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Banerjee S, Ghosh S, Chakraborty S, Sarkar D, Datta R, Bhattacharyya P. Synergistic impact of bioavailable PHEs and alkalinity on microbial diversity and traits in agricultural soil adjacent to chromium-asbestos mines. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 350:124021. [PMID: 38657890 DOI: 10.1016/j.envpol.2024.124021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 04/26/2024]
Abstract
Soil microbial communities undergo constant fluctuations, particularly in response to environmental factors. Although the deposition of toxic mine waste is recognized for introducing potentially hazardous elements (PHEs) into the soil, its specific impacts on microbial communities remain unclear. This study aims to explore the combined effects of soil alkalinity and bioavailable PHEs on microbial diversity and traits in agricultural soil adjacent to a chromium-asbestos mining area. By employing a comprehensive analysis, this study indicated that microbiological attributes were reduced in contaminated areas (zone 1), whereas both the levels of bioavailable PHEs (CrWs: 31.08 mg/kg, NiWs: 13.90 mg/kg) and alkalinity indices (CROSS, MCAR, MH) were significantly higher. The spatial distribution of soil alkalinity and bioavailable PHEs, primarily originating from chromium-asbestos mines, has been determined. This study also elucidates the negative relationship between soil stressors (Alkalinity and PHEs) and microbial activities (soil enzymatic activity, microbial respiration, and biomass carbon). The vector's length exhibited a notable difference between zone 1 (0.51) and zone 2 (0.32), indicating a substantial limitation on carbon (C). Also, the investigation of soil bacterial diversity unveiled notable disparities in the prevalence of microbial populations inside zone 1. Proteobacteria constituted 57.18% of the total population indicating a noteworthy prevalence in the contaminated soils. Finally, the random forest (RF) algorithm from machine learning was selected and proven to be a robust choice in Taylor diagrams for predicting the causative stressors responsible for the deterioration of soil microbial health. Therefore, this research offers insights into the health and resilience of soil microbial communities under synergistic stress conditions, which will aid environmentalists in planning future interventions and improving sustainable farming techniques.
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Affiliation(s)
- Sonali Banerjee
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Giridih, Jharkhand, 815301, India
| | - Saibal Ghosh
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Giridih, Jharkhand, 815301, India
| | - Shreya Chakraborty
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Giridih, Jharkhand, 815301, India
| | - Dibyendu Sarkar
- Stevens Institute of Technology, Department of Civil, Environmental, and Ocean Engineering, Hoboken, NJ, 07030, USA
| | - Rupali Datta
- Department of Biological Science, Michigan Technological University, Michigan, USA
| | - Pradip Bhattacharyya
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Giridih, Jharkhand, 815301, India.
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Feng K, Lu Y, Zhou W, Xu Z, Ye J, Zhang S, Chen J, Zhao J. Metagenomics revealing biomolecular insights into the enhanced toluene removal and electricity generation in PANI@CNT bioanode. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172402. [PMID: 38608888 DOI: 10.1016/j.scitotenv.2024.172402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/28/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024]
Abstract
Microbial fuel cells (MFCs) have significant potential for environmental remediation and energy recycling directly from refractory aromatic hydrocarbons. To boost the capacities of toluene removal and the electricity production in MFCs, this study constructed a polyaniline@carbon nanotube (PANI@CNT) bioanode with a three-dimensional framework structure. Compared with the control bioanode based on graphite sheet, the PANI@CNT bioanode increased the output voltage and toluene degradation kinetics by 2.27-fold and 1.40-fold to 0.399 V and 0.60 h-1, respectively. Metagenomic analysis revealed that the PANI@CNT bioanode promoted the selective enrichment of Pseudomonas, with the dual functions of degrading toluene and generating exogenous electrons. Additionally, compelling genomic evidence elucidating the relationship between functional genes and microorganisms was found. It was interesting that the genes derived from Pseudomonas related to extracellular electron transfer, tricarboxylic acid cycle, and toluene degradation were upregulated due to the existence of PANI@CNT. This study provided biomolecular insights into key genes and related microorganisms that effectively facilitated the organic pollutant degradation and energy recovery in MFCs, offering a novel alternative for high-performance bioanode.
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Affiliation(s)
- Ke Feng
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yi Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Weikang Zhou
- Zhejiang Engineering Survey and Design Institute Group Co., Ltd., Ningbo 315012, China
| | - Zijiong Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jiexu Ye
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shihan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jianmeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jingkai Zhao
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
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Chen X, Yang Y, Wang J, Pan C, Zhang Z, Chen S, Xie S. Impacts of o-cresol spill on composition and function of river sediment and soil microbial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:31978-31988. [PMID: 38641693 DOI: 10.1007/s11356-024-33043-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/19/2024] [Indexed: 04/21/2024]
Abstract
o-Cresol is a toxic substance with strong irritating and corrosive effects on skin and mucous membranes. To date, information on the effects of o-cresol on microbial communities in the natural environment is very limited. In the present study, 16S rRNA sequencing and metagenomic technique were carried out to elucidate the effects of the o-cresol spill on microbial communities in river sediments and nearby soils. o-Cresol spill induced the increase in the relative abundance of phyla Planctomycetes and Gemmatimonadetes, suggesting their resilience to o-cresol-induced stress. Uncultured Gemmatimonadetes genera and the MND1 genus exhibited enrichment, while the Pseudomonas genus dominated across all samples, indicating their potential pivotal roles in adapting to the o-cresol spill. Moreover, o-cresol spill impaired the metabolic functions of microbes but triggered their defense mechanisms. Under o-cresol pressure, microbial functions related to carbon fixation were upregulated and functions associated with sulfur metabolism were downregulated. In addition, the o-cresol spill led to an increase in functional genes related to the conversion of o-cresol to 3-methylcatechol. Several genes involved in the degradation of aromatic compounds were also identified, potentially contributing to the biodegradation of o-cresol. This study provides fresh insights into the repercussions of an abrupt o-cresol spill on microbial communities in natural environments, shedding light on their adaptability, defense mechanisms, and biodegradation potential.
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Affiliation(s)
- Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Yuyin Yang
- Ministry of Ecology and Environment (MEE), South China Institute of Environmental Sciences (SCIES), Guangzhou, 510655, China
| | - Ji Wang
- Ministry of Ecology and Environment (MEE), South China Institute of Environmental Sciences (SCIES), Guangzhou, 510655, China
| | - Chaoyi Pan
- Ministry of Ecology and Environment (MEE), South China Institute of Environmental Sciences (SCIES), Guangzhou, 510655, China
| | - Zhengke Zhang
- Ministry of Ecology and Environment (MEE), South China Institute of Environmental Sciences (SCIES), Guangzhou, 510655, China.
| | - Sili Chen
- Ministry of Ecology and Environment (MEE), South China Institute of Environmental Sciences (SCIES), Guangzhou, 510655, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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Belykh E, Maystrenko T, Velegzhaninov I, Tavleeva M, Rasova E, Rybak A. Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review. Microorganisms 2024; 12:733. [PMID: 38674676 PMCID: PMC11051952 DOI: 10.3390/microorganisms12040733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.
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Affiliation(s)
- Elena Belykh
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Tatiana Maystrenko
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Ilya Velegzhaninov
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Marina Tavleeva
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
- Department of Biology, Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prospekt, Syktyvkar 167001, Russia
| | - Elena Rasova
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Anna Rybak
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
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Sanyal SK, Etschmann B, Hore SB, Shuster J, Brugger J. Microbial adaptations and biogeochemical cycling of uranium in polymetallic tailings. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133334. [PMID: 38154188 DOI: 10.1016/j.jhazmat.2023.133334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023]
Abstract
Microorganisms inhabiting uranium (U)-rich environments have specific physiological and biochemical coping mechanisms to deal with U toxicity, and thereby play a crucial role in the U biogeochemical cycling as well as associated heavy metals. We investigated the diversity and functional capabilities of indigenous bacterial communities inhabiting historic U- and Rare-Earth-Elements-rich polymetallic tailings from the Mount Painter Inlier, Northern Flinders Ranges, South Australia. Bacterial diversity profiling identified Actinobacteria as the predominant phylum in all samples. GeoChip analyses revealed the presence of diverse functional genes associated with biogenic element cycling, metal homeostasis/resistance, stress response, and secondary metabolism. The high abundance of metal-resistance and stress-tolerance genes indicates the adaptation of bacterial communities to the "harsh" environmental (metal-rich and semi-arid) conditions of the Northern Flinders Ranges. Additionally, a viable bacterial consortium was enriched from polymetallic tailings. Laboratory experiments demonstrated that the consortium scrubbed uranyl from solution by precipitating a uranyl phosphate biomineral (chernikovite), thus contributing to U biogeochemical cycling. These specialised microbial communities reflect the high specificity of the mineralogy/geochemistry, and biogeography of these U-rich settings. This study provides the fundamental knowledge to develop future applications in securing long-term stability of polymetallic mine waste, and for reprocessing this "waste" to further extract critical minerals.
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Affiliation(s)
- Santonu K Sanyal
- School of Earth, Atmosphere and Environment, Monash University, Clayton, Victoria 3800 Australia.
| | - Barbara Etschmann
- School of Earth, Atmosphere and Environment, Monash University, Clayton, Victoria 3800 Australia
| | - Stephen B Hore
- Geological Survey of South Australia, Adelaide, South Australia 5001, Australia
| | - Jeremiah Shuster
- Department of Earth Sciences, Western University, London, Ontario N6A 3K7, Canada
| | - Joël Brugger
- School of Earth, Atmosphere and Environment, Monash University, Clayton, Victoria 3800 Australia.
