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Liu S, Liu J, She J, Xie Z, Zhou L, Dai Q, Zhang X, Wan Y, Yin M, Dong X, Zhao M, Chen D, Wang J. Microbial features with uranium pollution in artificial reservoir sediments at different depths under drought stress. Sci Total Environ 2024; 919:170694. [PMID: 38325477 DOI: 10.1016/j.scitotenv.2024.170694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/22/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
The uranium (U) containing leachate from uranium tailings dam into the natural settings, may greatly affect the downstream environment. To reveal such relationship between uranium contamination and microbial communities in the most affected downstream environment under drought stress, a 180 cm downstream artificial reservoir depth sediment profile was collected, and the microbial communities and related genes were analyzed by 16S rDNA and metagenomics. Besides, the sequential extraction scheme was employed to shed light on the distinct role of U geochemical speciations in shaping microbial community structures. The results showed that U content ranged from 28.1 to 70.1 mg/kg, with an average content of 44.9 mg/kg, significantly exceeding the value of background sediments. Further, U in all the studied sediments was related to remarkably high portions of mobile fractions, and U was likely deposited layer by layer depending on the discharge/leachate inputs from uranium-involving anthoropogenic facilities/activities upstream. The nexus between U speciation, physico-chemical indicators and microbial composition showed that Fe, S, and N metabolism played a vital role in microbial adaptation to U-enriched environment; meanwhile, the fraction of Ureducible and the Fe and S contents had the most significant effects on microbial community composition in the sediments under drought stress.
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Affiliation(s)
- Siyu Liu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Juan Liu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Jingye She
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Zhenyu Xie
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Lei Zhou
- School of Environment and Resource, Key Laboratory of Solid Waste Treatment and Resource Recycling, Ministry of Education, Southwest University of Science and Technology, Mianyang, China
| | - Qunwei Dai
- School of Environment and Resource, Key Laboratory of Solid Waste Treatment and Resource Recycling, Ministry of Education, Southwest University of Science and Technology, Mianyang, China
| | - Xing Zhang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Yuebing Wan
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Meiling Yin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Xinjiao Dong
- School of Life & Environmental Science, Wenzhou University, Wenzhou, China
| | - Min Zhao
- School of Life & Environmental Science, Wenzhou University, Wenzhou, China
| | - Diyun Chen
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China; Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, Guangzhou, China
| | - Jin Wang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China; Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, Guangzhou, China.
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Newman-Portela AM, Krawczyk-Bärsch E, Lopez-Fernandez M, Bok F, Kassahun A, Drobot B, Steudtner R, Stumpf T, Raff J, Merroun ML. Biostimulation of indigenous microbes for uranium bioremediation in former U mine water: multidisciplinary approach assessment. Environ Sci Pollut Res Int 2024; 31:7227-7245. [PMID: 38157180 PMCID: PMC10821841 DOI: 10.1007/s11356-023-31530-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/09/2023] [Indexed: 01/03/2024]
Abstract
Characterizing uranium (U) mine water is necessary to understand and design an effective bioremediation strategy. In this study, water samples from two former U-mines in East Germany were analysed. The U and sulphate (SO42-) concentrations of Schlema-Alberoda mine water (U: 1 mg/L; SO42-: 335 mg/L) were 2 and 3 order of magnitude higher than those of the Pöhla sample (U: 0.01 mg/L; SO42-: 0.5 mg/L). U and SO42- seemed to influence the microbial diversity of the two water samples. Microbial diversity analysis identified U(VI)-reducing bacteria (e.g. Desulfurivibrio) and wood-degrading fungi (e.g. Cadophora) providing as electron donors for the growth of U-reducers. U-bioreduction experiments were performed to screen electron donors (glycerol, vanillic acid, and gluconic acid) for Schlema-Alberoda U-mine water bioremediation purpose. Thermodynamic speciation calculations show that under experimental conditions, U(VI) is not coordinated to the amended electron donors. Glycerol was the best-studied electron donor as it effectively removed 99% of soluble U, 95% of Fe, and 58% of SO42- from the mine water, probably by biostimulation of indigenous microbes. Vanillic acid removed 90% of U, and no U removal occurred using gluconic acid.
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Affiliation(s)
- Antonio M Newman-Portela
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain.
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany.
| | - Evelyn Krawczyk-Bärsch
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Margarita Lopez-Fernandez
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain
| | - Frank Bok
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Andrea Kassahun
- WISMUT GmbH, Jagdschänkenstraße 29, 09117, Chemnitz, Germany
| | - Björn Drobot
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Robin Steudtner
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Thorsten Stumpf
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Johannes Raff
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain
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Ju Y, Baik MH, Lee SY, Lee KK, Kaown D, Shin D, Ryu JH. Identifying the origin and fate of dissolved U in the Boeun aquifer based on microbial signatures and C, O, Fe, S, and U isotopes. J Hazard Mater 2023; 459:132051. [PMID: 37467612 DOI: 10.1016/j.jhazmat.2023.132051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/12/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023]
Abstract
The uranium inventory in the Boeun aquifer is situated near an artificial reservoir (40-70 m apart) intended to supply water to nearby cities. However, toxic radionuclides can enter the reservoir. To determine the U mobility in the system, we analyzed groundwater and fracture-filling materials (FFMs) for environmental tracers, including microbial signatures, redox-sensitive elements and isotopes. In the site, U mass flux ranged from only 9.59 × 10-7 µg/L/y to 1.70 × 10-4 µg/L/y. The δ18O-H2O and 14C signatures showed that groundwater originated mainly from upland recharges and was not influenced by oxic surface water. We observed U accumulations (∼157 mg/kg) in shallow FFMs and Fe enrichments (∼226798 mg/kg) and anomalies in the 230Th/238U activity ratio (AR), 230Th/234U AR, δ56Fe and δ57Fe isotopes, suggesting that low U mobility in shallow depths is associated with a Fe-rich environment. At shallow depths, anaerobic Fe-oxidizers, Gallionella was prevalent in the groundwater, while Acidovorax was abundant near the U ore deposit depth. The Fe-rich environment at shallow depths was formed by sulfide dissolution, as demonstrated by δ34S-SO4 and δ18O-SO4 distribution. Overall, the Fe-rich aquifer including abundant sulfide minerals immobilizes dissolved U through biotic and abiotic processes, without significant leaching into nearby reservoirs.
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Affiliation(s)
- YeoJin Ju
- Disposal Safety Evaluation Research Division, Korea Atomic Energy Research Institute, Daejeon 34057, Republic of Korea
| | - Min Hoon Baik
- Disposal Safety Evaluation Research Division, Korea Atomic Energy Research Institute, Daejeon 34057, Republic of Korea
| | - Seung Yeop Lee
- Disposal Safety Evaluation Research Division, Korea Atomic Energy Research Institute, Daejeon 34057, Republic of Korea
| | - Kang-Kun Lee
- School of Earth and Environmental Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Dugin Kaown
- School of Earth and Environmental Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Dongbok Shin
- Department of Geoenvironmental Sciences, Kongju National University, Kongju 32588, Republic of Korea
| | - Ji-Hun Ryu
- Disposal Safety Evaluation Research Division, Korea Atomic Energy Research Institute, Daejeon 34057, Republic of Korea.
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Xu R, Kolton M, Tao W, Sun X, Su P, Huang D, Zhang M, Yang Z, Guo Z, Gao H, Wang Q, Li B, Chen C, Sun W. Anaerobic selenite-reducing bacteria and their metabolic potentials in Se-rich sediment revealed by the combination of DNA-stable isotope probing, metagenomic binning, and metatranscriptomics. J Hazard Mater 2023; 457:131834. [PMID: 37327607 DOI: 10.1016/j.jhazmat.2023.131834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 06/04/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
Microorganisms play a critical role in the biogeochemical cycling of selenium (Se) in aquatic environments, particularly in reducing the toxicity and bioavailability of selenite (Se(IV)). This study aimed to identify putative Se(IV)-reducing bacteria (SeIVRB) and investigate the genetic mechanisms underlying Se(IV) reduction in anoxic Se-rich sediment. Initial microcosm incubation confirmed that Se(IV) reduction was driven by heterotrophic microorganisms. DNA stable-isotope probing (DNA-SIP) analysis identified Pseudomonas, Geobacter, Comamonas, and Anaeromyxobacter as putative SeIVRB. High-quality metagenome-assembled genomes (MAGs) affiliated with these four putative SeIVRB were retrieved. Annotation of functional gene indicated that these MAGs contained putative Se(IV)-reducing genes such as DMSO reductase family, fumarate and sulfite reductases. Metatranscriptomic analysis of active Se(IV)-reducing cultures revealed significantly higher transcriptional levels of genes associated with DMSO reductase (serA/PHGDH), fumarate reductase (sdhCD/frdCD), and sulfite reductase (cysDIH) compared to those in cultures not amended with Se(IV), suggesting that these genes played important roles in Se(IV) reduction. The current study expands our knowledge of the genetic mechanisms involved in less-understood anaerobic Se(IV) bio-reduction. Additinally, the complementary abilities of DNA-SIP, metagenomics, and metatranscriptomics analyses are demonstrated in elucidating the microbial mechanisms of biogeochemical processes in anoxic sediment.
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Affiliation(s)
- Rui Xu
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, PR China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Max Kolton
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Wan Tao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Pingzhou Su
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Duanyi Huang
- College of Environmental Science and Engineering, Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Miaomiao Zhang
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Zhaohui Guo
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, PR China
| | - Hanbing Gao
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, PR China
| | - Qi Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Chengyu Chen
- College of Natural Resources and Environment, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, South China Agricultural University, Guangzhou 510642, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China; School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control (Ministry of Education), Henan Normal University, Xinxiang 453007, PR China.
