communities was positively correlated with the change in groundwater level (R = 0.47 and 0.39 in NH03B and NH05B, respectively, P < 0.01), implying that the latter could be a primary driver of the seasonal microbial dynamics. In response to the fluctuating groundwater level, iron (Fe) reducers within the Desulfuromonadales were dominant (9.9 ± 4.7% among different sampling sites) in groundwater microbial communities during the monsoon season and associated with high concentrations of Fe(II) and As, while the predominance (16.7 ± 15.2% among different sampling sites) of iron-oxidizers the Gallionellaceae was accompanied by low Fe(II) and As in the non-monsoon season. These results suggest that microbially-mediated iron reduction/oxidation may have governed the seasonal mobilization/scavenging of As in groundwater. Our results provide new insights into mechanisms responsible for seasonal variations in groundwater As concentrations in similar aquifer systems.
Collapse
Affiliation(s)
- Tianliang Zheng
- Geological Survey, China University of Geosciences, Wuhan, 430074, PR China
| | - Yamin Deng
- Geological Survey, China University of Geosciences, Wuhan, 430074, PR China; School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China.
| | - Yanxin Wang
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China.
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
| | - Edward J O'Loughlin
- Biosciences Division, Argonne National Laboratory, Argonne, IL, 60439-4843, United States
| | - Theodore M Flynn
- Biosciences Division, Argonne National Laboratory, Argonne, IL, 60439-4843, United States
| | - Yiqun Gan
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
| | - Teng Ma
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
| |
Collapse
|
32
|
Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes. mBio 2019; 10:mBio.02899-18. [PMID: 30808697 PMCID: PMC6391923 DOI: 10.1128/mbio.02899-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Naturally occurring plasmids constitute a major category of mobile genetic elements responsible for harboring and transferring genes important in survival and fitness. A targeted evaluation of plasmidomes can reveal unique adaptations required by microbial communities. We developed a model system to optimize plasmid DNA isolation procedures targeted to groundwater samples which are typically characterized by low cell density (and likely variations in the plasmid size and copy numbers). The optimized method resulted in successful identification of several hundred circular plasmids, including some large plasmids (11 plasmids more than 50 kb in size, with the largest being 1.7 Mb in size). Several interesting observations were made from the analysis of plasmid DNA isolated in this study. The plasmid pool (plasmidome) was more conserved than the corresponding microbiome distribution (16S rRNA based). The circular plasmids were diverse as represented by the presence of seven plasmid incompatibility groups. The genes carried on these groundwater plasmids were highly enriched in metal resistance. Results from this study confirmed that traits such as metal, antibiotic, and phage resistance along with toxin-antitoxin systems are encoded on abundant circular plasmids, all of which could confer novel and advantageous traits to their hosts. This study confirms the ecological role of the plasmidome in maintaining the latent capacity of a microbiome, enabling rapid adaptation to environmental stresses.IMPORTANCE Plasmidomes have been typically studied in environments abundant in bacteria, and this is the first study to explore plasmids from an environment characterized by low cell density. We specifically target groundwater, a significant source of water for human/agriculture use. We used samples from a well-studied site and identified hundreds of circular plasmids, including one of the largest sizes reported in plasmidome studies. The striking similarity of the plasmid-borne ORFs in terms of taxonomical and functional classifications across several samples suggests a conserved plasmid pool, in contrast to the observed variability in the 16S rRNA-based microbiome distribution. Additionally, the stress response to environmental factors has stronger conservation via plasmid-borne genes as marked by abundance of metal resistance genes. Last, identification of novel and diverse plasmids enriches the existing plasmid database(s) and serves as a paradigm to increase the repertoire of biological parts that are available for modifying novel environmental strains.
