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Kumar M, Saini HS. Deciphering Indigenous Bacterial Diversity of Co-Polluted Sites to Unravel Its Bioremediation Potential: A Metagenomic Approach. J Basic Microbiol 2024:e2400303. [PMID: 38988320 DOI: 10.1002/jobm.202400303] [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: 05/24/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 07/12/2024]
Abstract
Polluted drains across the globe are affected due to reckless disposal of untreated industrial effluents resulting in significant water pollution affecting microbial community structure/dynamics. To elucidate this, polluted samples were collected from Budha Nala (BN) drain, Tung Dhab (TD) drain, and wastewater treatment plant (WWTP) receiving an inflow of organic pollutants as well as heavy metals due to anthropogenic activities. The sample of unpolluted pristine soil (PS) was used as control, as there is no history of usage of organic chemicals at this site. The bacterial diversity of these samples was sequenced using the Illumina MiSeq platform by amplifying the V3/V4 region of 16S rRNA. The majority of operational taxonomic unit (OTUs) at polluted sites belonged to phyla Proteobacteria specifically Gammaproteobacteria class, followed by Actinobacteria, Bacteriodetes, Chloroflexi, Firmicutes, Planctomycetes, WS6, and TM7, whereas unpolluted site revealed the prevalence of Proteobacteria followed by Actinobacteria, Planctomycetes, Firmicutes, Acidobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, and Nitrospirae. The data sets decode unclassified species of the phyla Proteobacteria, Bacteriodetes, Chloroflexi, Firmicutes, and WS6, along with some unclassified bacterial species. The study provided a comparative study of changed microbial community structure, their possible functions across diverse geographical locations, and identifying specific bacterial genera as pollution bio-indicators of aged polluted drains.
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Affiliation(s)
- Manoj Kumar
- Department of Microbiology, Guru Nanak Dev University, Amritsar, India
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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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Li Q, Xiong Z, Xiang P, Zhou L, Zhang T, Wu Q, Zhao C. Effects of uranium mining on soil bacterial communities and functions in the Qinghai-Tibet plateau. CHEMOSPHERE 2024; 347:140715. [PMID: 37979803 DOI: 10.1016/j.chemosphere.2023.140715] [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: 05/10/2023] [Revised: 11/07/2023] [Accepted: 11/12/2023] [Indexed: 11/20/2023]
Abstract
The microecological effects of plateau uranium mining are still unknown. In this study, we used 16S rRNA high-throughput sequencing to analyze the impact of plateau uranium mining on the microbial diversity and community structure of tailings soil, tunnel soil, and soil at different depths in an open pit. The results showed that uranium mining significantly reduced soil microbial community richness and diversity indicators, including Chao1, Pielou evenness, and Shannon index (P < 0.05). Uranium mining activities significantly reduced the abundance of RB41, Vicinamidactaceae, and Nitrospira (P < 0.05). Interestingly, the abundance of Thiobacillus, Sphingomonas, and Sulfuriferula significantly increased in the soil samples from various environments and depths during uranium mining (P < 0.05). Beta diversity analysis found that uranium mining resulted in the differentiation of soil microbial communities. Functional enrichment analysis found that uranium mining resulted in the functional enrichment of DNA binding response regulator, DNA helicase, methyl-accepting chemotaxis protein, and Helicase conserved C-terminal domain, whereas cell wall synthesis, nonspecific serine/threonine protein kinase, RNA polymerase sigma-70 factor, and ATP binding cassette transporter were significantly affected by uranium mining (P < 0.05). In addition, we also found that different uranium mining environments and soil depths enriched diverse microbial populations and functions to cope with the environmental pressures that were elicited by uranium mining, including Gaiella, Gemmatimonas, Lysobacter, Pseudomonas, signal transformation histidine kinase, DNA-directed DNA polymerase, and iron complex outer membrane receptor protein functions (P < 0.05). The results have enhanced our understanding of the impact of uranium mining on plateau soil microecological stability and the mechanism of microbial response to uranium mining activities for the first time and aided us in screening microbial strains that can promote the environmental remediation of uranium mining in plateaus.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Zhuang Xiong
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Peng Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Lin Zhou
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China
| | - Ting Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Qian Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Changsong Zhao
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China.