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Chakraborty S, Ghosh S, Banerjee S, Kumar S, Bhattacharyya P. Elucidating the synergistic effect of acidity and metalloid poisoning on the microbiome through metagenomics and machine learning approaches. ENVIRONMENTAL RESEARCH 2024; 243:117885. [PMID: 38072100 DOI: 10.1016/j.envres.2023.117885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 02/06/2024]
Abstract
The abundance and diversity of the microflora in a complex environment such as soil is everchanging. Mica mining has led to metalloid poisoning and changes in soil biogeochemistry affecting the overall produce and leading to toxic dietary exposure. The study focuses on two prominent stressors acidity and arsenic, in mining-contaminated agricultural locations. Soil samples were collected from agricultural fields at a distance of 50 m (zone 1) and 500 m (zone 2) from active mines. Mean arsenic concentration was higher in zone 1 and pH was lower. Geostatistical and self-organizing maps were employed to report that the pattern of localization of soil acidity and arsenic content is similar indicating a causal relationship. Cluster and principal component analysis were further used to materialize a negative effect of soil acidity fractions and arsenic labile pool on soil enzymatic activity (fluorescein diacetate, dehydrogenase, β-1,4-glucosidase, phosphatase, and urease), respiration and Microbial biomass carbon. Soil metagenomic analysis revealed significant differences in the abundance of microbial populations with zone 1 (contaminated zone) having lower alpha and beta diversity. Finally, the efficacy of several machine-learning tools was tested using Taylor diagrams and an effort was made to select a potent algorithm to predict the causal stressors responsible for depreciating soil microbial health. Random Forrest had superior predictive power based on numerical evidence and was therefore chosen as the best-fitted model. The aforementioned insights into soil microbial health and sustenance in stressed conditions can be beneficial for predicting remedial strategies and practicing sustainable agriculture.
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Affiliation(s)
- Shreya Chakraborty
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Giridih, Jharkhand, 815301, India
| | - Saibal Ghosh
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Giridih, Jharkhand, 815301, India
| | - Sonali Banerjee
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Giridih, Jharkhand, 815301, India
| | - Sumit Kumar
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Giridih, Jharkhand, 815301, India
| | - Pradip Bhattacharyya
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Giridih, Jharkhand, 815301, India.
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7
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Higo M, Kang DJ, Isobe K. Root-associated microbial community and diversity in napiergrass across radiocesium-contaminated lands after the Fukushima-Daiichi nuclear disaster in Japan. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 342:123051. [PMID: 38043771 DOI: 10.1016/j.envpol.2023.123051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 11/18/2023] [Accepted: 11/25/2023] [Indexed: 12/05/2023]
Abstract
The microbiome derived from soil associated with plant roots help in plant growth and stress resistance. It exhibits potential benefits for soil remediation and restoration of radioactive-cesium (137Cs)-contaminated soils. However, there is still limited information about the community and diversity of root-associated microbiome in 137Cs-contaminated soil after the Fukushima-Daiichi Nuclear Power Plant (FDNPP) disaster. To address this, a comparative analysis of communities and diversity of root-associated microbiomes was conducted in two field types after the FDNPP disaster. In 2013, we investigated the community and diversity of indigenous root-associated microbiome of napiergrass (Pennisetum purpureum) grown in both grassland and paddy fields of 137Cs-contaminated land-use type within a 30-km radius around the FDNPP. Results showed that the root-associated bacterial communities in napiergrass belonged to 32 phyla, 75 classes, 174 orders, 284 families, and 521 genera, whereas the root-associated fungal communities belonged to 5 phyla, 11 classes, 31 orders, 59 families, and 64 genera. The most frequently observed phylum in both grassland and paddy field was Proteobacteria (47.4% and 55.9%, respectively), followed by Actinobacteriota (23.8% and 27.9%, respectively) and Bacteroidota (10.1% and 11.3%, respectively). The dominant fungal phylum observed in both grassland and paddy field was Basidiomycota (75.9% and 94.2%, respectively), followed by Ascomycota (24.0% and 5.8%, respectively). Land-use type significantly affected the bacterial and fungal communities that colonize the roots of napiergrass. Several 137Cs-tolerant bacterial and fungal taxa were also identified, which may be potentially applied for the phytoremediation of 137Cs-contaminated areas around FDNPP. These findings contribute to a better understanding of the distribution of microbial communities in 137Cs-contaminated lands and their long-term ecosystem benefits for phytoremediation efforts.
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Affiliation(s)
- Masao Higo
- College of Bioresource Sciences, Nihon University, Kameino, 1866, Fujisawa, Kanagawa, 252-0880, Japan.
| | - Dong-Jin Kang
- Teaching and Research Center for Bio-coexistence, Faculty of Agriculture and Life Sciences, Hirosaki University, Gosyogawara, Aomori, 037-0202, Japan.
| | - Katsunori Isobe
- College of Bioresource Sciences, Nihon University, Kameino, 1866, Fujisawa, Kanagawa, 252-0880, Japan
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Wang Y, Feng H, Wang R, Zhou L, Li N, He Y, Yang X, Lai J, Chen K, Zhu W. Non-targeted metabolomics and 16s rDNA reveal the impact of uranium stress on rhizosphere and non-rhizosphere soil of ryegrass. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2023; 258:107090. [PMID: 36565664 DOI: 10.1016/j.jenvrad.2022.107090] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/27/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
As a radioactive heavy metal element with a long half-life, uranium causes environmental pollution when it enters the surrounding soil. This study analyzed the changes about soil enzyme activity, non-targeted metabolomics, microbial community structure and function microbial community structure and function to assess the differences in the effects of uranium stress on rhizosphere and non-rhizosphere soil. Results showed that uranium stress significantly inhibited the activities of urease and sucrase in rhizosphere and non-rhizosphere, which had less effect on rhizosphere. Compare to the non-rhizosphere soil, the uranium stress induced the production of gibberellin A1, to promoted several metabolic pathways, such as nitrogen and PTS (Phosphotransferase system) metabolic in rhizosphere soil. The species and abundance of Aspergillus, Acidobacter, and Synechococcus in both rhizosphere and non-rhizosphere soil were decreased by uranium stress. However, the microorganisms in rhizosphere soil were less inhibited according to the soil metabolism and microbial network map analysis. Furthermore, the Chujaibacter in rhizosphere soil under uranium stress was found significantly positively correlated with lipid and organic oxygen compounds. Overall, the results indicated that ryegrass roots significantly alleviated the effects of uranium stress on soil microbial activity and population abundances, thus playing a protective role. The study also provided a theoretical basis for in-depth understanding of the biological effects, prevention and control mechanisms of uranium-contaminated soil.
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Affiliation(s)
- Yilin Wang
- State Key Laboratory of Environment-friendly Energy Materials, School of Life Science and Engineering, Sichuan Co-Innovation Center for New Energetic Materials, National Co-innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, Southwest University of Science and Technology, Mianyang, 621010, China; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Huachuan Feng
- State Key Laboratory of Environment-friendly Energy Materials, School of Life Science and Engineering, Sichuan Co-Innovation Center for New Energetic Materials, National Co-innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, Southwest University of Science and Technology, Mianyang, 621010, China; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Ruixiang Wang
- State Key Laboratory of Environment-friendly Energy Materials, School of Life Science and Engineering, Sichuan Co-Innovation Center for New Energetic Materials, National Co-innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, Southwest University of Science and Technology, Mianyang, 621010, China; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Li Zhou
- State Key Laboratory of Environment-friendly Energy Materials, School of Life Science and Engineering, Sichuan Co-Innovation Center for New Energetic Materials, National Co-innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, Southwest University of Science and Technology, Mianyang, 621010, China; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Nan Li
- State Key Laboratory of Environment-friendly Energy Materials, School of Life Science and Engineering, Sichuan Co-Innovation Center for New Energetic Materials, National Co-innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, Southwest University of Science and Technology, Mianyang, 621010, China; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Yizhou He
- State Key Laboratory of Environment-friendly Energy Materials, School of Life Science and Engineering, Sichuan Co-Innovation Center for New Energetic Materials, National Co-innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, Southwest University of Science and Technology, Mianyang, 621010, China; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Xu Yang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Jinlong Lai
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Ke Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Wenkun Zhu
- State Key Laboratory of Environment-friendly Energy Materials, School of Life Science and Engineering, Sichuan Co-Innovation Center for New Energetic Materials, National Co-innovation Center for Nuclear Waste Disposal and Environmental Safety, Nuclear Waste and Environmental Safety Key Laboratory of Defense, Southwest University of Science and Technology, Mianyang, 621010, China.
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Diversity and Antimicrobial Activities of Actinobacteria Isolated from Mining Soils in Midelt Region, Morocco. ScientificWorldJournal 2023; 2023:6106673. [PMID: 36733955 PMCID: PMC9889154 DOI: 10.1155/2023/6106673] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/25/2023] Open
Abstract
Multidrug-resistant bacteria have emerged as a serious global health threat that requires, more than ever before, an urgent need for novel and more effective drugs. In this regard, the present study sheds light on the diversity and antimicrobial potential of Actinobacteria isolates in mining ecosystems. We have indeed investigated the production of bioactive molecules by the Actinobacteria isolated from abandoned mining areas in Midelt, Morocco, where average contents of lead (Pb) and cadmium (Cd) are higher than normal world levels. One hundred and forty-five Actinobacteria isolates were isolated and characterized based on morphological, chemotaxonomical, biochemical, and molecular data. Most of the 145 isolates were identified as Streptomyces. Isolates affiliated to the genera Amycolatopsis, Lentzea, Actinopolymorpha, and Pseudonocardia were also found. Antimicrobial producing potentials of Actinobacteria isolates were assessed against eight test microorganisms Gram+ and Gram- bacteria and yeast. Out of 145 isolates, 51 showed antimicrobial activities against at least one test microorganism. 31 isolates inhibited only bacteria, 7 showed activity against bacteria and Candida albicans, and 13 displayed activity against C. albicans solely. Our findings suggest that Actinobacteria isolated from natural heavy metal ecosystems may be a valuable source of novel secondary metabolites and therefore of new biotechnologically promising antimicrobial compounds.