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Srivastava A, Verma D. Ganga River sediments of India predominate with aerobic and chemo-heterotrophic bacteria majorly engaged in the degradation of xenobiotic compounds. Environ Sci Pollut Res Int 2023; 30:752-772. [PMID: 35904740 DOI: 10.1007/s11356-022-22198-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Sediment provides a stagnant habitat to microbes that accumulate organic matter and other industrial pollutants from the upper layer of the water. The sediment of the Ganga River of India is overlooked for exploring the bacterial diversity despite their taxon richness over the water counterpart. To enrich the limited information on the bacterial diversity of the Ganga River sediment, the present study was planned that relies on amplicon-based bacterial diversity of the Ganga River sediment by using bacterial-specific 16S hypervariable region (V3-V4). The Illumina MiSeq2500 platform generated 1,769,226 raw reads from the metagenomes of various samples obtained from ten sites in five major cities of Uttar Pradesh and Uttarakhand regions traversing the Ganga River. Taxonomy level analysis assigned 58 phyla, 366 order, and 715 genera of bacterial type. The high values of various diversity indices (Chao1, Shannon, and Simpson) in Kanpur sediment indicate the high bacterial richness compared to the Rishikesh sediment. However, several other ecological parameters (Shannon index, Simpson index, enspie _vector, and Faith_pd) were comparatively higher in Rishikesh sediment which is a comparatively less disturbed region by human activities over the other sediments samples studied here. Ganga River sediment dominates with Gram-negative, chemo-heterotrophic, and aerobic bacteria that chiefly belong to Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidota. The abundance of Nitrospira, Hydrogenophaga, Thauera, Vicinamibacteraceae, and Latescibacterota in the Ganga River sediment could be considered as the ecological indicators that find a significant role in the degradation of xenobiotic compounds. The PICRUSt-based analysis showed that ~ 35% of genes were involved in benzoate and aminobenzoate degradation where a significant portion of genes belong to nitrotoluene degradation (14%). Thus, the study uncovers a new perspective in the lineage of bacterial communities and their functional characterization of the Ganga River sediment.
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Affiliation(s)
- Ankita Srivastava
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India, 226025
| | - Digvijay Verma
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India, 226025.
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Zhu F, Zhao B, Min W, Li J. Characteristics of groundwater microbial communities and the correlation with the environmental factors in a decommissioned acid in-situ uranium mine. Front Microbiol 2022; 13:1078393. [PMID: 36909843 PMCID: PMC9992980 DOI: 10.3389/fmicb.2022.1078393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/29/2022] [Indexed: 02/24/2023] Open
Abstract
Microorganisms play an important role in the bioremediation process for the decommissioned acid in-situ leaching uranium mine. It is crucial to understand the original microbial community characteristics before the in-situ bioremediation. However, there are limited studies on the groundwater microbial characteristics in the decommissioned acid in-situ uranium mine. To this end, we collected groundwater samples, including the groundwater that originally residual in the borehole (RW) and the aquifer water (AW), from a decommissioned acid in-situ uranium mine in the southern margin of Ili Basin in Xinjiang, China. The occurrence characteristics of the groundwater microbial communities and their correlation with environmental factors were systematically studied based on the high throughput 16S rRNA gene sequencing data and geochemical data. Results found that the AW samples had higher alpha- and beta- diversity than the RW samples. The relative abundance of Sporosarcina, Sulfobacillus, Pedobacter and Pseudomonas were significantly different in the AW and RW samples, which had significant correlation with pH, metals, and sulfate, etc. A series of reducing microorganisms were discovered, such as sulfate reduction (e.g., Desulfosporosinus) and metal reduction (e.g., Arthrobacter, Bacillus, Clostridium, Pseudomonas, and Rhodanobacter), which have the potential to attenuate sulfate and uranium in groundwater. In addition, we found that pH and redox potential (Eh) were the dominant environmental factors affecting the microbial composition. This study extends our knowledge of microbial community structure changes in the decommissioned acid in-situ uranium mine and has positive implications for assessing the potential of natural attenuation and bioremediation strategies.
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Affiliation(s)
- Fangfang Zhu
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang, Jiangxi, China.,School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, Jiangxi, China
| | - Bei Zhao
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China
| | - Wenwen Min
- School of Information Science and Engineering, Yunnan University, Kunming, Yunnan, China
| | - Jiang Li
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang, Jiangxi, China.,School of Chemistry, Biology and Materials Science, East China University of Technology, Nanchang, Jiangxi, China
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Ruen-Pham K, Graham LE, Satjarak A. Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand. Plants (Basel) 2021; 10:2266. [PMID: 34834629 PMCID: PMC8622721 DOI: 10.3390/plants10112266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022]
Abstract
Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.
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Affiliation(s)
- Karnjana Ruen-Pham
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Linda E. Graham
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA;
| | - Anchittha Satjarak
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
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Babich TL, Semenova EM, Sokolova DS, Tourova TP, Bidzhieva SK, Loiko NG, Avdonin GI, Lutsenko NI, Nazina TN. Phylogenetic Diversity and Potential Activity of Bacteria and Fungi in the Deep Subsurface Horizons of an Uranium Deposit. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721040032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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9
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Maertens L, Cherry P, Tilquin F, Van Houdt R, Matroule JY. Environmental Conditions Modulate the Transcriptomic Response of Both Caulobacter crescentus Morphotypes to Cu Stress. Microorganisms 2021; 9:1116. [PMID: 34064119 PMCID: PMC8224329 DOI: 10.3390/microorganisms9061116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022] Open
Abstract
Bacteria encounter elevated copper (Cu) concentrations in multiple environments, varying from mining wastes to antimicrobial applications of copper. As the role of the environment in the bacterial response to Cu ion exposure remains elusive, we used a tagRNA-seq approach to elucidate the disparate responses of two morphotypes of Caulobacter crescentus NA1000 to moderate Cu stress in a complex rich (PYE) medium and a defined poor (M2G) medium. The transcriptome was more responsive in M2G, where we observed an extensive oxidative stress response and reconfiguration of the proteome, as well as the induction of metal resistance clusters. In PYE, little evidence was found for an oxidative stress response, but several transport systems were differentially expressed, and an increased need for histidine was apparent. These results show that the Cu stress response is strongly dependent on the cellular environment. In addition, induction of the extracytoplasmic function sigma factor SigF and its regulon was shared by the Cu stress responses in both media, and its central role was confirmed by the phenotypic screening of a sigF::Tn5 mutant. In both media, stalked cells were more responsive to Cu stress than swarmer cells, and a stronger basal expression of several cell protection systems was noted, indicating that the swarmer cell is inherently more Cu resistant. Our approach also allowed for detecting several new transcription start sites, putatively indicating small regulatory RNAs, and additional levels of Cu-responsive regulation.
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Affiliation(s)
- Laurens Maertens
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (L.M.); (R.V.H.)
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium; (P.C.); (F.T.)
| | - Pauline Cherry
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium; (P.C.); (F.T.)
| | - Françoise Tilquin
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium; (P.C.); (F.T.)
| | - Rob Van Houdt
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (L.M.); (R.V.H.)
| | - Jean-Yves Matroule
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium; (P.C.); (F.T.)
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Flynn TM, Antonopoulos DA, Skinner KA, Brulc JM, Johnston E, Boyanov MI, Kwon MJ, Kemner KM, O’Loughlin EJ. Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment. PLoS One 2021; 16:e0251883. [PMID: 34014980 PMCID: PMC8136678 DOI: 10.1371/journal.pone.0251883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/04/2021] [Indexed: 11/19/2022] Open
Abstract
Iron reduction and sulfate reduction are two of the major biogeochemical processes that occur in anoxic sediments. Microbes that catalyze these reactions are therefore some of the most abundant organisms in the subsurface, and some of the most important. Due to the variety of mechanisms that microbes employ to derive energy from these reactions, including the use of soluble electron shuttles, the dynamics between iron- and sulfate-reducing populations under changing biogeochemical conditions still elude complete characterization. Here, we amended experimental bioreactors comprised of freshwater aquifer sediment with ferric iron, sulfate, acetate, and the model electron shuttle AQDS (9,10-anthraquinone-2,6-disulfonate) and monitored both the changing redox conditions as well as changes in the microbial community over time. The addition of the electron shuttle AQDS did increase the initial rate of FeIII reduction; however, it had little effect on the composition of the microbial community. Our results show that in both AQDS- and AQDS+ systems there was an initial dominance of organisms classified as Geobacter (a genus of dissimilatory FeIII-reducing bacteria), after which sequences classified as Desulfosporosinus (a genus of dissimilatory sulfate-reducing bacteria) came to dominate both experimental systems. Furthermore, most of the ferric iron reduction occurred under this later, ostensibly “sulfate-reducing” phase of the experiment. This calls into question the usefulness of classifying subsurface sediments by the dominant microbial process alone because of their interrelated biogeochemical consequences. To better inform models of microbially-catalyzed subsurface processes, such interactions must be more thoroughly understood under a broad range of conditions.
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Affiliation(s)
- Theodore M. Flynn
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | | | - Kelly A. Skinner
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Jennifer M. Brulc
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Eric Johnston
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Maxim I. Boyanov
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Man Jae Kwon
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
- Department of Earth and Environmental Sciences, Korea University, Seoul, South Korea
| | - Kenneth M. Kemner
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Edward J. O’Loughlin
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
- * E-mail:
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11
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Lopez‐Fernandez M, Jroundi F, Ruiz‐Fresneda MA, Merroun ML. Microbial interaction with and tolerance of radionuclides: underlying mechanisms and biotechnological applications. Microb Biotechnol 2021; 14:810-828. [PMID: 33615734 PMCID: PMC8085914 DOI: 10.1111/1751-7915.13718] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 11/26/2022] Open
Abstract
Radionuclides (RNs) generated by nuclear and civil industries are released in natural ecosystems and may have a hazardous impact on human health and the environment. RN-polluted environments harbour different microbial species that become highly tolerant of these elements through mechanisms including biosorption, biotransformation, biomineralization and intracellular accumulation. Such microbial-RN interaction processes hold biotechnological potential for the design of bioremediation strategies to deal with several contamination problems. This paper, with its multidisciplinary approach, provides a state-of-the-art review of most research endeavours aimed to elucidate how microbes deal with radionuclides and how they tolerate ionizing radiations. In addition, the most recent findings related to new biotechnological applications of microbes in the bioremediation of radionuclides and in the long-term disposal of nuclear wastes are described and discussed.