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Nayak T, Basak S, Deb A, Dhal PK. A systematic review on groundwater radon distribution with human health consequences and probable mitigation strategy. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2022; 247:106852. [PMID: 35305305 DOI: 10.1016/j.jenvrad.2022.106852] [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: 02/03/2022] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Groundwater radon contamination is a serious global concern for its eco-toxicological effects. The major health hazard occurs due to toxic indoor air inhalation and consumption of contaminated drinking water supplied from different distribution systems, especially groundwater. There are fragmented reports on the measurement of radon contamination and their health consequences with physical radon removal strategies as well as characterization of inhabitant microbial communities. As it concerned with human health, collective information is much essential on their groundwater distribution, their physicochemical properties and possible mitigation strategies, not done so far. In such prospect, this review summarizes the physicochemical properties of radon, their sources, global as well as Indian groundwater radon contamination scenario, health effects and inhabitant microbes along with their survival strategies. It also summarizes the physical radon removal techniques and especially emphasizes the microbes based bioremediation process as well as a combination of both as a future effective radon remediation process.
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Affiliation(s)
- Tilak Nayak
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700032, India
| | - Sohom Basak
- Department of Biotechnology, Bengal Institute of Technology, Kolkata, 700091, India
| | - Argha Deb
- School of Studies in Environmental Radiation and Archaeological Sciences & Department of Physics, Jadavpur University, Kolkata, 700032, India
| | - Paltu Kumar Dhal
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700032, India.
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Biomineralization by Extremely Halophilic and Metal-Tolerant Community Members from a Sulfate-Dominated Metal-Rich Environment. Microorganisms 2021; 10:microorganisms10010079. [PMID: 35056528 PMCID: PMC8780871 DOI: 10.3390/microorganisms10010079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 11/17/2022] Open
Abstract
The adaptation to adverse environmental conditions can lead to adapted microbial communities that may be screened for mechanisms involved in halophily and, in this case, metal tolerance. At a former uranium mining and milling site in Seelingstädt, Germany, microbial communities from surface waters and sediment soils were screened for isolates surviving high salt and metal concentrations. The high salt contents consisted mainly of chloride and sulfate, both in soil and riverbed sediment samples, accompanied by high metal loads with presence of cesium and strontium. The community structure was dominated by Chloroflexi, Proteobacteria and Acidobacteriota, while only at the highest contaminations did Firmicutes and Desulfobacterota reach appreciable percentages in the DNA-based community analysis. The extreme conditions providing high stress were mirrored by low numbers of cultivable strains. Thirty-four extremely halotolerant bacteria (23 Bacillus sp. and another 4 Bacillales, 5 Actinobacteria, and 1 Gamma-Proteobacterium) surviving 25 to 100 mM SrCl2, CsCl, and Cs2SO4 were further analyzed. Mineral formation of strontium- or cesium-struvite could be observed, reducing bioavailability and thereby constituting the dominant metal and salt resistance strategy in this environment.
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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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Complete Genome Sequence for Asinibacterium sp. Strain OR53 and Draft Genome Sequence for Asinibacterium sp. Strain OR43, Two Bacteria Tolerant to Uranium. Microbiol Resour Announc 2019; 8:8/14/e01701-18. [PMID: 30948472 PMCID: PMC6449563 DOI: 10.1128/mra.01701-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Asinibacterium sp. strains OR43 and OR53 belong to the phylum Bacteroidetes and were isolated from subsurface sediments in Oak Ridge, TN. Both strains grow at elevated levels of heavy metals. Here, we present the closed genome sequence of Asinibacterium sp. strain OR53 and the draft genome sequence of Asinibacterium sp. strain OR43.
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Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi. Sci Rep 2018; 8:14281. [PMID: 30250138 PMCID: PMC6155181 DOI: 10.1038/s41598-018-32688-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/11/2018] [Indexed: 02/08/2023] Open
Abstract
Organic and inorganic xenobiotic compounds can affect the potential ecological function of the soil, altering its biodiversity. Therefore, the response of microbial communities to environmental pollution is a critical issue in soil ecology. Here, a high-throughput sequencing approach was used to investigate the indigenous bacterial and fungal community structure as well as the impact of pollutants on their diversity and richness in contaminated and noncontaminated soils of a National Interest Priority Site of Campania Region (Italy) called "Terra dei Fuochi". The microbial populations shifted in the polluted soils via their mechanism of adaptation to contamination, establishing a new balance among prokaryotic and eukaryotic populations. Statistical analyses showed that the indigenous microbial communities were most strongly affected by contamination rather than by site of origin. Overabundant taxa and Actinobacteria were identified as sensitive biomarkers for assessing soil pollution and could provide general information on the health of the environment. This study has important implications for microbial ecology in contaminated environments, increasing our knowledge of the capacity of natural ecosystems to develop microbiota adapted to polluted soil in sites with high agricultural potential and providing a possible approach for modeling pollution indicators for bioremediation purposes.