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Zhao B, Sun Z, Guo Y, Zhou Z, Wang X, Ke P. Occurrence characteristics of uranium mineral-related substances in various environmental media in China: A critical review. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129856. [PMID: 36115096 DOI: 10.1016/j.jhazmat.2022.129856] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 08/17/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
The high demand and extensive exploitation of uranium resources resulted in the ubiquity and high detection levels of uranium mineral-related substances in various environment media in China. The potential adverse effects of uranium mineral-related substances on environment and human health have received extensive attention. Therefore, we reviewed the occurrence and spatial distribution of uranium mineral-related substances in various basins and environmental media in China to obtain an overall understanding. We collected information from over 70 papers reporting the occurrence and distribution of uranium mineral-related substances in multiple environments and 183 articles on the genesis of uranium deposits in China from 2001 to 2021. Then the occurrence of uranium mineral-related substances and corresponding correlation in different basins, environmental media and depth ranges were compared in detail. And this review assessed the uranium mineral-related pollution in China based on various environmental quality standards of China, EPA and WHO, and proposed the priority uranium mineral-related heavy metals and radioactive substances based on cluster analysis. This review showed that there were obvious differences in the occurrence characteristics of various uranium mineral-related substances in different environmental media, especially in the surrounding environment of sandstone type and hard rock type uranium deposits. These results will guide us to tackle the challenge of uranium mineral-related pollution in China. The correlation analysis of uranium mineral-related pollutants in different environmental media and the identification of priority pollutants will also provide instructions for us to control uranium mineral-related pollution. Finally, we put forward a series of urgent and practical suggestions on risk management and control of uranium mining according to the current situation of uranium mining environment in China, which is of guiding significance for the realization of "green uranium mining".
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Affiliation(s)
- Bei Zhao
- China University of Geosciences (Beijing), Beijing 100083, China
| | - Zhanxue Sun
- China University of Geosciences (Beijing), Beijing 100083, China; State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang 330013, China.
| | - Yadan Guo
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang 330013, China
| | - Zhongkui Zhou
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang 330013, China
| | - Xuegang Wang
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang 330013, China
| | - Pingchao Ke
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang 330013, China
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Zhou S, Xiong C, Su Y, Wang Y, Gao Y, Tang Z, Liu B, Wu Y, Duan Y. Antibiotic-resistant bacteria and antibiotic resistance genes in uranium mine: Distribution and influencing factors. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 304:119158. [PMID: 35304179 DOI: 10.1016/j.envpol.2022.119158] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/19/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Both heavy metals and radiation could affect the proliferation and dissemination of emerging antibiotic resistance pollutants. As an environmental medium rich in radioactive metals, the profile of antibiotic resistance in uranium mine remains largely unknown. A uranium mine in Guangdong province, China was selected to investigate the distribution and influencing factors of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) including intracellular ARGs (iARGs), adsorbed-extracellular ARGs (aeARGs), and free extracellular ARGs (feARGs). The result indicated that sulfonamide and tetracycline ARB could be generally detected in mining area with the absolute concentrations of 7.70 × 102-5.18 × 105 colony forming unit/g. The abundances of aeARGs in mine soil were significantly higher than those of iARGs (p < 0.05), highlighting the critical contribution of aeARGs to ARGs spread. The feARGs in mine drainage and its receiving river were abundant (3.38 × 104-1.86 × 107 copies/mL). ARB, aeARGs, and iARGs may correlate with nitrogen species and heavy metals (e.g., U and Mn), and feARGs presented a significant correlation with chemical oxygen demand (p < 0.05). These findings demonstrate the occurrence of ARB and ARGs in uranium mine for the first time, thereby contributing to the assessment and control of the ecological risk of antibiotic resistance in radioactive environments.
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Affiliation(s)
- Shuai Zhou
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China; School of Civil Engineering, University of South China, Hengyang, 421001, China; Hunan Province Key Laboratory of Rare Metal Minerals Exploitation and Geological Disposal of Wastes, University of South China, Hengyang, 421001, China
| | - Cong Xiong
- School of Civil Engineering, University of South China, Hengyang, 421001, China
| | - Yinglong Su
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, PR China
| | - Yuanyuan Gao
- Hunan Province Key Laboratory of Rare Metal Minerals Exploitation and Geological Disposal of Wastes, University of South China, Hengyang, 421001, China
| | - Zhenping Tang
- Hunan Province Key Laboratory of Rare Metal Minerals Exploitation and Geological Disposal of Wastes, University of South China, Hengyang, 421001, China
| | - Boyang Liu
- School of Civil Engineering, University of South China, Hengyang, 421001, China
| | - Yueyue Wu
- Institute of Pathogenic Biology, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Yi Duan
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China; School of Civil Engineering, University of South China, Hengyang, 421001, China.
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12
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Yu Z, Pei Y, Zhao S, Kakade A, Khan A, Sharma M, Zain H, Feng P, Ji J, Zhou T, Wang H, Wu J, Li X. Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1527-1537. [PMID: 33123966 DOI: 10.1007/s10646-020-02290-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
Heavy metals have been severely polluting the environment. However, the response mechanism of microbial communities to short-term heavy metals stress remains unclear. In this study, metagenomics (MG) and metatranscriptomics (MT) was performed to observe the microbial response to short-term Cr(VI) stress. MG data showed that 99.1% of species were similar in the control and Cr(VI) treated groups. However, MT data demonstrated that 83% of the microbes were active in which 58.7% increased, while the relative abundance of 41.3% decreased after short-term Cr(VI) incubation. The MT results also revealed 9% of microbes were dormant in samples. Genes associated with oxidative stress, Cr(VI) transport, resistance, and reduction, as well as genes with unknown functions were 2-10 times upregulated after Cr(VI) treatment. To further confirm the function of unknown genes, two genes (314 and 494) were selected to detect the Cr(VI) resistance and reduction ability. The results showed that these genes significantly increased the Cr(VI) remediation ability of Escherichia coli. MT results also revealed an increase in the expression of some rare genera (at least two times) after Cr(VI) treatment, indicating these rare species played a crucial role in microbial response to short-term Cr(VI) stress. In summary, MT is an efficient way to understand the role of active and dormant microbes in specific environmental conditions.
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Affiliation(s)
- Zhengsheng Yu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Yaxin Pei
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Shuai Zhao
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Apurva Kakade
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Aman Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Monika Sharma
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Hajira Zain
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Pengya Feng
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Jing Ji
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Tuoyu Zhou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Haoyang Wang
- McMaster University, 1280 Main Street West, Hamilton, ON, Canada
| | - Jingyuan Wu
- The First Clinical Medical College, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China.
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China.
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13
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Nayak T, Sengupta I, Dhal PK. A new era of radiation resistance bacteria in bioremediation and production of bioactive compounds with therapeutic potential and other aspects: An in-perspective review. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2021; 237:106696. [PMID: 34265519 DOI: 10.1016/j.jenvrad.2021.106696] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms that survive in extreme environmental conditions are known as 'extremophiles'. Recently, extremophiles draw an impression in biotechnology/pharmaceutical researches/industries because of their novel molecules, known as 'extremolytes'. The intriguing phenomenon of microbial radiation resistance probably arose independently throughout their evolution of selective pressures (e.g. UV, X-ray, Gamma radiation etc.). Radiation produces multiple types of damage/oxidation to nucleic acids, proteins and other crucial cellular components. Most of the literature on microbial radiation resistance is based on acute γ-irradiation experiments performed in the laboratory, typically involving pure cultures isolation and their application on bioremediation/therapeutic field. There is much less information other than bioremediation and therapeutic application of such promising microbes we called as 'new era'. Here we discus origin and diversity of radiation resistance bacteria as well as selective mechanisms by which microorganisms can sustain in radiation rich environment. Potential uses of these radiations resistant microbes in the field of bioremediation, bioactive compounds and therapeutic industry. Last but not the least, which is the new aspect of radiation resistance microbes. Our review suggest that resistance to chronic radiation is not limited to rare specialized strains from extreme environments, but can occur among common microbial taxa, perhaps due to overlap molecular mechanisms of resistance to radiation and other stressors. These stress tolerance potential make them potential for radionuclides remediation, their extremolytes can be useful as anti-oxidant and anti-proliferative agents. In current scenario they can be useful in various fields from natural dye synthesis to nanoparticles production and anti-cancer treatment.
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Affiliation(s)
- Tilak Nayak
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700032, India.
| | - Indraneel Sengupta
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700032, India.
| | - Paltu Kumar Dhal
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700032, India.
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14
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Wang Q, Zeng Y, Zeng X, Wang X, Wang Y, Dai C, Li J, Huang P, Huang J, Hussain T, Zhu M, Yang H. Effects of Dietary Energy Levels on Rumen Fermentation, Gastrointestinal Tract Histology, and Bacterial Community Diversity in Fattening Male Hu Lambs. Front Microbiol 2021; 12:695445. [PMID: 34566905 PMCID: PMC8460862 DOI: 10.3389/fmicb.2021.695445] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/02/2021] [Indexed: 12/11/2022] Open
Abstract
This study investigated rumen fermentation and histological and microbial diversity in male Hu lamb fed diets with different metabolizable energy (ME) levels (MEA, 9.17 MJ/kg, MEB, 10.00 MJ/kg, and MEC, 10.82 MJ/kg). Thirty-six male Hu lambs were randomly allotted to three treatments, and the feeding trial lasted for 67 days. Rumen fermentation results suggest that the iso-valerate had a significant effect on dietary energy level. The papillary height (PH) of rumen was the highest in the MEB group, the crypt depth (CD) was significantly increased in the duodenum and jejunum, and the villus height (VH)-to-CD ratio (VH/CD) was significantly decreased in the duodenum by increasing dietary energy levels; the VH, villus width (VW), and VH/CD also had significant differences in the ileum. 16S rRNA sequencing results showed that the operational taxonomic units (OTUs) number, the ACE, and Chao1 indices were linearly decreased by increasing dietary energy level; 24 phyla including 124 genera were identified, and the relative abundance of Papillibacter and Quinella linearly decreased by increasing the dietary energy level. Compared to MEA and MEB groups, the relative abundance of unidentified_Veillonellaceae and Anaerovibrio was significantly increased in the MEC group at the genus level. The relative abundance of the carbohydrate metabolism pathway predicted by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was linearly increased by increasing the dietary energy levels. Three metabolic pathways identified in Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 were significantly influenced as the dietary energy level increased. In summary, these results demonstrated that the dietary energy levels affected the rumen fermentation parameters, morphological structures of the gastrointestinal tract (GIT), and the composition and function of rumen microflora in male Hu sheep.