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Affiliation(s)
- Margarita Lopez‐Fernandez
- Department of MicrobiologyUniversity of GranadaAvenida Fuentenueva s/nGranada18071Spain
- Present address:
Institute of Resource EcologyHelmholtz‐Zentrum Dresden‐RossendorfBautzner Landstraße 400Dresden01328Germany
| | - Fadwa Jroundi
- Department of MicrobiologyUniversity of GranadaAvenida Fuentenueva s/nGranada18071Spain
| | - Miguel A. Ruiz‐Fresneda
- Department of MicrobiologyUniversity of GranadaAvenida Fuentenueva s/nGranada18071Spain
- Present address:
Departamento de Cristalografía y Biología EstructuralCentro Superior de Investigaciones Científicas (CSIC)Instituto de Química‐Física Rocasolano (IQFR)Calle Serrano 119Madrid28006Spain
| | - Mohamed L. Merroun
- Department of MicrobiologyUniversity of GranadaAvenida Fuentenueva s/nGranada18071Spain
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12
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Safonov AV, Boguslavsky AE, Gaskova OL, Boldyrev KA, Shvartseva OS, Khvashchevskaya AA, Popova NM. Biogeochemical Modelling of Uranium Immobilization and Aquifer Remediation Strategies Near NCCP Sludge Storage Facilities. Applied Sciences 2021; 11:2875. [DOI: 10.3390/app11062875] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nitrate is a substance which influences the prevailing redox conditions in groundwater, and in turn the behaviour of U. The study of groundwater in an area with low-level radioactive sludge storage facilities has shown their contamination with sulphate and nitrate anions, uranium, and some associated metals. The uranyl ion content in the most contaminated NO3–Cl–SO4–Na borehole is 2000 times higher (1.58 mg/L) than that in the background water. At the same time, assessment of the main physiological groups of microorganisms showed a maximum number of denitrifying and sulphate-reducing bacteria (e.g., Sulfurimonas) in the water from the same borehole. Biogenic factors of radionuclide immobilization on sandy rocks of upper aquifers have been experimentally investigated. Different reduction rates of NO3−, SO42−, Fe(III) and U(VI) with stimulated microbial activity were dependent on the pollution degree. Moreover, 16S rRNA gene analysis of the microbial community after whey addition revealed a significant decrease in microbial diversity and the activation of nonspecific nitrate-reducing bacteria (genera Rhodococcus and Rhodobacter). The second influential factor can be identified as the formation of microbial biofilms on the sandy loam samples, which has a positive effect on U sorption (an increase in Kd value is up to 35%). As PHREEQC physicochemical modelling numerically confirmed, the third most influential factor that drives U mobility is the biogenic-mediated formation of a sulphide redox buffer. This study brings important information, which helps to assess the long-term stability of U in the environment of radioactive sludge storage facilities.
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Morrison KD, Zavarin M, Kersting AB, Begg JD, Mason HE, Balboni E, Jiao Y. Influence of Uranium Concentration and pH on U-Phosphate Biomineralization by Caulobacter OR37. Environ Sci Technol 2021; 55:1626-1636. [PMID: 33471994 DOI: 10.1021/acs.est.0c05437] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Uranium contamination of soils and groundwater in the United States represents a significant health risk and will require multiple remediation approaches. Microbial phosphatase activity coupled to the addition of an organic P source has recently been studied as a remediation strategy that provides an extended release of inorganic P (Pi) into U-contaminated sites, resulting in the precipitation of meta-autunite minerals. Previous laboratory- and field-based biomineralization studies have investigated environments with relatively high U concentrations (>20 μM). However, most contaminated sites have much lower U concentrations (<2 μM). The Environmental Protection Agency (EPA) limit for U in drinking water is 0.126 μM. Reaching this regulatory limit becomes challenging as U concentrations approach autunite solubility. We studied the precipitation of U(VI)-phosphate minerals by an environmental isolate of Caulobacter sp. (strain OR37) from an Oak Ridge, Tennessee, U-contaminated site. Abiotic U(VI) solubility experiments reveal that U(VI)-phosphate minerals do not form in the presence of excess Pi (500 μM) when U(VI) concentrations are <1 μM and pH is <5. When OR37 cells are reacted under the same conditions with Pi or glycerol-2-phosphate, U(VI)-phosphate mineral formation was observed, along with the formation of intracellular polyphosphate granules. These results show that bacteria provide supersaturated microenvironments needed for U(VI)-phosphate mineralization while hydrolyzing organic P sources. This provides a pathway to lower U concentrations to below EPA limits for drinking water.
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14
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Mollaei M, Timmers PHA, Suarez-Diez M, Boeren S, van Gelder AH, Stams AJM, Plugge CM. Comparative proteomics of Geobacter sulfurreducens PCA T in response to acetate, formate and/or hydrogen as electron donor. Environ Microbiol 2020; 23:299-315. [PMID: 33185968 PMCID: PMC7894505 DOI: 10.1111/1462-2920.15311] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/19/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022]
Abstract
Geobacter sulfurreducens is a model bacterium to study the degradation of organic compounds coupled to the reduction of Fe(III). The response of G. sulfurreducens to the electron donors acetate, formate, hydrogen and a mixture of all three with Fe(III) citrate as electron acceptor was studied using comparative physiological and proteomic approaches. Variations in the supplied electron donors resulted in differential abundance of proteins involved in the citric acid cycle (CAC), gluconeogenesis, electron transport, and hydrogenases and formate dehydrogenase. Our results provided new insights into the electron donor metabolism of G. sulfurreducens. Remarkably, formate was the preferred electron donor compared to acetate, hydrogen, or acetate plus hydrogen. When hydrogen was the electron donor, formate was formed, which was associated with a high abundance of formate dehydrogenase. Notably, abundant proteins of two CO2 fixation pathways (acetyl-CoA pathway and the reversed oxidative CAC) corroborated chemolithoautotrophic growth of G. sulfurreducens with formate or hydrogen and CO2 , and provided novel insight into chemolithoautotrophic growth of G. sulfurreducens.
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Affiliation(s)
- Monir Mollaei
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Peer H A Timmers
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Antonie H van Gelder
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.,Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Caroline M Plugge
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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15
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Wilpiszeski RL, Gionfriddo CM, Wymore AM, Moon JW, Lowe KA, Podar M, Rafie S, Fields MW, Hazen TC, Ge X, Poole F, Adams MWW, Chakraborty R, Fan Y, Van Nostrand JD, Zhou J, Arkin AP, Elias DA. In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations. PLoS One 2020; 15:e0232437. [PMID: 32986713 DOI: 10.1371/journal.pone.0232437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [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.
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16
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Pathak A, Jaswal R, Xu X, White JR, Edwards B, Hunt J, Brooks S, Rathore RS, Agarwal M, Chauhan A. Characterization of Bacterial and Fungal Assemblages From Historically Contaminated Metalliferous Soils Using Metagenomics Coupled With Diffusion Chambers and Microbial Traps. Front Microbiol 2020; 11:1024. [PMID: 32655505 PMCID: PMC7325934 DOI: 10.3389/fmicb.2020.01024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/27/2020] [Indexed: 01/05/2023] Open
Abstract
The majority of environmental microbiomes are not amenable to cultivation under standard laboratory growth conditions and hence remain uncharacterized. For environmental applications, such as bioremediation, it is necessary to isolate microbes performing the desired function, which may not necessarily be the fast growing or the copiotroph microbiota. Toward this end, cultivation and isolation of microbial strains using diffusion chambers (DC) and/or microbial traps (MT) have both been recently demonstrated to be effective strategies because microbial enrichment is facilitated by soil nutrients and not by synthetically defined media, thus simulating their native habitat. In this study, DC/MT chambers were established using soils collected from two US Department of Energy (DOE) sites with long-term history of heavy metal contamination, including mercury (Hg). To characterize the contamination levels and nutrient status, soils were first analyzed for total mercury (THg), methylmercury (MeHg), total carbon (TC), total nitrogen (TN), and total phosphorus (TP). Multivariate statistical analysis on these measurements facilitated binning of soils under high, medium and low levels of contamination. Bacterial and fungal microbiomes that developed within the DC and MT chambers were evaluated using comparative metagenomics, revealing Chthoniobacter, Burkholderia and Bradyrhizobium spp., as the predominant bacteria while Penicillium, Thielavia, and Trichoderma predominated among fungi. Many of these core microbiomes were also retrieved as axenic isolates. Furthermore, canonical correspondence analysis (CCA) of biogeochemical measurements, metal concentrations and bacterial communities revealed a positive correlation of Chthoniobacter/Bradyrhizobium spp., to THg whereas Burkholderia spp., correlated with MeHg. Penicillium spp., correlated with THg whereas Trichoderma spp., and Aspergillus spp., correlated with MeHg, from the MT approach. This is the first metagenomics-based assessment, isolation and characterization of soil-borne bacterial and fungal communities colonizing the diffusion chambers (DC) and microbial traps (MT) established with long-term metal contaminated soils. Overall, this study provides proof-of-concept for the successful application of DC/MT based assessment of mercury resistant (HgR) microbiomes in legacy metal-contaminated soils, having complex contamination issues. Overall, this study brings out the significance of microbial communities and their relevance in context to heavy metal cycling for better stewardship and restoration of such historically contaminated systems.
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Affiliation(s)
- Ashish Pathak
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Rajneesh Jaswal
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Xiaoyu Xu
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States
| | - John R White
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Bobby Edwards
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Jaden Hunt
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Scott Brooks
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Rajesh Singh Rathore
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Meenakshi Agarwal
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Ashvini Chauhan
- School of the Environment, Florida A&M University, Tallahassee, FL, United States
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Jroundi F, Descostes M, Povedano-Priego C, Sánchez-Castro I, Suvannagan V, Grizard P, Merroun ML. Profiling native aquifer bacteria in a uranium roll-front deposit and their role in biogeochemical cycle dynamics: Insights regarding in situ recovery mining. Sci Total Environ 2020; 721:137758. [PMID: 32179349 DOI: 10.1016/j.scitotenv.2020.137758] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 05/13/2023]
Abstract
A uranium-mineralized sandy aquifer, planned for mining by means of uranium in situ recovery (U ISR), harbors a reservoir of bacterial life that may influence the biogeochemical cycles surrounding uranium roll-front deposits. Since microorganisms play an important role at all stages of U ISR, a better knowledge of the resident bacteria before any ISR actuations is essential to face environmental quality assessment. The focus here was on the characterization of bacteria residing in an aquifer surrounding a uranium roll-front deposit that forms part of an ISR facility project at Zoovch Ovoo (Mongolia). Water samples were collected following the natural redox zonation inherited in the native aquifer, including the mineralized orebody, as well as compartments located both upstream (oxidized waters) and downstream (reduced waters) of this area. An imposed chemical zonation for all sensitive redox elements through the roll-front system was observed. In addition, high-throughput sequencing data showed that the bacterial community structure was shaped by the redox gradient and oxygen availability. Several interesting bacteria were identified, including sulphate-reducing (e.g. Desulfovibrio, Nitrospira), iron-reducing (e.g. Gallionella, Sideroxydans), iron-oxidizing (e.g. Rhodobacter, Albidiferax, Ferribacterium), and nitrate-reducing bacteria (e.g. Pseudomonas, Aquabacterium), which may also be involved in metal reduction (e.g. Desulfovibrio, Ferribacterium, Pseudomonas, Albidiferax, Caulobacter, Zooglea). Canonical correspondence analysis (CCA) and co-occurrence patterns confirmed strong correlations among the bacterial genera, suggesting either shared/preferred environmental conditions or the performance of similar/complementary functions. As a whole, the bacterial community residing in each aquifer compartment would appear to define an ecologically functional ecosystem, containing suitable microorganisms (e.g. acidophilic bacteria) prone to promote the remediation of the acidified aquifer by natural attenuation. Assessing the composition and structure of the aquifer's native bacteria is a prerequisite for understanding natural attenuation and predicting the role of bacterial input in improving ISR efficiency.