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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: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 11/28/2022]
Abstract
There is a strong interest in knowing how various microbial systems respond to the presence of uranium (U), largely in the context of bioremediation. There is no known biological role for uranium so far. Uranium is naturally present in rocks and minerals. The insoluble nature of the U(IV) minerals keeps uranium firmly bound in the earth's crust minimizing its bioavailability. However, anthropogenic nuclear reaction processes over the last few decades have resulted in introduction of uranium into the environment in soluble and toxic forms. Microbes adsorb, accumulate, reduce, oxidize, possibly respire, mineralize and precipitate uranium. This review focuses on the microbial responses to uranium exposure which allows the alteration of the forms and concentrations of uranium within the cell and in the local environment. Detailed information on the three major bioprocesses namely, biosorption, bioprecipitation and bioreduction exhibited by the microbes belonging to various groups and subgroups of bacteria, fungi and algae is provided in this review elucidating their intrinsic and engineered abilities for uranium removal. The survey also highlights the instances of the field trials undertaken for in situ uranium bioremediation. Advances in genomics and proteomics approaches providing the information on the regulatory and physiologically important determinants in the microbes in response to uranium challenge have been catalogued here. Recent developments in metagenomics and metaproteomics indicating the ecologically relevant traits required for the adaptation and survival of environmental microbes residing in uranium contaminated sites are also included. A comprehensive understanding of the microbial responses to uranium can facilitate the development of in situ U bioremediation strategies.
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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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Corbett MK, Eksteen JJ, Niu XZ, Watkin ELJ. Syntrophic effect of indigenous and inoculated microorganisms in the leaching of rare earth elements from Western Australian monazite. Res Microbiol 2018; 169:558-568. [PMID: 29852218 DOI: 10.1016/j.resmic.2018.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/16/2018] [Accepted: 05/19/2018] [Indexed: 10/14/2022]
Abstract
The unique physiochemical properties exhibited by rare earth elements (REEs) and their increasing application in high-tech industries has created a demand for secure supply lines with established recovery procedures that create minimal environmental damage. Bioleaching experiments conducted on a non-sterile monazite concentrate with a known phosphate solubilising microorganism (PSM) resulted in greater mobilisation of REEs into solution in comparison to experiments conducted on sterile monazite. By combining the native consortia with an introduced PSM, a syntrophic effect between the populations effectively leached a greater amount of REEs than either a single PSM or the indigenous population alone. With sterile monazite, Penicillium sp.CF1 inoculated experiments released a total REE concentration of 12.32 mg L-1 after incubation for 8 days, whereas on non-sterile ore, double the soluble REE concentration was recorded (23.7 mg L-1). Comparable effects were recorded with Enterobacter aerogenes, Pantoea agglomerans and Pseudomonas putida. Alterations in the microbial populations during bioleaching of the monazite ore were determined by diversity profiling and demonstrated noticeable changes in community inhabitants over 14 days. The presence of native Firmicutes on the monazite appears to greatly contribute to the increased leaching recorded when using non-sterile monazite for REE recovery.