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Affiliation(s)
- Qiye Wang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China.,Hubei Zhiqinghe Agriculture and Animal Husbandry Co., Ltd., Yichang, China
| | - Yutong Zeng
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xianglin Zeng
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xin Wang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yancan Wang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Chunpeng Dai
- Hubei Zhiqinghe Agriculture and Animal Husbandry Co., Ltd., Yichang, China
| | - Jianzhong Li
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Pengfei Huang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jing Huang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Tarique Hussain
- Animal Sciences Division, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Mingzhi Zhu
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Huansheng Yang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China.,Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Engineering Research Center of Healthy Livestock, Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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15
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Response and Dynamic Change of Microbial Community during Bioremediation of Uranium Tailings by Bacillus sp. MINERALS 2021. [DOI: 10.3390/min11090967] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bacillus sp. is widely used in the remediation of uranium-contaminated sites. However, little is known about the competitive process of microbial community in the environment during bioremediation. The bioremediation of uranium tailings using Bacillus sp. was explored, and the bacterial community was analyzed by high-throughput sequencing at different stages of remediation. Bacillus sp. reduced the leaching of uranium from uranium tailings. The lowest uranium concentration was 17.25 μg/L. Alpha diversity revealed that the abundance and diversity of microorganisms increased with the extension of the culture time. The microbial abundance and diversity were higher in the treatment group than in the control group. The dominant species at the phyla level were Firmicutes and Proteobacteria in the uranium tailings environment, whereas the phylum of Proteobacteria was significantly increased in the treatment group. Based on the genus level, the proportions of Arthrobacter, Rhodococcus and Paenarthrobacter decreased significantly, whereas those of Clostridium sp., Bacillus and Pseudomonas increased dramatically. Hence, the remediation of uranium contamination in the environment was due to the functional microorganisms, which gradually became the dominant strain in the treatment, such as Desulfotomaculum, Desulfosporporosinus, Anaerocolumna, Ruminiclostridium and Burkholderia. These findings provided a promising outlook of the potential for remediation strategies of soil contaminated by uranium. The dynamic characteristics of the microbial community are likely to provide a foundation for the bioremediation process in practice.
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16
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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] [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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17
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Kolhe N, Kulkarni A, Zinjarde S, Acharya C. Transcriptome Response of the Tropical Marine Yeast Yarrowia lipolytica on Exposure to Uranium. Curr Microbiol 2021; 78:2033-2043. [PMID: 33772621 DOI: 10.1007/s00284-021-02459-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/11/2021] [Indexed: 11/30/2022]
Abstract
In our earlier investigation, we reported the consequences of uranium (U)-induced oxidative stress and cellular defense mechanisms alleviating uranium toxicity in the marine yeast Yarrowia lipolytica NCIM 3589. However, there is lack of information on stress response towards uranium toxicity at molecular level in this organism. To gain an insight on this, transcriptional response of Y. lipolytica after exposure to 50 µM uranium was investigated by RNA sequencing at the global level in this study. The de novo transcriptome analysis (in triplicates) revealed 56 differentially expressed genes with significant up-regulation and down-regulation of 33 and 23 transcripts, respectively, in U-exposed yeast cells as compared to the control, U-unexposed cells. Highly up-regulated genes under U-treated condition were identified to be primarily involved in transport, DNA damage repair and oxidative stress. The major reaction of Y. lipolytica to uranium exposure was the activation of oxidative stress response mechanisms to protect the important biomolecules of the cells. On the other hand, genes involved in cell wall and cell cycle regulation were significantly down-regulated. Overall, the transcriptional profiling by RNA sequencing to stress-inducing concentration of uranium sheds light on the various responses of Y. lipolytica for coping with uranium toxicity, providing a foundation for understanding the molecular interactions between uranium and this marine yeast.
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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
| | - Abhijeet Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, 411007, India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, 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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18
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Massello FL, Donati E. Effect of heavy metal-induced stress on two extremophilic microbial communities from Caviahue-Copahue, Argentina. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115709. [PMID: 33010675 DOI: 10.1016/j.envpol.2020.115709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 09/03/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
Metal pollution is a great concern worldwide and the development of new technologies for more sustainable extraction methods as well as for the remediation of polluted sites is essential. Extremophilic microorganisms are attractive for this purpose since they have poly-resistance mechanisms which make them versatile. In this work, we sampled an acidic river and a hot spring of Caviahue-Copahue volcanic environment. The indigenous microbial communities were exposed to five heavy metals (Cd, Co, Cu, Ni and Zn) in batch-cultures favouring different metabolisms of biotechnological interest. Remarkably, high tolerance values were reached in all the cultures, even though most of the metals studied were not present in the environmental sample. Particularly, outstanding tolerances were exhibited by acidophiles, which grew at concentrations as high as 400 mM of Zn and Ni. High-throughput amplicon sequencing of 16S rRNA gene was used to study the indigenous communities and the resistant consortia. We took three approaches for the analysis: phylotypes, OTUs and amplicon sequence variants (ASVs). Interestingly, similar conclusions were drawn in all three cases. Analysing the phylogenetic structure and functional potential of the adapted consortia, we found that the strongest selection was exerted by the culture media. Notably, there was a poor correlation between alpha diversity and metal stress; furthermore, metal stress did not seem to harm the functional potential of the consortia. All these results reveal a great adaptability and versatility. At the end, 25 metal-resistant extremophilic consortia with potential uses in bioremediation, bioleaching or biomonitoring processes were obtained.
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Affiliation(s)
- Francisco L Massello
- CINDEFI (CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
| | - Edgardo Donati
- CINDEFI (CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
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19
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Komatsu K, Shiba T, Takeuchi Y, Watanabe T, Koyanagi T, Nemoto T, Shimogishi M, Shibasaki M, Katagiri S, Kasugai S, Iwata T. Discriminating Microbial Community Structure Between Peri-Implantitis and Periodontitis With Integrated Metagenomic, Metatranscriptomic, and Network Analysis. Front Cell Infect Microbiol 2020; 10:596490. [PMID: 33425781 PMCID: PMC7793907 DOI: 10.3389/fcimb.2020.596490] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022] Open
Abstract
Peri-implantitis and periodontitis are both polymicrobial diseases induced by subgingival plaque accumulation, with some differing clinical features. Studies on the microbial and gene transcription activity of peri-implantitis microbiota are limited. This study aimed to verify the hypothesis that disease-specific microbial and gene transcription activity lead to disease-specific clinical features, using an integrated metagenomic, metatranscriptomic, and network analysis. Metagenomic data in peri-implantitis and periodontitis were obtained from the same 21 subjects and metatranscriptomic data from 12 subjects were obtained from a database. The microbial co-occurrence network based on metagenomic analysis had more diverse species taxa and correlations than the network based on the metatranscriptomic analysis. Solobacterium moorei and Prevotella denticola had high activity and were core species taxa specific to peri-implantitis in the co-occurrence network. Moreover, the activity of plasmin receptor/glyceraldehyde-3-phosphate dehydrogenase genes was higher in peri-implantitis. These activity differences may increase complexity in the peri-implantitis microbiome and distinguish clinical symptoms of the two diseases. These findings should help in exploring a novel biomarker that assist in the diagnosis and preventive treatment design of peri-implantitis.
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Affiliation(s)
- Keiji Komatsu
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuo Takeuchi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takayasu Watanabe
- Department of Chemistry, Nihon University School of Dentistry, Tokyo, Japan
| | - Tatsuro Koyanagi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takashi Nemoto
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masahiro Shimogishi
- Oral Implantology and Regenerative Dental Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masaki Shibasaki
- Oral Implantology and Regenerative Dental Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shohei Kasugai
- Oral Implantology and Regenerative Dental Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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20
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Wang Q, Wang Y, Wang X, Dai C, Tang W, Li J, Huang P, Li Y, Ding X, Huang J, Hussain T, Yang H, Zhu M. Effects of dietary energy levels on rumen fermentation, microbiota, and gastrointestinal morphology in growing ewes. Food Sci Nutr 2020; 8:6621-6632. [PMID: 33312546 PMCID: PMC7723210 DOI: 10.1002/fsn3.1955] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/24/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023] Open
Abstract
This study investigated whether dietary metabolizable energy (ME) could generate dynamical effects on rumen fermentation, gastrointestinal tract (GIT) morphology, and microbial composition of growing ewes. A total of twenty-eight female Hu lambs were randomly allotted to two treatments with different dietary ME levels: 9.17 (FEA) and 10.41 MJ/kg (FEB). These lambs were further made ready for a 67-day feeding trial. Results showed that the molar proportions of butyrate (p = .020), iso-valerate (p = .028), and valerate (p = .005) were significantly higher in the FEB group than those in the FEA group. The results of the GIT morphologic properties showed that the villus height (VH) (p = .005) was significantly higher and crypt depth was significantly deeper (CD) (p = .005) in the duodenum and that the rumen papillary height (PH) was significantly higher (p = .020) in FEB group compared with the FEA group. High-throughput sequencing results showed that 1826 operational taxonomic units (OTUs) were obtained and that the OTU number (p = .039), the ACE (p = .035), and Chao1 indices (p = .005) were lower in the FEB group. Moreover, 76 genera belonging to 21 phyla were detected in all samples; the relative abundance of Papillibacter (p = .036) and Flexilinea (p = .046) was significantly lower in the high energy group, whereas the relative abundance of unidentified Lachnospiraceae (p = .019), Acetitomaculum (p = .029), unidentified Veillonellaceae (p = .017), Anaerovibrio (p = .005), and Succinivibrio (p = .035) was significantly higher in the FEB group at the genus level. Furthermore, the relative abundance of genes and metabolic pathways were predicted by PICRUSt. The relative abundance of gene families related to carbohydrate metabolism was particularly higher (p = .027) in the FEB group. In summary, these results reveal that the dietary energy levels altered the composition and function of rumen microbiota and GIT morphology in growing female Hu sheep and provide a reference for optimizing diet formula and 10.41MJ/kg of ME level has been recommended in the growing period.