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Affiliation(s)
- Fadwa Jroundi
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain.
| | | | - Cristina Povedano-Priego
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain.
| | - Iván Sánchez-Castro
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain.
| | | | - Pierre Grizard
- ORANO Mining, 125 avenue de Paris, F-92330 Châtillon, France.
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain.
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18
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Ho Y. Comments on: Li et al. (2019) “Bioelectrochemical Systems for Groundwater Remediation: The Development Trend and Research Front Revealed by Bibliometric Analysis” Water, 11, 1532. Water 2020; 12:1586. [DOI: 10.3390/w12061586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Li et al. (2019) used inappropriate searching words and method to publish a bibliometric paper in Water. The results show a huge difference from the results by using an appropriate method. This comment points out each of problems.
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Nazina T, Babich T, Kostryukova N, Sokolova D, Abdullin R, Tourova T, Kadnikov V, Mardanov A, Ravin N, Grouzdev D, Poltaraus A, Kalmykov S, Safonov A, Zakharova E, Novikov A, Kato K. Ultramicrobacteria from Nitrate- and Radionuclide-Contaminated Groundwater. Sustainability 2020; 12:1239. [DOI: 10.3390/su12031239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The goal of the present work was to investigate the physicochemical and radiochemical conditions and the microbial diversity in groundwater collected near the Lake Karachai (Russia), which was formerly used for the disposal of liquid radioactive waste, to isolate the dominant bacteria, and to determine their taxonomy and the physiological characteristics responsible for their adaptation to this environment. Groundwater samples contained high concentrations of acetate, oxalate, nitrate, and sulfate, as well as radionuclides. High-throughput sequencing and analysis of the clone libraries revealed lower microbial diversity in the most strongly contaminated groundwater and a predominance of bacteria of the genera Polynucleobacter, Pusillimonas, Candidatus Pelagibacter, and of the candidate phylum Parcubacteria; these groups include species with an ultra small cell size. Archaeal sequences in the libraries belonged to ammonium oxidizers of the phylum Thaumarchaeota and methanogens of the phylum Euryarchaeota. Pure cultures of obligate and facultative ultramicrobacteria belonging to the genera Chryseobacterium, Microbacterium, Salinibacterium, Pusillimonas, Roseomonas, and Janibacter were isolated from water samples. In genomes of Pusillimonas and Roseomonas strains the genes associated with nitrate reduction, resistance to heavy metals and metalloids were revealed. Several isolates are able to participate in the geochemical process of nitrate conversion to N2 using acetate; this results in decreasing redox potential, which in turn may stimulate radionuclide reduction and decrease radionuclide migration in groundwater.
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Jaswal R, Pathak A, Chauhan A. Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils. Microorganisms 2019; 7:E324. [PMID: 31489900 DOI: 10.3390/microorganisms7090324] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/27/2019] [Accepted: 09/02/2019] [Indexed: 01/06/2023] Open
Abstract
Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the “core” microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired “core” microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis of the DC/MT generations also revealed that enrichment and stable populations of the desired “core” bacterial and fungal microbiomes develop within the first 20 days of incubation and the practice of subsequent transfers for second and third generations, as is standard in previous studies, may be unnecessary. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies, which were run for months. In summation, it was concluded that, using the diffusion chamber-based enrichment techniques, growth of desired microbiota possessing environmentally relevant functions can be achieved in a much shorter time frame than has been previously shown.
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Jaswal R, Pathak A, Edwards B III, Lewis R III, Seaman JC, Stothard P, Krivushin K, Blom J, Rupp O, Chauhan A. Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA. Genes (Basel) 2019; 10:E325. [PMID: 31035394 DOI: 10.3390/genes10050325] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/19/2019] [Accepted: 04/24/2019] [Indexed: 11/17/2022] Open
Abstract
Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.
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Zhao X, Huang J, Lu J, Sun Y. Study on the influence of soil microbial community on the long-term heavy metal pollution of different land use types and depth layers in mine. Ecotoxicol Environ Saf 2019; 170:218-226. [PMID: 30529916 DOI: 10.1016/j.ecoenv.2018.11.136] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 05/27/2023]
Abstract
To understand the importance of the response of soil microbial communities to the stress of heavy metals around mining areas by assessing the feedback of soil ecosystems in different soil habitats, this article selected different land use types (Mining area, Dressing area, Heap mine area, Tailings area and Vegetable field) and surface soil samples of different depths (0-10 cm, 10-20 cm, 20-30 cm) as the variables related to the mining activities in the Shizishan mining area in Tongling, Anhui Province, China. Soil physicochemical properties and heavy metal concentrations of the different land use types and soil depths were compared. Illumina MiSeq. 2500 Sequencing Technology was used to analyze the abundance and structural diversity of the microbial community in soil samples. The relationship between mine soil pollution characteristics and microbial community were investigated. The results showed that soil physicochemical properties and heavy metals significantly affected the microbial community. The microbial community structure was significantly variable in vertical soil depth-layer habitats. The relative abundance (1%) of the soil microbial community at the phylum level was represented by a total of 14 phyla, where the two most dominant phyla were Proteobacteria (41.71%) and Firmicutes (20.44%). The two bacteria were positively related with Cu, Zn, Pb, and pH but negatively associated with soil organic matter (SOM), available potassium (AK), and moisture content (MC). Therefore, Proteobacteria and Firmicutes were highly resistant to heavy metals. These results increased our understanding of microbial variation and assembly pattern under different land use types in heavy metals contaminated mining soils.
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Affiliation(s)
- Xingqing Zhao
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, PR China.
| | - Jian Huang
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, PR China
| | - Jin Lu
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, PR China
| | - Yu Sun
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, PR China
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Lacerda-Júnior GV, Noronha MF, Cabral L, Delforno TP, de Sousa STP, Fernandes-Júnior PI, Melo IS, Oliveira VM. Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest. Front Microbiol 2019; 10:648. [PMID: 31024471 PMCID: PMC6461016 DOI: 10.3389/fmicb.2019.00648] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/14/2019] [Indexed: 12/21/2022] Open
Abstract
Drylands occupy approximately 41% of the Earth's terrestrial surface. Climate change and land use practices are expected to affect biogeochemical cycling by the soil microbiome in these ecosystems. Understanding how soil microbial community might respond to these drivers is extremely important to mitigate the processes of land degradation and desertification. The Caatinga, an exclusively Brazilian biome composed of an extensive seasonal tropical dry forest, is exposed to variable spatiotemporal rainfall patterns as well as strong human-driven pressures. Herein, an integrated analysis of shotgun metagenomics approach coupled to meteorological data was employed to unravel the impact of seasonality and land use change on soil microbiome from preserved and agriculture-affected experimental fields in Caatinga drylands. Multivariate analysis suggested that microbial communities of preserved soils under seasonal changes were shaped primarily by water deficit, with a strong increase of Actinobacteria and Proteobacteria members in the dry and rainy seasons, respectively. In contrast, nutrient availability notably played a critical role in driving the microbial community in agriculture-affected soils. The strong enrichment of bacterial genera belonging to the poorly-known phylum Acidobacteria ('Candidatus Solibacter' and 'Candidatus Koribacter') in soils from dry season affected by ferti-irrigation practices presupposes a contrasting copiotrophic lifestyle and ecological role in mitigating the impact of chemical fertilization. Functional analyses identify overrepresented genes related to osmotic stress response (synthesis of osmoprotectant compounds, accumulation of potassium ions) and preferential carbon and nitrogen utilization when comparing the microbiome of preserved soils under seasonal changes, reflecting differences in the genetic potential for nutrient cycling and C acquisition in the environment. However, the prevalence of nitrosative stress and denitrification functions in irrigation/fertilization-affected soils of the dry season clearly suggest that nutrient input and disruption of natural water regime may impact biogeochemical cycles linked to the microbial processes, with potential impacts on the ecosystem functionality. These findings help to better understand how natural seasonality and agricultural management differentially affect soil microbial ecology from dry forests, providing support for the development of more sustainable land management in dryland ecosystems.