Collapse
|
33
|
Zeng T, Li L, Mo G, Wang G, Liu H, Xie S. Analysis of uranium removal capacity of anaerobic granular sludge bacterial communities under different initial pH conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:5613-5622. [PMID: 30612368 DOI: 10.1007/s11356-018-4017-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
The bacterial community of an anaerobic granular sludge associated with uranium depletion was investigated following its exposure to uranium under different initial pH conditions (pH 4.5, 5.5, and 6.5). The highest uranium removal efficiency (98.1%) was obtained for the sample with an initial pH of 6.5, which also supported the highest bacterial community richness and diversity. Venn diagrams visualized the decrease in the number of genera present in both the inoculum and the uranium-exposed biomass as the initial pH decreased from 6.5 to 4.5. Compared with the inoculum, a significant increase in the abundances of the phyla Chloroflexi and Proteobacteria was observed following uranium exposure. At initial pH conditions of 6.5 to 4.5, the proportions of the taxa Anaerolineaceae, Chryseobacterium, Acinetobacter, Pseudomonas, and Sulfurovum increased significantly, likely contributing to the observed uranium removal. Uranium exposure induced a greater level of dynamic diversification of bacterial abundances than did the initial pH difference.
Collapse
Affiliation(s)
- Taotao Zeng
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, People's Republic of China.
| | - Licheng Li
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, People's Republic of China
| | - Guanhai Mo
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, People's Republic of China
| | - Guohua Wang
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, People's Republic of China
| | - Haiyan Liu
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, People's Republic of China
| | - Shuibo Xie
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, People's Republic of China.
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, People's Republic of China.
| |
Collapse
|
34
|
Niño de Guzmán GT, Hapeman CJ, Millner PD, Torrents A, Jackson D, Kjellerup BV. Presence of organohalide-respiring bacteria in and around a permeable reactive barrier at a trichloroethylene-contaminated Superfund site. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:766-776. [PMID: 30228068 DOI: 10.1016/j.envpol.2018.08.095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/29/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Trichloroethylene (TCE) is one of the most common groundwater contaminants in the United States; however clean-up efforts are a challenge due to its physical and chemical properties. TCE and several of its degradation products were detected in the groundwater of the Beaver Dam Road Landfill site (Beltsville, MD) at concentrations above accepted maximum contaminant levels. A permeable reactive barrier (i.e., biowall) was installed to remediate the groundwater. Microbial infiltration and colonization of the biowall with native site bacteria was expected to occur. An array of molecular biological tools was applied to survey the microbial community for presence of organohalide-respiring microorganisms at the site. Microorganisms belonging to methanogens, acetogens, sulfate-reducing bacteria, and chlorinated aliphatic hydrocarbon-metabolizing bacteria were identified, thus making way for the application of the microbial populations in the biowall bioaugmentation efforts. In concomitant laboratory studies, molecular approaches were used to monitor continuously-fed column reactors containing saturated biowall material spiked with a commercially-available, Dehalococcoides-containing culture (SDC-9), with or without zero-valent iron (ZVI) shavings. The column without ZVI had the highest abundance of Dehalococcoides spp. (2.7 × 106 cells g-1 material, S.D. = 3.8 × 105 cells g-1 material), while the addition of ZVI did not affect the overall population. Although the addition of ZVI and biostimulation did change ratios of the Dehalococcoides strains, the results suggests that if ZVI would be applied as a biowall material amendment, biostimulation would not be required to maintain a Dehalococcoides population. These experimental results will be utilized in future remediation and/or biowall expansion plans to utilize the natural resources most effectively at the biowall site.
Collapse
Affiliation(s)
| | - Cathleen J Hapeman
- US Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
| | - Patricia D Millner
- US Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
| | - Alba Torrents
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, USA
| | - Dana Jackson
- US Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
| | - Birthe V Kjellerup
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, USA.
| |
Collapse
|
35
|
Smith HJ, Zelaya AJ, De León KB, Chakraborty R, Elias DA, Hazen TC, Arkin AP, Cunningham AB, Fields MW. Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments. FEMS Microbiol Ecol 2018; 94:5107865. [PMID: 30265315 PMCID: PMC6192502 DOI: 10.1093/femsec/fiy191] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/26/2018] [Indexed: 12/12/2022] Open
Abstract
Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.