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Affiliation(s)
- Qiye Wang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan International Joint Laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangshaHunanChina
- Hubei Zhiqinghe Agriculture and Animal Husbandry Co., LtdYichangHubeiChina
| | - Yancan Wang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan International Joint Laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangshaHunanChina
| | - Xin Wang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan International Joint Laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangshaHunanChina
| | - Chunpeng Dai
- Hubei Zhiqinghe Agriculture and Animal Husbandry Co., LtdYichangHubeiChina
| | - Wensheng Tang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan International Joint Laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangshaHunanChina
| | - Jianzhong Li
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan International Joint Laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangshaHunanChina
| | - Pengfei Huang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan International Joint Laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangshaHunanChina
| | - Yali Li
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan International Joint Laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangshaHunanChina
| | - Xueqin Ding
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan International Joint Laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangshaHunanChina
| | - Jing Huang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan International Joint Laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangshaHunanChina
| | - Tarique Hussain
- Animal Sciences DivisionNuclear Institute for Agriculture and Biology (NIAB)FaisalabadPakistan
| | - Huansheng Yang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan International Joint Laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangshaHunanChina
- Key Laboratory of Agro‐ecological Processes in Subtropical RegionHunan Provincial Engineering Research Center of Healthy LivestockScientific Observing and Experimental Station of Animal Nutrition and Feed Science in South‐CentralMinistry of AgricultureInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaHunanChina
| | - Mingzhi Zhu
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from BotanicalsCo‐Innovation Center of Education Ministry for Utilization of Botanical Functional IngredientsCollege of HorticultureHunan Agricultural UniversityChangshaChina
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21
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Petit PCM, Pible O, Eesbeeck VV, Alban C, Steinmetz G, Mysara M, Monsieurs P, Armengaud J, Rivasseau C. Direct Meta-Analyses Reveal Unexpected Microbial Life in the Highly Radioactive Water of an Operating Nuclear Reactor Core. Microorganisms 2020; 8:E1857. [PMID: 33255667 PMCID: PMC7760952 DOI: 10.3390/microorganisms8121857] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 02/04/2023] Open
Abstract
The pools of nuclear reactor facilities constitute harsh environments for life, bathed with ionizing radiation, filled with demineralized water and containing toxic radioactive elements. The very few studies published to date have explored water pools used to store spent nuclear fuels. Due to access restrictions and strong handling constraints related to the high radioactivity level, nothing is presently known about life in water pools that directly cool nuclear cores. In this work, we investigated the microbial communities in the cooling pool of the French Osiris nuclear reactor using direct meta-omics approaches, namely, DNA metabarcoding and proteotyping based on 16S ribosomal RNA gene sequencing and on peptide analysis, respectively. We identified 25 genera in the highly radioactive core water supply during operation with radionuclide activity higher than 3 × 109 Bq/m3. The prevailing genera Variovorax and Sphingomonas at operation were supplanted by Methylobacterium, Asanoa, and Streptomyces during shutdown. Variovorax might use dihydrogen produced by water radiolysis as an energy source.
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Affiliation(s)
- Pauline C. M. Petit
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), CNRS, INRAE, Université Grenoble Alpes, F-38054 Grenoble, France; (P.C.M.P.); (C.A.)
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris-Saclay, F-30200 Bagnols-sur-Cèze, France; (O.P.); (G.S.); (J.A.)
| | - Valérie Van Eesbeeck
- Microbiology Unit, The Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, B-2400 Mol, Belgium; (V.V.E.); (M.M.); (P.M.)
| | - Claude Alban
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), CNRS, INRAE, Université Grenoble Alpes, F-38054 Grenoble, France; (P.C.M.P.); (C.A.)
| | - Gérard Steinmetz
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris-Saclay, F-30200 Bagnols-sur-Cèze, France; (O.P.); (G.S.); (J.A.)
| | - Mohamed Mysara
- Microbiology Unit, The Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, B-2400 Mol, Belgium; (V.V.E.); (M.M.); (P.M.)
| | - Pieter Monsieurs
- Microbiology Unit, The Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, B-2400 Mol, Belgium; (V.V.E.); (M.M.); (P.M.)
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris-Saclay, F-30200 Bagnols-sur-Cèze, France; (O.P.); (G.S.); (J.A.)
| | - Corinne Rivasseau
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), CNRS, INRAE, Université Grenoble Alpes, F-38054 Grenoble, France; (P.C.M.P.); (C.A.)
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22
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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] [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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23
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Zeng T, Mo G, Hu Q, Wang G, Liao W, Xie S. Microbial characteristic and bacterial community assessment of sediment sludge upon uranium exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 261:114176. [PMID: 32088436 DOI: 10.1016/j.envpol.2020.114176] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/29/2020] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
The microbial characteristics and bacterial communities of sediment sludge upon different concentrations of exposure to uranium were investigated by high solution transmission electron microscopy (HRTEM), energy dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS) and high-throughput sequencing. After exposure to initial uranium concentrations of 10-50 μM for 24 h in synthetic wastewater, the removal efficiencies of uranium reached 80.7%-96.5%. The spherical and short rod bacteria were dominant in the sludge exposed to uranium. HRTEM-EDS and XPS analyses indicated that reduction and adsorption were the main mechanisms for uranium removal. Short-term exposure to low concentrations of uranium resulted in a decrease in bacterial richness but an increase in diversity. A dramatic change in the composition and abundances of the bacterial community were present in the sediment sludge exposed to uranium. The highest removal efficiency was identified in the sediment sludge exposed to 30 μM uranium, and the dominant bacteria included Acinetobacter (44.9%), Klebsiella (20.0%), Proteiniclasticum (6.7%), Enterobacteriaceae (6.6%), Desulfovibrio (4.4%), Porphyromonadaceae (4.1%), Comamonas (2.4%) and Sedimentibacter (2.3%). By comparison to the inoculum sediment sludge, exposure to uranium caused a substantial difference in the majority of bacterial abundance.
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Affiliation(s)
- Taotao Zeng
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China.
| | - Guanhai Mo
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China
| | - Qing Hu
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China
| | - Guohua Wang
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China
| | - Wei Liao
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China
| | - Shuibo Xie
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China; Key Discipline Laboratory for National Defence for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, China
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24
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Liu T, He X, Jia G, Xu J, Quan X, You S. Simultaneous nitrification and denitrification process using novel surface-modified suspended carriers for the treatment of real domestic wastewater. CHEMOSPHERE 2020; 247:125831. [PMID: 31935576 DOI: 10.1016/j.chemosphere.2020.125831] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/31/2019] [Accepted: 01/02/2020] [Indexed: 05/27/2023]
Abstract
Moving-bed biofilm reactor (MBBR) is a well-established technology for simultaneous nitrification and denitrification (SND). In MBBR, biofilm development and pollutant removal performance are strictly governed by the physico-chemical properties of the carriers. In this study, novel surface-modified carriers with enhanced hydrophilicity (surface contact angle of 60.2 ± 2.3°) and positively-charged surfaces (+11.7 ± 1.1 mV, pH 7.0) had been prepared successfully via polymer blending, and they had also been implemented in SND system for the treatment of real domestic wastewater. Results showed that accelerated startup of SND with more biomass on the carriers was observed in MBBR system filled with surface-modified carriers. At low DO level (0.6-0.8 mg L-1) and low C/N ratio (≤5), highly efficient organics removal and SND performance could be achieved with COD removal, TN removal and SND efficiencies of 79.3-85.7%, 62.0-75.9% and 58.5-71.8%, respectively. The efficient performance of SND in MBBR system filled with surface-modified carriers was mainly attributed to the coexistence of enriched mixtrophic nitrifiers and denitrifiers like autotrophic nitrifers (Nitrosomonas, Nitrospira, Nitrobacter), heterotrophic nitrifers (Rudaea), aerobicdenitrifiers (Dokdonella, Terrimonas), anoxic denitrifiers (Gemmobacter, Ottowia, Methyloversatilis, Thermomonas) and N2O producer (Mesorhizobium).
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Affiliation(s)
- Tao Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| | - Xiaolu He
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Guangyue Jia
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Jiawei Xu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Xie Quan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Shijie You
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
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25
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Khare D, Kumar R, Acharya C. Genomic and functional insights into the adaptation and survival of Chryseobacterium sp. strain PMSZPI in uranium enriched environment. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 191:110217. [PMID: 32001422 DOI: 10.1016/j.ecoenv.2020.110217] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/11/2019] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
Metal enriched areas represent important and dynamic microbiological ecosystems. In this study, the draft genome of a uranium (U) tolerant bacterium, Chryseobacterium sp. strain PMSZPI, isolated from the subsurface soil of Domiasiat uranium ore deposit in Northeast India, was analyzed. The strain revealed a genome size of 3.8 Mb comprising of 3346 predicted protein-coding genes. The analysis indicated high abundance of genes associated with metal resistance and efflux, transporters, phosphatases, antibiotic resistance, polysaccharide synthesis, motility, protein secretion systems, oxidoreductases and DNA repair. Comparative genomics with other closely related Chryseobacterium strains led to the identification of unique inventory of genes which were of adaptive significance in PMSZPI. Consistent with the genome analysis, PMSZPI showed superior tolerance to uranium and other heavy metals. The metal exposed cells exhibited transcriptional induction of metal translocating PIB ATPases suggestive of their involvement in metal resistance. Efficient U binding (~90% of 100 μM U) and U bioprecipitation (~93-94% of 1 mM U at pH 5, 7 and 9) could be attributed as uranium tolerance strategies in PMSZPI. The strain demonstrated resistance to a large number of antibiotics which was in agreement with in silico prediction. Reduced gliding motility in the presence of cadmium and uranium, enhanced biofilm formation on uranium exposure and tolerance to 1.5 kGy of 60Co gamma radiation were perceived as adaptive responses in PMSZPI. Overall, the positive correlation observed between uranium/metal tolerance abilities predicted using genome analysis and the functional characterization reinforced the multifaceted adaptation strategies employed by PMSZPI for its survival in the soil of uranium ore deposit comprising of high concentrations of uranium and other heavy metals.