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Affiliation(s)
- Gileno V. Lacerda-Júnior
- Brazilian Agricultural Research Corporation, Embrapa Meio Ambiente, Jaguariúna, Brazil
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
| | - Melline F. Noronha
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
| | - Lucélia Cabral
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Tiago P. Delforno
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
| | - Sanderson Tarciso Pereira de Sousa
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
| | | | - Itamar S. Melo
- Brazilian Agricultural Research Corporation, Embrapa Meio Ambiente, Jaguariúna, Brazil
| | - Valéria M. Oliveira
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
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Agarwal M, Pathak A, Rathore RS, Prakash O, Singh R, Jaswal R, Seaman J, Chauhan A. Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress. Cells 2018; 7:cells7120269. [PMID: 30545132 PMCID: PMC6315756 DOI: 10.3390/cells7120269] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 01/15/2023] Open
Abstract
Two Burkholderia spp. (strains SRS-25 and SRS-46) were isolated from high concentrations of uranium (U) from the U.S. Department of Energy (DOE)-managed Savannah River Site (SRS). SRS contains soil gradients that remain co-contaminated by heavy metals from previous nuclear weapons production activities. Uranium (U) is one of the dominant contaminants within the SRS impacted soils, which can be microbially transformed into less toxic forms. We established microcosms containing strains SRS-25 and SRS-46 spiked with U and evaluated the microbially-mediated depletion with concomitant genomic and proteomic analysis. Both strains showed a rapid depletion of U; draft genome sequences revealed SRS-25 genome to be of approximately 8,152,324 bp, a G + C content of 66.5, containing a total 7604 coding sequences with 77 total RNA genes. Similarly, strain SRS-46 contained a genome size of 8,587,429 bp with a G + C content of 67.1, 7895 coding sequences, with 73 total RNA genes, respectively. An in-depth, genome-wide comparisons between strains 25, 46 and a previously isolated strain from our research (Burkholderia sp. strain SRS-W-2-2016), revealed a common pool of 3128 genes; many were found to be homologues to previously characterized metal resistance genes (e.g., for cadmium, cobalt, and zinc), as well as for transporter, stress/detoxification, cytochromes, and drug resistance functions. Furthermore, proteomic analysis of strains with or without U stress, revealed the increased expression of 34 proteins from strain SRS-25 and 52 proteins from strain SRS-46; similar to the genomic analyses, many of these proteins have previously been shown to function in stress response, DNA repair, protein biosynthesis and metabolism. Overall, this comparative proteogenomics study confirms the repertoire of metabolic and stress response functions likely rendering the ecological competitiveness to the isolated strains for colonization and survival in the heavy metals contaminated SRS soil habitat.
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Affiliation(s)
- Meenakshi Agarwal
- Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA.
| | - Ashish Pathak
- Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA.
| | - Rajesh Singh Rathore
- Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA.
| | - Om Prakash
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India.
| | - Rakesh Singh
- Translational Science Lab, College of Medicine, Florida State University, Tallahassee, FL 32304, USA.
| | - Rajneesh Jaswal
- Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA.
| | - John Seaman
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA.
| | - Ashvini Chauhan
- Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA.
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Hershey OS, Kallmeyer J, Wallace A, Barton MD, Barton HA. High Microbial Diversity Despite Extremely Low Biomass in a Deep Karst Aquifer. Front Microbiol 2018; 9:2823. [PMID: 30534116 PMCID: PMC6275181 DOI: 10.3389/fmicb.2018.02823] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
Despite the importance of karst aquifers as a source of drinking water, little is known about the role of microorganisms in maintaining the quality of this water. One of the limitations in exploring the microbiology of these environments is access, which is usually limited to wells and surface springs. In this study, we compared the microbiology of the Madison karst aquifer sampled via the potentiometric lakes of Wind Cave with surface sampling wells and a spring. Our data indicated that only the Streeter Well (STR), which is drilled into the same hydrogeologic domain as the Wind Cave Lakes (WCL), allowed access to water with the same low biomass (1.56-9.25 × 103 cells mL-1). Filtration of ∼300 L of water from both of these sites through a 0.2 μm filter allowed the collection of sufficient cells for DNA extraction, PCR amplification of 16S rRNA gene sequences, and identification through pyrosequencing. The results indicated that bacteria (with limited archaea and no detectable eukaryotic organisms) dominated both water samples; however, there were significant taxonomic differences in the bacterial populations of the samples. The STR sample was dominated by a single phylotype within the Gammaproteobacteria (Order Acidithiobacillales), which dramatically reduced the overall diversity and species richness of the population. In WCL, despite less organic carbon, the bacterial population was significantly more diverse, including significant contributions from the Gammaproteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Planctomycetes, Fusobacter, and Omnitrophica phyla. Comparisons with similar oligotrophic environments suggest that karst aquifers have a greater species richness than comparable surface environs. These data also demonstrate that Wind Cave provides a unique opportunity to sample a deep, subterranean aquifer directly, and that the microbiology of such aquifers may be more complex than previously anticipated.
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Affiliation(s)
- Olivia S Hershey
- Department of Biology, University of Akron, Akron, OH, United States
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Andrew Wallace
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, United States
| | | | - Hazel A Barton
- Department of Biology, University of Akron, Akron, OH, United States.,Department of Geosciences, University of Akron, Akron, OH, United States
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Safonov AV, Babich TL, Sokolova DS, Grouzdev DS, Tourova TP, Poltaraus AB, Zakharova EV, Merkel AY, Novikov AP, Nazina TN. Microbial Community and in situ Bioremediation of Groundwater by Nitrate Removal in the Zone of a Radioactive Waste Surface Repository. Front Microbiol 2018; 9:1985. [PMID: 30190715 PMCID: PMC6115527 DOI: 10.3389/fmicb.2018.01985] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/07/2018] [Indexed: 12/26/2022] Open
Abstract
The goal of the present work was to investigate the physicochemical and radiochemical conditions and the composition of the microbial community in the groundwater of a suspended surface repository for radioactive waste (Russia) and to determine the possibility of in situ groundwater bioremediation by removal of nitrate ions. Groundwater in the repository area (10-m depth) had elevated concentrations of strontium, tritium, nitrate, sulfate, and bicarbonate ions. High-throughput sequencing of the V3-V4/V4 region of the 16S rRNA gene revealed the presence of members of the phyla Proteobacteria (genera Acidovorax, Simplicispira, Thermomonas, Thiobacillus, Pseudomonas, Brevundimonas, and uncultured Oxalobacteraceae), Firmicutes (genera Bacillus and Paenibacillus), and Actinobacteria (Candidatus Planktophila, Gaiella). Canonical correspondence analysis suggested that major contaminant - nitrate, uranium, and sulfate shaped the composition of groundwater microbial community. Groundwater samples contained culturable aerobic organotrophic, as well as anaerobic fermenting, iron-reducing, and denitrifying bacteria. Pure cultures of 33 bacterial strains belonging to 15 genera were isolated. Members of the genera Pseudomonas, Rhizobium, Cupriavidus, Shewanella, Ensifer, and Thermomonas reduced nitrate to nitrite and/or dinitrogen. Application of specific primers revealed the nirS and nirK genes encoding nitrite reductases in bacteria of the genera Pseudomonas, Rhizobium, and Ensifer. Nitrate reduction by pure bacterial cultures resulted in decreased ambient Eh. Among the organic substrates tested, sodium acetate and milk whey were the best for stimulation of denitrification by the microcosms with groundwater microorganisms. Injection of these substrates into the subterranean horizon (single-well push-pull test) resulted in temporary removal of nitrate ions in the area of the suspended radioactive waste repository and confirmed the possibility for in situ application of this method for bioremediation.
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Affiliation(s)
- Alexey V. Safonov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
- V.I. Vernadsky Institute of Geochemistry and Analytical Chemistry of Russian Academy of Sciences, Moscow, Russia
| | - Tamara L. Babich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Diyana S. Sokolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Denis S. Grouzdev
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Tatiyana P. Tourova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey B. Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena V. Zakharova
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
- V.I. Vernadsky Institute of Geochemistry and Analytical Chemistry of Russian Academy of Sciences, Moscow, Russia
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander P. Novikov
- V.I. Vernadsky Institute of Geochemistry and Analytical Chemistry of Russian Academy of Sciences, Moscow, Russia
| | - Tamara N. Nazina
- V.I. Vernadsky Institute of Geochemistry and Analytical Chemistry of Russian Academy of Sciences, Moscow, Russia
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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28
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Field EK, Blaskovich JP, Peyton BM, Gerlach R. Carbon-dependent chromate toxicity mechanism in an environmental Arthrobacter isolate. J Hazard Mater 2018; 355:162-169. [PMID: 29800910 DOI: 10.1016/j.jhazmat.2018.05.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 05/08/2018] [Accepted: 05/10/2018] [Indexed: 06/08/2023]
Abstract
Arthrobacter spp. are widespread in soil systems and well-known for their Cr(VI) reduction capabilities making them attractive candidates for in situ bioremediation efforts. Cellulose drives carbon flow in soil systems; yet, most laboratory studies evaluate Arthrobacter-Cr(VI) interactions solely with nutrient-rich media or glucose. This study aims to determine how various cellulose degradation products and biostimulation substrates influence Cr(VI) toxicity, reduction, and microbial growth of an environmental Arthrobacter sp. isolate. Laboratory culture-based studies suggest there is a carbon-dependent Cr(VI) toxicity mechanism that affects subsequent Cr(VI) reduction by strain LLW01. Strain LLW01 could only grow in the presence of, and reduce, 50 μM Cr(VI) when glucose or lactate were provided. Compared to lactate, Cr(VI) was at least 30-fold and 10-fold more toxic when ethanol or butyrate was the sole carbon source, respectively. The addition of sulfate mitigated toxicity somewhat, but had no effect on the extent of Cr(VI) reduction. Cell viability studies indicated that a small fraction of cells were viable after 8 days suggesting cell growth and subsequent Cr(VI) reduction may resume. These results suggest when designing bioremediation strategies with Arthrobacter spp. such as strain LLW01, carbon sources such as glucose and lactate should be considered over ethanol and butyrate.
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Affiliation(s)
- Erin K Field
- Department of Biology, East Carolina University, Greenville, NC, 27858, United States; Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, United States.
| | - John P Blaskovich
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, United States; Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, United States
| | - Brent M Peyton
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, United States; Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, United States
| | - Robin Gerlach
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, United States; Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, United States.
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29
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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: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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30
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Lopez-Fernandez M, Romero-González M, Günther A, Solari PL, Merroun ML. Effect of U(VI) aqueous speciation on the binding of uranium by the cell surface of Rhodotorula mucilaginosa, a natural yeast isolate from bentonites. Chemosphere 2018; 199:351-360. [PMID: 29453061 DOI: 10.1016/j.chemosphere.2018.02.055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 02/06/2018] [Accepted: 02/08/2018] [Indexed: 06/08/2023]
Abstract
This study presents the effect of aqueous uranium speciation (U-hydroxides and U-hydroxo-carbonates) on the interaction of this radionuclide with the cells of the yeast Rhodotorula mucigilanosa BII-R8. This strain was isolated from Spanish bentonites considered as reference materials for the engineered barrier components of the future deep geological repository of radioactive waste. X-ray absorption and infrared spectroscopy showed that the aqueous uranium speciation has no effect on the uranium binding process by this yeast strain. The cells bind mobile uranium species (U-hydroxides and U-hydroxo-carbonates) from solution via a time-dependent process initiated by the adsorption of uranium species to carboxyl groups. This leads to the subsequent involvement of organic phosphate groups forming uranium complexes with a local coordination similar to that of the uranyl mineral phase meta-autunite. Scanning transmission electron microscopy with high angle annular dark field analysis showed uranium accumulations at the cell surface associated with phosphorus containing ligands. Moreover, the effect of uranium mobile species on the cell viability and metabolic activity was examined by means of flow cytometry techniques, revealing that the cell metabolism is more affected by higher concentrations of uranium than the cell viability. The results obtained in this work provide new insights on the interaction of uranium with bentonite natural yeast from genus Rhodotorula under deep geological repository relevant conditions.