Collapse
Affiliation(s)
- H J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A J Zelaya
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - K B De León
- Department of Biochemistry, University of Missouri, Columbia, MO
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - R Chakraborty
- Climate and Ecosystems Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - D A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - T C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A P Arkin
- Department of Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, CA
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A B Cunningham
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Civil Engineering, Montana State University, Montana State University, Bozeman, MT
| | - M W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| |
Collapse
|
36
|
Caglar MU, Hockenberry AJ, Wilke CO. Predicting bacterial growth conditions from mRNA and protein abundances. PLoS One 2018; 13:e0206634. [PMID: 30388153 PMCID: PMC6214550 DOI: 10.1371/journal.pone.0206634] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 10/16/2018] [Indexed: 01/30/2023] Open
Abstract
Cells respond to changing nutrient availability and external stresses by altering the expression of individual genes. Condition-specific gene expression patterns may thus provide a promising and low-cost route to quantifying the presence of various small molecules, toxins, or species-interactions in natural environments. However, whether gene expression signatures alone can predict individual environmental growth conditions remains an open question. Here, we used machine learning to predict 16 closely-related growth conditions using 155 datasets of E. coli transcript and protein abundances. We show that models are able to discriminate between different environmental features with a relatively high degree of accuracy. We observed a small but significant increase in model accuracy by combining transcriptome and proteome-level data, and we show that measurements from stationary phase cells typically provide less useful information for discriminating between conditions as compared to exponentially growing populations. Nevertheless, with sufficient training data, gene expression measurements from a single species are capable of distinguishing between environmental conditions that are separated by a single environmental variable.
Collapse
Affiliation(s)
- M. Umut Caglar
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Adam J. Hockenberry
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Claus O. Wilke
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
| |
Collapse
|
37
|
Kolhe N, Zinjarde S, Acharya C. Responses exhibited by various microbial groups relevant to uranium exposure. Biotechnol Adv 2018; 36:1828-1846. [PMID: 30017503 DOI: 10.1016/j.biotechadv.2018.07.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 11/28/2022]
Abstract
There is a strong interest in knowing how various microbial systems respond to the presence of uranium (U), largely in the context of bioremediation. There is no known biological role for uranium so far. Uranium is naturally present in rocks and minerals. The insoluble nature of the U(IV) minerals keeps uranium firmly bound in the earth's crust minimizing its bioavailability. However, anthropogenic nuclear reaction processes over the last few decades have resulted in introduction of uranium into the environment in soluble and toxic forms. Microbes adsorb, accumulate, reduce, oxidize, possibly respire, mineralize and precipitate uranium. This review focuses on the microbial responses to uranium exposure which allows the alteration of the forms and concentrations of uranium within the cell and in the local environment. Detailed information on the three major bioprocesses namely, biosorption, bioprecipitation and bioreduction exhibited by the microbes belonging to various groups and subgroups of bacteria, fungi and algae is provided in this review elucidating their intrinsic and engineered abilities for uranium removal. The survey also highlights the instances of the field trials undertaken for in situ uranium bioremediation. Advances in genomics and proteomics approaches providing the information on the regulatory and physiologically important determinants in the microbes in response to uranium challenge have been catalogued here. Recent developments in metagenomics and metaproteomics indicating the ecologically relevant traits required for the adaptation and survival of environmental microbes residing in uranium contaminated sites are also included. A comprehensive understanding of the microbial responses to uranium can facilitate the development of in situ U bioremediation strategies.
Collapse
Affiliation(s)
- Nilesh Kolhe
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India; Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India; Department of Microbiology, Savitribai Phule Pune University, Pune 411007, India.
| | - Celin Acharya
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Trombay, Mumbai 400094, India.
| |
Collapse
|