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Affiliation(s)
- Devanshi Khare
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India
| | - Celin Acharya
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
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26
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Hou R, Luo X, Liu C, Zhou L, Wen J, Yuan Y. Enhanced degradation of triphenyl phosphate (TPHP) in bioelectrochemical systems: Kinetics, pathway and degradation mechanisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:113040. [PMID: 31421579 DOI: 10.1016/j.envpol.2019.113040] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 08/09/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
Triphenyl phosphate (TPHP) is one of the major organophosphate esters (OPEs) with increasing consumption. Considering its largely distribution and high toxicity in aquatic environment, it is important to explore an efficient treatment for TPHP. This study aimed to investigate the accelerated degradation of TPHP in a three-electrode single chamber bioelectrochemical system (BES). Significant increase of degradation efficiency of TPHP in the BES was observed compared with open circuit and abiotic controls. The one-order degradation rates of TPHP (1.5 mg L-1) were increased with elevating sodium acetate concentrations and showed the highest value (0.054 ± 0.010 h-1) in 1.0 g L-1 of sodium acetate. This result indicated bacterial metabolism of TPHP was enhanced by the application of micro-electrical field and addition acetate as co-substrates. TPHP could be degraded into diphenyl phosphate (DPHP), hydroxyl triphenyl phosphate (OH-TPHP) and three byproducts. DPHP was the most accumulated degradation product in BES, which accounted more than 35.5% of the initial TPHP. The composition of bacterial community in BES electrode was affected by the acclimation by TPHP, with the most dominant bacteria of Azospirillum, Petrimonas, Pseudomonas and Geobacter at the genera level. Moreover, it was found that the acute toxic effect of TPHP to Vibrio fischeri was largely removed after the treatment, which revealed that BES is a promising technology to remove TPHP threaten in aquatic environment.
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Affiliation(s)
- Rui Hou
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Xiaoshan Luo
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Chuangchuang Liu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Lihua Zhou
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Junlin Wen
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Yong Yuan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
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27
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Khalid NA, Rajandas H, Parimannan S, Croft LJ, Loke S, Chong CS, Bruce NC, Yahya A. Insights into microbial community structure and diversity in oil palm waste compost. 3 Biotech 2019; 9:364. [PMID: 31588388 DOI: 10.1007/s13205-019-1892-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 08/31/2019] [Indexed: 11/26/2022] Open
Abstract
Empty fruit bunch (EFB) and palm oil mill effluent (POME) are the major wastes generated by the oil palm industry in Malaysia. The practice of EFB and POME digester sludge co-composting has shown positive results, both in mitigating otherwise environmentally damaging waste streams and producing a useful product (compost) from these streams. In this study, the bacterial ecosystems of 12-week-old EFB-POME co-compost and POME biogas sludge from Felda Maokil, Johor were analysed using 16S metagenome sequencing. Over ten phyla were detected, with Chloroflexi being the predominant phylum, representing approximately 53% of compost and 23% of the POME microbiome reads. The main bacterial lineage found in the compost and POME was Anaerolinaceae (Chloroflexi) with 30% and 18% of the total gene fragments, respectively. The significant differences between compost and POME communities were abundances of Syntrophobacter, Sulfuricurvum and Coprococcus. No methanogens were identified due to the bias in general 16S primers to eubacteria. The preponderance of anaerobic species in the compost and high abundance of secondary metabolite fermenting bacteria is due to an extended composting time, with anaerobic collapse of the pile due to the tropical heat. Predictive functional profiles of the metagenomes using 16S rRNA marker genes suggest that the presence of enzymes involved in degradation of polysaccharides such as glucoamylase, endoglucanase and arabinofuranosidase, all of which were strongly active in POME. Eubacterial species associated with cellulytic methanogenesis were present in both samples.
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Affiliation(s)
- Nurshafika Abd Khalid
- 1Biorefinery Technology Laboratory, Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Heera Rajandas
- 2Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, 08100 Bedong, Kedah Malaysia
| | - Sivachandran Parimannan
- 2Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, 08100 Bedong, Kedah Malaysia
| | - Laurence J Croft
- 3Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220 Australia
| | - Stella Loke
- 4School of Life and Environmental Sciences, Deakin University, Burwood Campus, Building M, 221 Burwood Hwy, Burwood, Victoria 3125 Australia
| | - Chun Shiong Chong
- 1Biorefinery Technology Laboratory, Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Neil C Bruce
- 5Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York, YO10 5DD UK
| | - Adibah Yahya
- 1Biorefinery Technology Laboratory, Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
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28
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Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils. Microorganisms 2019; 7:microorganisms7090324. [PMID: 31489900 PMCID: PMC6780890 DOI: 10.3390/microorganisms7090324] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [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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Hoyos-Hernandez C, Courbert C, Simonucci C, David S, Vogel TM, Larose C. Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima. FEMS Microbiol Lett 2019; 366:5556529. [DOI: 10.1093/femsle/fnz180] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 08/26/2019] [Indexed: 12/19/2022] Open
Abstract
ABSTRACT
Chernobyl and Fukushima were subjected to radionuclide (RN) contamination that has led to environmental problems. In order to explore the ability of microorganisms to survive in these environments, we used a combined 16S rRNA and metagenomic approach to describe the prokaryotic community structure and metabolic potential over a gradient of RN concentrations (137Cs 1680–0.4 and 90Sr 209.1–1.9 kBq kg−1) in soil samples. The taxonomic results showed that samples with low 137Cs content (37.8–0.4 kBq kg−1) from Fukushima and Chernobyl clustered together. In order to determine the effect of soil chemical parameters such as organic carbon (OC), Cesium-137 (137Cs) and Strontium-90 (90Sr) on the functional potential of microbial communities, multiple predictor model analysis using piecewiseSEM was carried out on Chernobyl soil metagenomes. The model identified 46 genes that were correlated to these parameters of which most have previously been described as mechanisms used by microorganisms under stress conditions. This study provides a baseline taxonomic and metagenomic dataset for Fukushima and Chernobyl, respectively, including physical and chemical characteristics. Our results pave the way for evaluating the possible RN selective pressure that might contribute to shaping microbial community structure and their functions in contaminated soils.
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Affiliation(s)
- Carolina Hoyos-Hernandez
- Laboratoire sur le devenir des pollutions de sites radioactifs, Institut de Radioprotection et de Sûreté Nucléaire, 31 avenue de la Division Leclerc, 92320, Fontenay-aux-Roses Cedex, France
| | - Christelle Courbert
- Laboratoire sur le devenir des pollutions de sites radioactifs, Institut de Radioprotection et de Sûreté Nucléaire, 31 avenue de la Division Leclerc, 92320, Fontenay-aux-Roses Cedex, France
| | - Caroline Simonucci
- Laboratoire sur le devenir des pollutions de sites radioactifs, Institut de Radioprotection et de Sûreté Nucléaire, 31 avenue de la Division Leclerc, 92320, Fontenay-aux-Roses Cedex, France
- Laboratoire d'expertise et d'intervention en radioprotection Nord, Institut de Radioprotection et de Sûreté Nucléaire, 31 avenue de la Division Leclerc, 92320 Fontenay aux Roses, France
| | - Sebastien David
- Environmental Microbial Genomics, Laboratoire Ampere, Ecole Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue 69134, Ecully, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampere, Ecole Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue 69134, Ecully, France
| | - Catherine Larose
- Environmental Microbial Genomics, Laboratoire Ampere, Ecole Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue 69134, Ecully, France
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Xi W, Gao Y, Cheng Z, Chen C, Han M, Yang P, Xiong G, Ning K. Using QC-Blind for Quality Control and Contamination Screening of Bacteria DNA Sequencing Data Without Reference Genome. Front Microbiol 2019; 10:1560. [PMID: 31354662 PMCID: PMC6637319 DOI: 10.3389/fmicb.2019.01560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 06/21/2019] [Indexed: 11/13/2022] Open
Abstract
Quality control for next generation sequencing (NGS) has become increasingly important with the ever increasing importance of sequencing data for omics studies. Tools have been developed for filtering possible contaminants from species with known reference genome. Unfortunately, reference genomes for all the species involved, including the contaminants, are required for these tools to work. This precludes many real-life samples that have no information about the complete genome of the target species, and are contaminated with unknown microbial species. In this work we proposed QC-Blind, a novel quality control pipeline for removing contaminants without any use of reference genomes. The pipeline merely requires the information about a few marker genes of the target species. The entire pipeline consists of unsupervised read assembly, contig binning, read clustering, and marker gene assignment. When evaluated on in silico, ab initio and in vivo datasets, QC-Blind proved effective in removing unknown contaminants with high specificity and accuracy, while preserving most of the genomic information of the target bacterial species. Therefore, QC-Blind could serve well in situations where limited information is available for both target and contamination species.
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Affiliation(s)
- Wang Xi
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangyu Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Chaoyun Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maozhen Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guangzhou Xiong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA. Genes (Basel) 2019; 10:genes10050325. [PMID: 31035394 PMCID: PMC6562407 DOI: 10.3390/genes10050325] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [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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Zeng T, Li L, Mo G, Wang G, Liu H, Xie S. Analysis of uranium removal capacity of anaerobic granular sludge bacterial communities under different initial pH conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:5613-5622. [PMID: 30612368 DOI: 10.1007/s11356-018-4017-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
The bacterial community of an anaerobic granular sludge associated with uranium depletion was investigated following its exposure to uranium under different initial pH conditions (pH 4.5, 5.5, and 6.5). The highest uranium removal efficiency (98.1%) was obtained for the sample with an initial pH of 6.5, which also supported the highest bacterial community richness and diversity. Venn diagrams visualized the decrease in the number of genera present in both the inoculum and the uranium-exposed biomass as the initial pH decreased from 6.5 to 4.5. Compared with the inoculum, a significant increase in the abundances of the phyla Chloroflexi and Proteobacteria was observed following uranium exposure. At initial pH conditions of 6.5 to 4.5, the proportions of the taxa Anaerolineaceae, Chryseobacterium, Acinetobacter, Pseudomonas, and Sulfurovum increased significantly, likely contributing to the observed uranium removal. Uranium exposure induced a greater level of dynamic diversification of bacterial abundances than did the initial pH difference.