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Affiliation(s)
| | | | - Alix Günther
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Pier L Solari
- MARS Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette Cedex, France
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31
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Sutcliffe B, Chariton AA, Harford AJ, Hose GC, Stephenson S, Greenfield P, Midgley DJ, Paulsen IT. Insights from the Genomes of Microbes Thriving in Uranium-Enriched Sediments. Microb Ecol 2018; 75:970-984. [PMID: 29128951 DOI: 10.1007/s00248-017-1102-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/26/2017] [Indexed: 06/07/2023]
Abstract
Elevated uranium dose (4 g kg-1) causes a shift in billabong sediment communities that result in the enrichment of five bacterial species. These taxa include Geobacter, Geothrix and Dyella species, as well as a novel-potentially predatory-Bacteroidetes species, and a new member of class Anaerolineae (Chloroflexi). Additionally, a population of methanogenic Methanocella species was also identified. Genomic reconstruction and metabolic examination of these taxa reveal a host of divergent life strategies and putative niche partitioning. Resistance-nodulation-division heavy metal efflux (RND-HME) transporters are implicated as potential uranium tolerance strategies among the bacterial taxa. Potential interactions, uranium tolerance and ecologically relevant catabolism are presented in a conceptual model of life in this environment.
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Affiliation(s)
- Brodie Sutcliffe
- Macquarie University, Sydney, NSW, 2109, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), PO BOX 52, North Ryde, NSW, 1670, Australia
| | | | - Andrew J Harford
- Supervising Scientist Branch, Department of the Environment and Energy, Darwin, NT, Australia
| | - Grant C Hose
- Macquarie University, Sydney, NSW, 2109, Australia
| | - Sarah Stephenson
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), PO BOX 52, North Ryde, NSW, 1670, Australia
| | - Paul Greenfield
- Macquarie University, Sydney, NSW, 2109, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), PO BOX 52, North Ryde, NSW, 1670, Australia
| | - David J Midgley
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), PO BOX 52, North Ryde, NSW, 1670, Australia
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Krawczyk-Bärsch E, Gerber U, Müller K, Moll H, Rossberg A, Steudtner R, Merroun ML. Multidisciplinary characterization of U(VI) sequestration by Acidovorax facilis for bioremediation purposes. J Hazard Mater 2018; 347:233-241. [PMID: 29324323 DOI: 10.1016/j.jhazmat.2017.12.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 12/04/2017] [Accepted: 12/10/2017] [Indexed: 06/07/2023]
Abstract
The contamination of the environment by U may affect plant life and consequently may have an impact on animal and human health. The present work describes U(VI) sequestration by Acidovorax facilis using a multidisciplinary approach combining wet chemistry, transmission electron microscopy, and spectroscopy methods (e.g. cryo-time resolved laser-induced fluorescence spectroscopy, extended X-ray absorption fine structure spectroscopy, and in-situ attenuated total reflection Fourier transform infrared spectroscopy). This bacterial strain is widely distributed in nature including U-contaminated sites. In kinetic batch experiments cells of A. facilis were contacted for 5 min to 48 h with 0.1 mM U(VI). The results show that the local coordination of U species associated with the cells depends upon time contact. U is bound mainly to phosphate groups of lipopolysaccharide (LPS) at the outer membrane within the first hour. And, that both, phosphoryl and carboxyl functionality groups of LPS and peptidoglycan of A. facilis cells may effectuate the removal of high U amounts from solution at 24-48 h of incubation. It is clearly demonstrated that A. facilis may play an important role in predicting the transport behaviour of U in the environment and that the results will contribute to the improvement of bioremediation methods of U-contaminated sites.
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Affiliation(s)
- E Krawczyk-Bärsch
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, D-01328 Dresden, Germany.
| | - U Gerber
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, D-01328 Dresden, Germany
| | - K Müller
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, D-01328 Dresden, Germany
| | - H Moll
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, D-01328 Dresden, Germany
| | - A Rossberg
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, D-01328 Dresden, Germany
| | - R Steudtner
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, D-01328 Dresden, Germany
| | - M L Merroun
- University of Granada, Department of Microbiology, Campus Fuentenueva, E-18071 Granada, Spain
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33
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Christensen GA, Moon J, Veach AM, Mosher JJ, Wymore AM, van Nostrand JD, Zhou J, Hazen TC, Arkin AP, Elias DA. Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition. PLoS One 2018; 13:e0194663. [PMID: 29558522 PMCID: PMC5860781 DOI: 10.1371/journal.pone.0194663] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/07/2018] [Indexed: 02/01/2023] Open
Abstract
Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion of the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems.
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Affiliation(s)
- Geoff A. Christensen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - JiWon Moon
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Allison M. Veach
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jennifer J. Mosher
- Marshall University, Biological Sciences, Huntington, West Virginia, United States of America
| | - Ann M. Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | | | - Jizhong Zhou
- University of Oklahoma, Norman, Oklahoma, United States of America
| | - Terry C. Hazen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- University of Tennessee, Knoxville, Tennessee, United States of America
| | - Adam P. Arkin
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- University of California at Berkeley, Berkeley, California, United States of America
| | - Dwayne A. Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail:
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Hillesland KL. Evolution on the bright side of life: microorganisms and the evolution of mutualism. Ann N Y Acad Sci 2017; 1422:88-103. [PMID: 29194650 DOI: 10.1111/nyas.13515] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/05/2017] [Accepted: 09/11/2017] [Indexed: 01/15/2023]
Abstract
Mutualistic interactions, where two interacting species have a net beneficial effect on each other's fitness, play a crucial role in the survival and evolution of many species. Despite substantial empirical and theoretical work in past decades, the impact of these interactions on natural selection is not fully understood. In addition, mutualisms between microorganisms have been largely ignored, even though they are ecologically important and can be used as tools to bridge the gap between theory and empirical work. Here, I describe two problems with our current understanding of natural selection in mutualism and highlight the properties of microbial mutualisms that could help solve them. One problem is that bias and methodological problems have limited our understanding of the variety of mechanisms by which species may adapt to mutualism. Another problem is that it is rare for experiments testing coevolution in mutualism to address whether each species has adapted to evolutionary changes in its partner. These problems can be addressed with genome resequencing and time-shift experiments, techniques that are easier to perform in microorganisms. In addition, microbial mutualisms may inspire novel insights and hypotheses about natural selection in mutualism.
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Sutcliffe B, Chariton AA, Harford AJ, Hose GC, Greenfield P, Elbourne LDH, Oytam Y, Stephenson S, Midgley DJ, Paulsen IT. Effects of uranium concentration on microbial community structure and functional potential. Environ Microbiol 2017. [DOI: 10.1111/1462-2920.13839] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Brodie Sutcliffe
- Macquarie UniversitySydney New South Wales, 2109 Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)Canberra Australia
| | | | - Andrew J. Harford
- Supervising Scientist Branch, Department of the Environment and EnergyDarwin Northern Territory Australia
| | - Grant C. Hose
- Macquarie UniversitySydney New South Wales, 2109 Australia
| | - Paul Greenfield
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)Canberra Australia
| | | | - Yalchin Oytam
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)Canberra Australia
| | - Sarah Stephenson
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)Canberra Australia
| | - David J. Midgley
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)Canberra Australia
| | - Ian T. Paulsen
- Macquarie UniversitySydney New South Wales, 2109 Australia
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Zhang P, He Z, Van Nostrand JD, Qin Y, Deng Y, Wu L, Tu Q, Wang J, Schadt CW, W Fields M, Hazen TC, Arkin AP, Stahl DA, Zhou J. Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer. Environ Sci Technol 2017; 51:3609-3620. [PMID: 28300407 DOI: 10.1021/acs.est.6b02980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
To further understand the diversity and dynamics of SRB in response to substrate amendment, we sequenced genes coding for the dissimilatory sulfite reductase (dsrA) in groundwater samples collected after an emulsified vegetable oil (EVO) amendment, which sustained U(VI)-reducing conditions for one year in a fast-flowing aquifer. EVO amendment significantly altered the composition of groundwater SRB communities. Sequences having no closely related-described species dominated (80%) the indigenous SRB communities in nonamended wells. After EVO amendment, Desulfococcus, Desulfobacterium, and Desulfovibrio, known for long-chain-fatty-acid, short-chain-fatty-acid and H2 oxidation and U(VI) reduction, became dominant accounting for 7 ± 2%, 21 ± 8%, and 55 ± 8% of the SRB communities, respectively. Succession of these SRB at different bioactivity stages based on redox substrates/products (acetate, SO4-2, U(VI), NO3-, Fe(II), and Mn(II)) was observed. Desulfovibrio and Desulfococcus dominated SRB communities at 4-31 days, whereas Desulfobacterium became dominant at 80-140 days. By the end of the experiment (day 269), the abundance of these SRB decreased but the overall diversity of groundwater SRB was still higher than non-EVO controls. Up to 62% of the SRB community changes could be explained by groundwater geochemical variables, including those redox substrates/products. A significant (P < 0.001) correlation was observed between groundwater U(VI) concentrations and Desulfovibrio abundance. Our results showed that the members of SRB and their dynamics were correlated significantly with slow EVO biodegradation, electron donor production and maintenance of U(VI)-reducing conditions in the aquifer.
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Affiliation(s)
- Ping Zhang
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Yujia Qin
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Ye Deng
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
- Research Center for Eco-Environmental Science, Chinese Academy of Sciences , Beijing 100085, China
| | - Liyou Wu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Qichao Tu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
- Department of Marine Sciences, Ocean College, Zhejiang University , Zhejiang, China
| | - Jianjun Wang
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences , Nanjing 210008, China
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University , Bozeman, Montana 59717, United States
| | - Terry C Hazen
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Adam P Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington , Seattle, Washington 98105, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, Oklahoma 73019, United States
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University , Beijing 100084, China
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King AJ, Preheim SP, Bailey KL, Robeson MS, Roy Chowdhury T, Crable BR, Hurt RA, Mehlhorn T, Lowe KA, Phelps TJ, Palumbo AV, Brandt CC, Brown SD, Podar M, Zhang P, Lancaster WA, Poole F, Watson DB, W Fields M, Chandonia JM, Alm EJ, Zhou J, Adams MWW, Hazen TC, Arkin AP, Elias DA. Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation. Environ Sci Technol 2017; 51:2879-2889. [PMID: 28112946 DOI: 10.1021/acs.est.6b04751] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads), and biogeochemical parameters are monitored by quantifying 53 metals, 12 organic acids, 14 anions, and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community and responded to DO. This also directly influenced the pH, and so the biotic impacts of DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part not only by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.