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Affiliation(s)
- Taotao Zeng
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, People's Republic of China.
| | - Licheng Li
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, People's Republic of China
| | - Guanhai Mo
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, People's Republic of China
| | - Guohua Wang
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, People's Republic of China
| | - Haiyan Liu
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, People's Republic of China
| | - Shuibo Xie
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, People's Republic of China.
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, People's Republic of China.
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Hemmat-Jou MH, Safari-Sinegani AA, Mirzaie-Asl A, Tahmourespour A. Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach. ECOTOXICOLOGY (LONDON, ENGLAND) 2018; 27:1281-1291. [PMID: 30242595 DOI: 10.1007/s10646-018-1981-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/01/2018] [Indexed: 06/08/2023]
Abstract
Soil pollution occurring at mining sites has adverse impacts on soil microbial diversity. New approaches, such as metagenomics approach, have become a powerful tool to investigate biodiversity of soil microbial communities. In the current study, metagenomics approach was used to investigate the microbial diversity of soils contaminated with different concentrations of lead (Pb) and zinc (Zn). The contaminated soils were collected from a Pb and Zn mine. The soil total DNA was extracted and 16S rDNA genes were amplified using universal primers. The PCR amplicons were sequenced and bioinformatic analysis of metagenomes was conducted to identify prokaryotic diversity in the Pb- and Zn-contaminated soils. The results indicated that the ten most abundant bacteria in all samples were Solirubrobacter (Actinobacteria), Geobacter (Proteobacteria), Edaphobacter (Acidobacteria), Pseudomonas (Proteobacteria), Gemmatiomonas (Gemmatimonadetes), Nitrosomonas, Xanthobacter, and Sphingomonas (Proteobacteria), Pedobacter (Bacterioidetes), and Ktedonobacter (Chloroflexi), descendingly. Archaea were also numerous, and Nitrososphaerales which are important in the nitrogen cycle had the highest abundance in the samples. Although, alpha and beta diversity showed negative effects of Pb and Zn contamination on soil microbial communities, microbial diversity of the contaminated soils was not subjected to a significant change. This study provided valuable insights into microbial composition in heavy metals-contaminated soils.
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Affiliation(s)
- M H Hemmat-Jou
- Department of Soil Science, College of Agriculture, Bu-Ali Sina University, Hamedan, 6517838695, Iran.
| | - A A Safari-Sinegani
- Department of Soil Science, College of Agriculture, Bu-Ali Sina University, Hamedan, 6517838695, Iran
| | - A Mirzaie-Asl
- Department of Biotechnology, College of Agriculture, Bu-Ali Sina University, Hamedan, 6517838695, Iran
| | - A Tahmourespour
- Department of Basic Medical Sciences, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
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Zeng T, Zhang S, Gao X, Wang G, Lens PNL, Xie S. Assessment of Bacterial Community Composition of Anaerobic Granular Sludge in Response to Short-Term Uranium Exposure. MICROBIAL ECOLOGY 2018; 76:648-659. [PMID: 29417188 DOI: 10.1007/s00248-018-1152-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
The effect of 10-50 μM uranium (U(VI)) on the bacterial community of anaerobic granular sludge was investigated by 24-h exposure tests, after which the bacterial community was analyzed by high-throughput sequencing. The specific U(VI) reducing activity of the anaerobic granular sludge ranged between 3.1 to 19.7 μM U(VI) g-1(VSS) h-1, independently of the initial U(VI) concentration. Alpha diversity revealed that microbial richness and diversity was the highest for anaerobic granular sludge upon 10 μM uranium exposure. Compared with the original biomass, the phylum of Euryarchaeota was significantly affected, whereas the Bacteroidetes, Firmicutes, and Synergistetes phyla were only slightly affected. However, the abundance of Chloroflexi and Proteobacteria phyla clearly increased after 24 h uranium exposure. Based on the genus level analysis, significant differences appeared in the bacterial abundance after uranium exposure. The proportions of Pseudomonas, Acinetobacter, Parabacteroides, Brevundimonas, Sulfurovum, and Trichococcus increased significantly, while the abundance of Paludibacter and Erysipelotrichaceae incertae sedis decreased dramatically. This study shows a dynamic diversification of the bacterial composition as a response to a short time (24 h) U(VI) exposure (10-50 μM).
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Affiliation(s)
- Taotao Zeng
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, People's Republic of China.
- UNESCO-IHE Institute for Water Education, Delft, The Netherlands.
| | - Shiqi Zhang
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, People's Republic of China
| | - Xiang Gao
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, People's Republic of China
| | - Guohua Wang
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, People's Republic of China
| | - Piet N L Lens
- UNESCO-IHE Institute for Water Education, Delft, The Netherlands
| | - Shuibo Xie
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, People's Republic of China
- Key Discipline Laboratory for National Defence for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, People's Republic of China
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Mumtaz S, Streten C, Parry DL, McGuinness KA, Lu P, Gibb KS. Soil uranium concentration at Ranger Uranium Mine Land Application Areas drives changes in the bacterial community. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2018; 189:14-23. [PMID: 29549875 DOI: 10.1016/j.jenvrad.2018.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/08/2018] [Accepted: 03/08/2018] [Indexed: 06/08/2023]
Abstract
Soil microorganisms may respond to metal stress by a shift in the microbial community from metal sensitive to metal resistant microorganisms. We assessed the bacterial community from low (2-20 mg kg-1), medium (200-400 mg kg-1), high (500-900 mg kg-1) and very high (>900 mg kg-1) uranium soils at Ranger Uranium Mine in northern Australia through pyrosequencing. Proteobacteria (28.85%) was the most abundant phylum at these sites, followed by Actinobacteria (9.31%), Acidobacteria (7.33%), Verrucomicrobia (2.11%), Firmicutes (2.02%), Chloroflexi (1.11%), Cyanobacteria (0.93%), Planctomycetes (0.82%), Bacteroidetes (0.46%) and Candidate_division_WS3 (Latescibacteria) (0.21%). However, 46.79% of bacteria were unclassified. Bacteria at low U soils differed from soils with elevated uranium. Bacterial OTUs closely related to Kitasatospora spp., Sphingobacteria spp. and Rhodobium spp. were only present at higher uranium concentrations and the bacterial community also changed with seasonal and temporal changes in soil uranium and physicochemical variables. This study using next generation sequencing in association with environmental variables at a uranium mine has laid a foundation for further studies of soil-microbe-metal interactions which may be useful for developing sustainable management and rehabilitation strategies. Furthermore, bacterial species associated with higher uranium may serve as useful indicators of uranium contamination in the wet-dry tropics.
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Affiliation(s)
- Saqib Mumtaz
- Charles Darwin University, Darwin, NT, Australia.
| | | | - David L Parry
- Charles Darwin University, Darwin, NT, Australia; Australian Institute of Marine Science, Darwin, NT, Australia
| | | | - Ping Lu
- Charles Darwin University, Darwin, NT, Australia; Energy Resources of Australia, Darwin, NT, Australia
| | - Karen S Gibb
- Charles Darwin University, Darwin, NT, Australia
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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: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 11/28/2022]
Abstract
There is a strong interest in knowing how various microbial systems respond to the presence of uranium (U), largely in the context of bioremediation. There is no known biological role for uranium so far. Uranium is naturally present in rocks and minerals. The insoluble nature of the U(IV) minerals keeps uranium firmly bound in the earth's crust minimizing its bioavailability. However, anthropogenic nuclear reaction processes over the last few decades have resulted in introduction of uranium into the environment in soluble and toxic forms. Microbes adsorb, accumulate, reduce, oxidize, possibly respire, mineralize and precipitate uranium. This review focuses on the microbial responses to uranium exposure which allows the alteration of the forms and concentrations of uranium within the cell and in the local environment. Detailed information on the three major bioprocesses namely, biosorption, bioprecipitation and bioreduction exhibited by the microbes belonging to various groups and subgroups of bacteria, fungi and algae is provided in this review elucidating their intrinsic and engineered abilities for uranium removal. The survey also highlights the instances of the field trials undertaken for in situ uranium bioremediation. Advances in genomics and proteomics approaches providing the information on the regulatory and physiologically important determinants in the microbes in response to uranium challenge have been catalogued here. Recent developments in metagenomics and metaproteomics indicating the ecologically relevant traits required for the adaptation and survival of environmental microbes residing in uranium contaminated sites are also included. A comprehensive understanding of the microbial responses to uranium can facilitate the development of in situ U bioremediation strategies.
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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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Effects of microbial diversity on nitrite concentration in pao cai , a naturally fermented cabbage product from China. Food Microbiol 2018; 72:185-192. [DOI: 10.1016/j.fm.2017.12.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/28/2017] [Accepted: 12/06/2017] [Indexed: 11/21/2022]
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Wang Z, Zhang W, Wang B, Zhang F, Shao Y. Influence of Bactrian camel milk on the gut microbiota. J Dairy Sci 2018; 101:5758-5769. [PMID: 29705422 DOI: 10.3168/jds.2017-13860] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/18/2018] [Indexed: 12/31/2022]
Abstract
Bactrian camel milk has become popular in the market as an important source of nutrients with diverse functional effects. In this study, the influence of Bactrian camel milk on the gut microbiota of mice was studied using metagenomic-based sequencing of the V3 and V4 hypervariable regions of the 16S rRNA gene. Bioinformatics analysis showed that Firmicutes and Bacteroidetes were the predominant phyla, accounting for more than 80% of the bacteria present. At the genus level, Allobaculum, Akkermansia, Romboutsia, Bifidobacterium, and Lactobacillus were most abundant in the gut microbiota; of these, Allobaculum and Akkermansia were the predominant genera, representing 40.42 and 7.85% of all the bacteria present, respectively. Camel milk was found to reduce relative abundance of Romboutsia, Lactobacillus, Turicibacter, and Desulfovibrio (decreased by 50.88, 34.78, 26.67, and 54.55%, respectively) in the gut microbiota compared with the control. However, some genera such as Allobaculum, Akkermansia, and Bifidobacterium in the gastrointestinal flora increased in abundance in the presence of camel milk; these genera are correlated with beneficial effects for organisms. Our research suggests that the gut microbiota should be taken into account when conducting functional studies on camel milk, and this work provides a useful foundation for further study on functions of camel milk.
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Affiliation(s)
- Zhaoxia Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, Inner Mongolia, P. R. China
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, Inner Mongolia, P. R. China
| | - Bini Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Fuxin Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China.
| | - Yuyu Shao
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China.
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Shen Y, Zheng X, Wang X, Wang T. The biomineralization process of uranium(VI) by Saccharomyces cerevisiae - transformation from amorphous U(VI) to crystalline chernikovite. Appl Microbiol Biotechnol 2018; 102:4217-4229. [PMID: 29564524 DOI: 10.1007/s00253-018-8918-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 11/30/2022]
Abstract
Microorganisms play a significant role in uranium(VI) biogeochemistry and influence U(VI) transformation through biomineralization. In the present work, the process of uranium mineralization was investigated by Saccharomyces cerevisiae. The toxicity experiments showed that the viability of cell was not significantly affected by 100 mg L-1 U(VI) under 4 days of exposure time. The batch experiments showed that the phosphate concentration and pH value increased over time during U(VI) adsorption. Meanwhile, thermodynamic calculations demonstrated that the adsorption system was supersaturated with respect to UO2HPO4. The X-ray powder diffraction spectroscopy (XRD), field emission scanning electron microscopy (FE-SEM) equipped with energy dispersive spectroscopy (EDX), Fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS) analyses indicated that the U(VI) was first attached onto the cell surface and reacted with hydroxyl, carboxyl, and phosphate groups through electrostatic interactions and complexation. As the immobilization of U(VI) transformed it from the ionic to the amorphous state, lamellar uranium precipitate was formed on the cell surface. With the prolongation of time, the amorphous uranium compound disappeared, and there were some crystalline substances observed extracellularly, which were well-characterized as tetragonal-chernikovite. Furthermore, the size of chernikovite was regulated at nano-level by cells, and the perfect crystal was formed finally. These findings provided an understanding of the non-reductive transformation process of U(VI) from the amorphous to crystalline state within microbe systems, which would be beneficial for the U(VI) treatment and reuse of nuclides and heavy metals.
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Affiliation(s)
- Yanghao Shen
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Xinyan Zheng
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Xiaoyu Wang
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Tieshan Wang
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, 730000, China.
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Woody forages effect the intestinal bacteria diversity of golden pompano Trachinotus ovatus. AMB Express 2018; 8:29. [PMID: 29484505 PMCID: PMC5826908 DOI: 10.1186/s13568-018-0550-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 02/05/2018] [Indexed: 01/07/2023] Open
Abstract
To understand the effect of woody forages on golden pompano (Trachinotus ovatus) intestinal bacteria diversity and exploit new aquafeed ingredients, the diets of Moringa oleifera Lam (MOL), Broussonetia papyrifera (BP), Neolamarckia cadamba (NC) and Folium mori (FM) formulated with 70% of reference (Ref) diet and 30% of the four woody plants leaves were fed to golden pompano with initial body weight of 34.4 ± 0.5 g for 56 days, respectively. Bacteria diversity of golden pompano intestine and tank water (W) samples were analyzed using high-throughput illumina sequencing and the result indicated that the dominate phyla of golden pompano intestine were Proteobacteria, Bacteroidetes, Firmicutes and Fusobacteria. Proteobacteria in BP was significantly higher than those in NC (P < 0.05). Firmicutes in NC were significantly higher than those in BP and FM (P < 0.05). At genera level, Lactobacillus in NC was significantly higher than those in BP, MOL and FM groups (P < 0.05). The PCoA and heat map analyses showed that the intestinal bacteria community of golden pompano fed with woody forages and Ref diet presented higher similarity and the bacteria community of golden pompano intestine were clearly distinguished from those of W. Phylogenetic investigation of communities by reconstruction of unobserved states showed that the intestinal bacteria dominant metabolism pathways of golden pompano fed with woody forages and Ref diet were biosynthesis of amino acids and carbon metabolism. Overall, the present study first successfully characterized the intestinal bacteria diversity of golden pompano.
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Zhang F, Wang Z, Lei F, Wang B, Jiang S, Peng Q, Zhang J, Shao Y. Bacterial diversity in goat milk from the Guanzhong area of China. J Dairy Sci 2017; 100:7812-7824. [DOI: 10.3168/jds.2017-13244] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 06/21/2017] [Indexed: 12/31/2022]
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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] [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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Theodorakopoulos N, Février L, Barakat M, Ortet P, Christen R, Piette L, Levchuk S, Beaugelin-Seiller K, Sergeant C, Berthomieu C, Chapon V. Soil prokaryotic communities in Chernobyl waste disposal trench T22 are modulated by organic matter and radionuclide contamination. FEMS Microbiol Ecol 2017. [DOI: 10.1093/femsec/fix079] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Liu B, Peng T, Sun H, Yue H. Release behavior of uranium in uranium mill tailings under environmental conditions. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2017; 171:160-168. [PMID: 28254525 DOI: 10.1016/j.jenvrad.2017.02.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 02/17/2017] [Accepted: 02/21/2017] [Indexed: 06/06/2023]
Abstract
Uranium contamination is observed in sedimentary geochemical environments, but the geochemical and mineralogical processes that control uranium release from sediment are not fully appreciated. Identification of how sediments and water influence the release and migration of uranium is critical to improve the prevention of uranium contamination in soil and groundwater. To understand the process of uranium release and migration from uranium mill tailings under water chemistry conditions, uranium mill tailing samples from northwest China were investigated with batch leaching experiments. Results showed that water played an important role in uranium release from the tailing minerals. The uranium release was clearly influenced by contact time, liquid-solid ratio, particle size, and pH under water chemistry conditions. Longer contact time, higher liquid content, and extreme pH were all not conducive to the stabilization of uranium and accelerated the uranium release from the tailing mineral to the solution. The values of pH were found to significantly influence the extent and mechanisms of uranium release from minerals to water. Uranium release was monitored by a number of interactive processes, including dissolution of uranium-bearing minerals, uranium desorption from mineral surfaces, and formation of aqueous uranium complexes. Considering the impact of contact time, liquid-solid ratio, particle size, and pH on uranium release from uranium mill tailings, reducing the water content, decreasing the porosity of tailing dumps and controlling the pH of tailings were the key factors for prevention and management of environmental pollution in areas near uranium mines.
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Affiliation(s)
- Bo Liu
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang 621010, Sichuan, PR China; Institute of Mineral Materials and Application, Southwest University of Science and Technology, Mianyang 621010, Sichuan, PR China; Key Laboratory of Solid Waste Treatment and Resource Recycle, Southwest University of Science and Technology, Ministry of Education, Mianyang 621010, Sichuan, PR China
| | - Tongjiang Peng
- Institute of Mineral Materials and Application, Southwest University of Science and Technology, Mianyang 621010, Sichuan, PR China; Key Laboratory of Solid Waste Treatment and Resource Recycle, Southwest University of Science and Technology, Ministry of Education, Mianyang 621010, Sichuan, PR China.
| | - Hongjuan Sun
- Key Laboratory of Solid Waste Treatment and Resource Recycle, Southwest University of Science and Technology, Ministry of Education, Mianyang 621010, Sichuan, PR China
| | - Huanjuan Yue
- Key Laboratory of Solid Waste Treatment and Resource Recycle, Southwest University of Science and Technology, Ministry of Education, Mianyang 621010, Sichuan, PR China
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Wang Y, Cao P, Wang L, Zhao Z, Chen Y, Yang Y. Bacterial community diversity associated with different levels of dietary nutrition in the rumen of sheep. Appl Microbiol Biotechnol 2017; 101:3717-3728. [PMID: 28175950 DOI: 10.1007/s00253-017-8144-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 01/02/2017] [Accepted: 01/27/2017] [Indexed: 01/16/2023]
Abstract
The sheep rumen microbial community plays an important role in animal performance and the environment. Few studies have paid close attention to the impact of different levels of dietary nutrition on rumen microbial populations. A total of 112 healthy Tan sheep were selected and randomly allotted to one of four dietary treatments (groups I, II, III, and IV). Each treatment included four replicated pens with seven sheep each for a total of 28 sheep per treatment. The sheep were fed four diets with nutrient levels that were 84, 96, 108, or 120% of the recommendation. In this study, a next-generation sequencing strategy and quantitative real-time PCR analysis were applied to investigate changes in whole ruminal bacteria with increased dietary energy and protein levels. The study observed 133 genera belonging to 16 phyla distributed throughout the rumen samples, with Firmicutes and Bacteroidetes predominating. Additionally, the higher nutritional dietary level linearly increased (P < 0.05) the number of Bacteroidetes and Proteobacteria but linearly decreased (P < 0.05) the Firmicutes richness. At the species level, the abundance of Prevotella ruminicola, Ruminococcus flavefaciens, and Succinivibrio dextrinosolvens linearly increased (P < 0.05), whereas the abundance of Selenomonas ruminantium and Veillonella parvula did not (P > 0.05). Furthermore, we predicted the potential functions of rumen bacteria. In particular, the relative abundances of the genes related to carbohydrates were overrepresented, and the genes involved in amino acid metabolism linearly increased (P < 0.05). These findings provide the first deep insights into the rumen microbial composition and the targeted improvement of dietary protein and energy use efficiency in Tan sheep.
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Affiliation(s)
- Yaoyue Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Pinghua Cao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan, People's Republic of China
| | - Lei Wang
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, Qinghai, People's Republic of China
| | - Zhaoyan Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China.
| | - Yuxin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China.
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Majumder ELW, Wall JD. Uranium Bio-Transformations: Chemical or Biological Processes? ACTA ACUST UNITED AC 2017. [DOI: 10.4236/ojic.2017.72003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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