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Affiliation(s)
- Andrew J King
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Sarah P Preheim
- Department of Environmental Health and Enginering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Kathryn L Bailey
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Michael S Robeson
- Fish, Wildlife and Conservation Biology, Colorado State University , Fort Collins, Colorado 80523, United States
| | - Taniya Roy Chowdhury
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Bryan R Crable
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Richard A Hurt
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Tonia Mehlhorn
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Kenneth A Lowe
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Tommy J Phelps
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Anthony V Palumbo
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Craig C Brandt
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Ping Zhang
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States
| | - Farris Poole
- Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States
| | - David B Watson
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Matthew W Fields
- Department of Microbiology & Immunology, Montana State University , Bozeman, Montana 59717, United States
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkley National Laboratory , Berkley, California 94720, United States
| | - Eric J Alm
- Civil and Environmental Engineering and Biological Engineering, Massachusets Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States
| | - Terry C Hazen
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkley National Laboratory , Berkley, California 94720, United States
| | - Dwayne A Elias
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
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Sánchez-Castro I, Amador-García A, Moreno-Romero C, López-Fernández M, Phrommavanh V, Nos J, Descostes M, Merroun ML. Screening of bacterial strains isolated from uranium mill tailings porewaters for bioremediation purposes. J Environ Radioact 2017; 166:130-141. [PMID: 27068793 DOI: 10.1016/j.jenvrad.2016.03.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 03/07/2016] [Accepted: 03/21/2016] [Indexed: 06/05/2023]
Abstract
The present work characterizes at different levels a number of bacterial strains isolated from porewaters sampled in the vicinity of two French uranium tailing repositories. The 16S rRNA gene from 33 bacterial isolates, corresponding to the different morphotypes recovered, was almost fully sequenced. The resulting sequences belonged to 13 bacterial genera comprised in the phyla Firmicutes, Actinobacteria and Proteobacteria. Further characterization at physiological level and metals/metalloid tolerance provided evidences for an appropriate selection of bacterial strains potentially useful for immobilization of uranium and other common contaminants. By using High Resolution Transmission Electron Microscope (HRTEM), this potential ability to immobilize uranium as U phosphate mineral phases was confirmed for the bacterial strains Br3 and Br5 corresponding to Arthrobacter sp. and Microbacterium oxydans, respectively. Scanning Transmission Electron Microscope- High-Angle Annular Dark-Field (STEM-HAADF) analysis showed U accumulates on the surface and within bacterial cytoplasm, in addition to the extracellular space. Energy Dispersive X-ray (EDX) element-distribution maps demonstrated the presence of U and P within these accumulates. These results indicate the potential of certain bacterial strains isolated from porewaters of U mill tailings for immobilizing uranium, likely as uranium phosphates. Some of these bacterial isolates might be considered as promising candidates in the design of uranium bioremediation strategies.
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Affiliation(s)
- Iván Sánchez-Castro
- Departamento de Microbiología, Campus de Fuentenueva, Universidad de Granada, 18071, Granada, Spain.
| | - Ahinara Amador-García
- Departamento de Microbiología, Campus de Fuentenueva, Universidad de Granada, 18071, Granada, Spain
| | - Cristina Moreno-Romero
- Departamento de Microbiología, Campus de Fuentenueva, Universidad de Granada, 18071, Granada, Spain
| | | | | | - Jeremy Nos
- R&D Department, AREVA Mines, La Défense, 92084, Paris, France
| | | | - Mohamed L Merroun
- Departamento de Microbiología, Campus de Fuentenueva, Universidad de Granada, 18071, Granada, Spain
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Czaplicki LM, Gunsch CK. Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics. J Environ Eng (New York) 2016; 142:10.1061/(ASCE)EE.1943-7870.0001141. [PMID: 28348455 PMCID: PMC5364726 DOI: 10.1061/(asce)ee.1943-7870.0001141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/31/2016] [Indexed: 05/30/2023]
Abstract
Bioremediation is generally viewed as a cost effective and sustainable technology because it relies on microbes to transform pollutants into benign compounds. Advances in molecular biological analyses allow unprecedented microbial detection and are increasingly incorporated into bioremediation. Throughout history, state-of-the-art techniques have informed bioremediation strategies. However, the insights those techniques provided were not as in depth as those provided by recently developed omics tools. Advances in next generation sequencing (NGS) have now placed metagenomics and metatranscriptomics within reach of environmental engineers. As NGS costs decrease, metagenomics and metatranscriptomics have become increasingly feasible options to rapidly scan sites for specific degradative functions and identify microorganisms important in pollutant degradation. These omic techniques are capable of revolutionizing biological treatment in environmental engineering by allowing highly sensitive characterization of previously uncultured microorganisms. Omics enables the discovery of novel microorganisms for use in bioaugmentation and supports systematic optimization of biostimulation strategies. This review describes the omics journey from roots in biology and medicine to its current status in environmental engineering including potential future directions in commercial application.
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Affiliation(s)
- Lauren M. Czaplicki
- Ph.D. Candidate, Department of Civil & Environmental Engineering, Duke University, Durham, NC 27708-0287 USA
| | - Claudia K. Gunsch
- Associate Professor, Department of Civil & Environmental Engineering, Duke University, Durham, NC 27708-0287 USA
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Dellagnezze BM, Vasconcellos SP, Angelim AL, Melo VMM, Santisi S, Cappello S, Oliveira VM. Bioaugmentation strategy employing a microbial consortium immobilized in chitosan beads for oil degradation in mesocosm scale. Mar Pollut Bull 2016; 107:107-117. [PMID: 27158046 DOI: 10.1016/j.marpolbul.2016.04.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 04/06/2016] [Accepted: 04/08/2016] [Indexed: 05/22/2023]
Abstract
A bacterial consortium composed by four metagenomic clones and Bacillus subtilis strain CBMAI 707, all derived from petroleum reservoirs, was entrapped in chitosan beads and evaluated regarding hydrocarbon degradation capability. Experiments were carried out in mesocosm scale (3000L) with seawater artificially polluted with crude oil. At different time intervals, mesocosms were sampled and subjected to GC-FID and microbiological analyses, as total and heterotrophic culturable bacterial abundance (DAPI and CFU count), biological oxygen demand (BOD) and taxonomic diversity (massive sequencing of 16S rRNA genes). The results obtained showed that degradation of n-alkane hydrocarbons was similar between both treatments. However, aromatic compound degradation was more efficient in bioaugmentation treatment, with biodegradation percentages reaching up to 99% in 30days. Community dynamics was different between treatments and the consortium used in the bioaugmentation treatment contributed to a significant increase in aromatic hydrocarbon degradation.
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Affiliation(s)
- B M Dellagnezze
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, CP 6171, CEP 13081-970 Campinas, SP, Brazil.
| | - S P Vasconcellos
- Federal University of São Paulo (UNIFESP), Rua Prof. Artur Riedel, 275, CEP 09972-270, Jd. Eldorado, Diadema, SP, Brazil
| | - A L Angelim
- Lembiotech (UFC), Federal University of Ceará, Av. Humberto Monte, 2977, Campus do Pici, Bloco 909, 60455-000, Fortaleza, CE, Brazil
| | - V M M Melo
- Lembiotech (UFC), Federal University of Ceará, Av. Humberto Monte, 2977, Campus do Pici, Bloco 909, 60455-000, Fortaleza, CE, Brazil
| | - S Santisi
- Institute for Coastal Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR) of Messina, Messina, Italy
| | - S Cappello
- Institute for Coastal Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR) of Messina, Messina, Italy
| | - V M Oliveira
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, CP 6171, CEP 13081-970 Campinas, SP, Brazil
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Stone W, Kroukamp O, Moes A, Mckelvie J, Korber DR, Wolfaardt GM. Measuring microbial metabolism in atypical environments: Bentonite in used nuclear fuel storage. J Microbiol Methods 2016; 120:79-90. [DOI: 10.1016/j.mimet.2015.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/09/2015] [Accepted: 11/09/2015] [Indexed: 11/19/2022]
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Zhang P, Van Nostrand JD, He Z, Chakraborty R, Deng Y, Curtis D, Fields MW, Hazen TC, Arkin AP, Zhou J. A Slow-Release Substrate Stimulates Groundwater Microbial Communities for Long-Term in Situ Cr(VI) Reduction. Environ Sci Technol 2015; 49:12922-12931. [PMID: 25835088 DOI: 10.1021/acs.est.5b00024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Cr(VI) is a widespread environmental contaminant that is highly toxic and soluble. Previous work indicated that a one-time amendment of polylactate hydrogen-release compound (HRC) reduced groundwater Cr(VI) concentrations for >3.5 years at a contaminated aquifer; however, microbial communities responsible for Cr(VI) reduction are poorly understood. In this study, we hypothesized that HRC amendment would significantly change the composition and structure of groundwater microbial communities, and that the abundance of key functional genes involved in HRC degradation and electron acceptor reduction would increase long-term in response to this slowly degrading, complex substrate. To test these hypotheses, groundwater microbial communities were monitored after HRC amendment for >1 year using a comprehensive functional gene microarray. The results showed that the overall functional composition and structure of groundwater microbial communities underwent sequential shifts after HRC amendment. Particularly, the abundance of functional genes involved in acetate oxidation, denitrification, dissimilatory nitrate reduction, metal reduction, and sulfate reduction significantly increased. The overall community dynamics was significantly correlated with changes in groundwater concentrations of microbial biomass, acetate, NO3-, Cr(VI), Fe(II) and SO4(2-). Our results suggest that HRC amendment primarily stimulated key functional processes associated with HRC degradation and reduction of multiple electron acceptors in the aquifer toward long-term Cr(VI) reduction.
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Affiliation(s)
- Ping Zhang
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Zhili He
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Romy Chakraborty
- Earth Science Division, Lawrence Berkeley National Laboratory , Berkeley, California 94270, United States
| | - Ye Deng
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
| | - Daniel Curtis
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University , Bozeman, Montana 59717, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee , Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831-6342, United States
| | - Adam P Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
- Earth Science Division, Lawrence Berkeley National Laboratory , Berkeley, California 94270, United States
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University , Beijing 100084, China
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Hemme CL, Tu Q, Shi Z, Qin Y, Gao W, Deng Y, Nostrand JDV, Wu L, He Z, Chain PSG, Tringe SG, Fields MW, Rubin EM, Tiedje JM, Hazen TC, Arkin AP, Zhou J. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front Microbiol 2015; 6:1205. [PMID: 26583008 PMCID: PMC4628106 DOI: 10.3389/fmicb.2015.01205] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/16/2015] [Indexed: 11/15/2022] Open
Abstract
To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301) and contaminated groundwater (FW106) samples from the Oak Ridge Integrated Field Research Center (OR-IFRC) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas) are the most abundant lineages in the pristine community, though a significant proportion ( >55%) of the community is composed of poorly characterized low abundance (individually <1%) lineages. The phylogenetic diversity of the pristine community contributed to a broader diversity of metabolic networks than the contaminated community. In addition, the pristine community encodes redundant and mostly complete geochemical cycles distributed over multiple lineages and appears capable of a wide range of metabolic activities. In contrast, many geochemical cycles in the contaminated community appear truncated or minimized due to decreased biodiversity and dominance by Rhodanobacter populations capable of surviving the combination of stresses at the site. These results indicate that the pristine site contains more robust and encodes more functional redundancy than the stressed community, which contributes to more efficient nutrient cycling and adaptability than the stressed community.
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Affiliation(s)
- Christopher L Hemme
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Qichao Tu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Zhou Shi
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Yujia Qin
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Weimin Gao
- The Biodesign Institute, Arizona State University, Tempe AZ, USA
| | - Ye Deng
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA ; CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Liyou Wu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos NM, USA
| | - Susannah G Tringe
- United States Department of Energy, Joint Genome Institute, Walnut Creek CA, USA
| | - Matthew W Fields
- Department of Microbiology, Montana State University, Bozeman MT, USA
| | - Edward M Rubin
- United States Department of Energy, Joint Genome Institute, Walnut Creek CA, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing MI, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee-Knoxville, Knoxville TN, USA ; Department of Earth and Planetary Sciences, University of Tennessee-Knoxville, Knoxville TN, USA ; Department of Microbiology, University of Tennessee-Knoxville, Knoxville TN, USA ; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN, USA
| | - Adam P Arkin
- Department of Bioengineering, Lawrence Berkeley National Laboratory, Berkeley CA, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA ; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, USA ; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University Beijing, China
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46
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Yan X, Luo X, Zhao M. Metagenomic analysis of microbial community in uranium-contaminated soil. Appl Microbiol Biotechnol 2015; 100:299-310. [PMID: 26433967 DOI: 10.1007/s00253-015-7003-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/31/2015] [Accepted: 09/10/2015] [Indexed: 10/23/2022]
Abstract
Uranium tailing is a serious pollution challenge for the environment. Based on metagenomic sequencing analysis, we explored the functional and structural diversity of the microbial community in six soil samples taken at different soil depths from uranium-contaminated and uncontaminated areas. Kyoto Encyclopedia of Genes and Genomes Orthology (KO) groups were obtained using a Basic Local Alignment Search Tool search based on the universal protein resource database. The KO-pathway network was then constructed using the selected KOs. Finally, alpha and beta diversity analyses were performed to explore the differences in soil bacterial diversity between the radioactive soil and uncontaminated soil. In total, 30-68 million high-quality reads were obtained. Sequence assembly yielded 286,615 contigs; and these contigs mostly annotated to 1699 KOs. The KO distributions were similar among the six soil samples. Moreover, the proportion of the metabolism of other amino acids (e.g., beta-alanine, taurine, and hypotaurine) and signal transduction was significantly lower in radioactive soil than in uncontaminated soil, whereas the proportion of membrane transport and carbohydrate metabolism was higher. Additionally, KOs were mostly enriched in ATP-binding cassette transporters and two-component systems. According to diversity analyses, Actinobacteria and Proteobacteria were the dominant phyla in radioactive and uncontaminated soil, and Robiginitalea, Microlunatus, and Alicyclobacillus were the dominant genera in radioactive soil. Taken together, these results demonstrate that soil microbial community, structure, and functions show significant changes in uranium-contaminated soil. The dominant categories such as Actinobacteria and Proteobacteria may be applied in environmental governance for uranium-contaminated soil in southern China.
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Affiliation(s)
- Xun Yan
- Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, China.,College of Chemistry and Chemical Engineering, Qiqihar University Qiqihar, Heilongjiang, 161006, China
| | - Xuegang Luo
- Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, China.
| | - Min Zhao
- College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, 150040, China
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47
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Ke X, Wang C, Jing D, Zhang Y, Zhang H. Assessing water quality by ratio of the number of dominant bacterium species between surface/subsurface sediments in Haihe River Basin. Mar Pollut Bull 2015; 98:267-273. [PMID: 26164783 DOI: 10.1016/j.marpolbul.2015.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 05/30/2015] [Accepted: 06/01/2015] [Indexed: 06/04/2023]
Abstract
Sedimentary microorganisms can be used as a sensitive indicator of integrated aquatic environment quality assessment and indicate long-term water quality or toxicity. According to the Chinese National Standards of GB 3838-2002 and GB 18918-2002, the comprehensive water quality in Haihe River Basin has been described. Results showed that the comprehensive water quality in 6 sites, 4 sites, and 20 sites were good, bad, and medium. Furthermore, 162 dominant bacterial species were identified in surface and subsurface sediments in the 30 sampling sites. As revealed by two initial models constructed by logistic regression, the comprehensive water quality exhibited a pattern from good to bad as the ratio of the number of dominant bacterial species in surface sediments to that in subsurface sediments increased from 1 to 2.1. This finding possibly bridged a traditional gap between aquatic microbe indicators and water quality assessment or monitoring techniques.
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Affiliation(s)
- Xin Ke
- College of Energy and Environment, Shenyang Aerospace University, Shenyang 110136, China
| | - Chunyong Wang
- College of Energy and Environment, Shenyang Aerospace University, Shenyang 110136, China
| | - Debing Jing
- College of Life Sciences, Capital Normal University, Beijing 100048, China; Xiang Yang Forestry Bureau, Xiangyang 441100, China.
| | - Yun Zhang
- College of Land and Environment, Shenyang Agriculture University, Shenyang 110161, China.
| | - Haijun Zhang
- College of Energy and Environment, Shenyang Aerospace University, Shenyang 110136, China
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48
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Mhuantong W, Wongwilaiwalin S, Laothanachareon T, Eurwilaichitr L, Tangphatsornruang S, Boonchayaanant B, Limpiyakorn T, Pattaragulwanit K, Punmatharith T, McEvoy J, Khan E, Rachakornkij M, Champreda V. Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing. PLoS One 2015; 10:e0128043. [PMID: 26020967 PMCID: PMC4447364 DOI: 10.1371/journal.pone.0128043] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 04/21/2015] [Indexed: 11/18/2022] Open
Abstract
The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas.
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Affiliation(s)
- Wuttichai Mhuantong
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sarunyou Wongwilaiwalin
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
| | - Thanaporn Laothanachareon
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
| | - Lily Eurwilaichitr
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sithichoke Tangphatsornruang
- Genome Institute, National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Benjaporn Boonchayaanant
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
- Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
| | - Tawan Limpiyakorn
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
- Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
| | - Kobchai Pattaragulwanit
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
| | - Thantip Punmatharith
- Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
| | - John McEvoy
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, ND 58108, United States of America
| | - Eakalak Khan
- Department of Civil and Environmental Engineering, North Dakota State University, Fargo, ND 58108, United States of America
| | - Manaskorn Rachakornkij
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
- Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
| | - Verawat Champreda
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
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49
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Koribanics NM, Tuorto SJ, Lopez-Chiaffarelli N, McGuinness LR, Häggblom MM, Williams KH, Long PE, Kerkhof LJ. Spatial distribution of an uranium-respiring betaproteobacterium at the Rifle, CO field research site. PLoS One 2015; 10:e0123378. [PMID: 25874721 PMCID: PMC4395306 DOI: 10.1371/journal.pone.0123378] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 02/13/2015] [Indexed: 11/21/2022] Open
Abstract
The Department of Energy’s Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reduction with specific microbiota has been indirect. Here, we report on the cultivation of a microorganism from the Rifle IFRC that reduces uranium and appears to utilize it as a terminal electron acceptor for respiration with acetate as electron donor. Furthermore, this bacterium constitutes a significant proportion of the subsurface sediment community prior to biostimulation based on TRFLP profiling of 16S rRNA genes. 16S rRNA gene sequence analysis indicates that the microorganism is a betaproteobacterium with a high similarity to Burkholderia fungorum. This is, to our knowledge, the first report of a betaproteobacterium capable of uranium respiration. Our results indicate that this microorganism occurs commonly in alluvial sediments located between 3-6 m below ground surface at Rifle and may play a role in the initial reduction of uranium at the site.
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Affiliation(s)
- Nicole M. Koribanics
- Inst. of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Steven J. Tuorto
- Inst. of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Nora Lopez-Chiaffarelli
- Inst. of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
- Dept. of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Lora R. McGuinness
- Inst. of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Max M. Häggblom
- Dept. of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Kenneth H. Williams
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Philip E. Long
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Lee J. Kerkhof
- Inst. of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail:
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50
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Zhang P, Wu WM, Van Nostrand JD, Deng Y, He Z, Gihring T, Zhang G, Schadt CW, Watson D, Jardine P, Criddle CS, Brooks S, Marsh TL, Tiedje JM, Arkin AP, Zhou J. Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction. Appl Environ Microbiol 2015; 81:4164-72. [PMID: 25862231 DOI: 10.1128/AEM.00043-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/05/2015] [Indexed: 11/20/2022] Open
Abstract
A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this study, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using a comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO3 (-), Mn(IV), Fe(III), U(VI), and SO4 (2-) significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO3 (-), Mn(II), Fe(II), U(VI), and SO4 (2-). Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. This study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction.
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