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Affiliation(s)
- Melissa K Corbett
- School of Pharmacy and Biomedical Sciences, CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
| | - Jacques J Eksteen
- Western Australian School of Mines, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
| | - Xi-Zhi Niu
- Curtin Water Quality Research Centre, Department of Chemistry, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
| | - Elizabeth L J Watkin
- School of Pharmacy and Biomedical Sciences, CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
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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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Basu S, Paul T, Yadav P, Debnath A, Sarkar K. Molecular Study of Indigenous Bacterial Community Composition on Exposure to Soil Arsenic Concentration Gradient. Pol J Microbiol 2017; 66:209-221. [PMID: 28735305 DOI: 10.5604/01.3001.0010.7838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Community structure of bacteria present in arsenic contaminated agricultural soil was studied with qPCR (quantitative PCR) and DGGE (Denaturing Gradient Gel Electrophoresis) as an indicator of extreme stresses. Copy number of six common bacterial taxa (Acidobacteria, Actinobacteria, α-, β- and γ-Proteobacteria, Firmicutes) was calculated using group specific primers of 16S rDNA. It revealed that soil contaminated with low concentration of arsenic was dominated by both Actinobacteria and Proteobacteria but a shift towards Proteobacteria was observed with increasing arsenic concentration, and number of Actinobacteria eventually decreases. PCA (Principle Component Analysis) plot of bacterial community composition indicated a distinct resemblance among high arsenic content samples, while low arsenic content samples remained separated from others. Cluster analysis of soil parameters identifies three clusters, each of them was related to the arsenic content. Further, cluster analysis of 16S rDNA based DGGE fingerprint markedly distributed the soil bacterial populations into low (< 10 ppm) and high (> 10 ppm) arsenic content subgroups. Following analysis of diversity indices shows significant variation in bacterial community structure. MDS (Multi Dimensional Scaling) plot revealed distinction in the distribution of each sample denoting variation in bacterial diversity. Phylogenetic sequence analysis of fragments excised from DGGE gel revealed the presence of γ-Proteobacteria group across the study sites. Collectively, our experiments indicated that gradient of arsenic contamination affected the shape of the soil bacterial population by significant structural shift.
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Affiliation(s)
- Semanti Basu
- Department of Microbiology, University of Kalyani, Nadia, West Bengal, India
| | - Tanima Paul
- Department of Microbiology, University of Kalyani, Nadia, West Bengal, India
| | - Priya Yadav
- Department of Microbiology, University of Kalyani, Nadia, West Bengal, India
| | - Abhijit Debnath
- Department of Agricultural Chemistry and Soil Science, BCKV, Mohanpur, Nadia, West Bengal, India
| | - Keka Sarkar
- Department of Microbiology, University of Kalyani, Nadia, West Bengal, India
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Suriya J, Chandra Shekar M, Nathani NM, Suganya T, Bharathiraja S, Krishnan M. Assessment of bacterial community composition in response to uranium levels in sediment samples of sacred Cauvery River. Appl Microbiol Biotechnol 2016; 101:831-841. [PMID: 27812801 DOI: 10.1007/s00253-016-7945-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 10/09/2016] [Accepted: 10/13/2016] [Indexed: 01/20/2023]
Abstract
Global industrialization is a major cause of effluent discharge from industries up to alarming concentrations. Especially, uranium concentrations in water bodies are of great concern, as its radioactivity significantly affects the persistent diversity of microbiota. Recently, continuous application of pesticides in the agricultural lands and accumulation of quartz that enter the Cauvery River has significantly increased the concentration of uranium (U) and other heavy metals. To perceive the impact of uranium on bacterial diversity in Cauvery River, sediment samples collected from polluted (UP) site with 32.4 Bq/K of U concentration and control (UNP) site were scrutinized for bacterial diversity through metagenomic analysis of the V3 region of 16S rDNA by Illumina sequencing. Taxonomic assignment revealed that the unpolluted sample was dominated by Bacteroidetes (27.7 %), and Firmicutes (25.9 %), while sediment sample from the highly polluted site revealed abundance of Proteobacteria (47.5 %) followed by Bacteroidetes (22.4 %) and Firmicutes (14.6 %). Among Proteobacteria, Gammaproteobacteria was the most prevalent group followed by alpha, delta, epsilon, and beta in the uranium-polluted sample. Rare and abundant species analysis revealed that species like Idiomarina loihiensis was abundant in the pollutant sample; however, it was rare (<0.1 %) in the sample from pristine environment. Similarly, the species distribution in both the samples varied, with the bacteria potentially active in redox activity and biosorption potential dominating in the polluted sample. Outcomes of the present study demonstrated the impact of uranium and metal accumulation on the bacterial communities and further confirmed the promising candidature of specific bacterial species as bioindicators of contamination.
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Affiliation(s)
- Jayaraman Suriya
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
| | - Mootapally Chandra Shekar
- CAS in Marine Biology, Annamalai University, Porto Novo, Tamil Nadu, 608502, India.,Department of Marine Science, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, 364002, India
| | - Neelam Mustakali Nathani
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India.,Department of Life Sciences, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, 364002, India
| | - Thangaiyan Suganya
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
| | | | - Muthukalingan Krishnan
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
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Fan M, Lin Y, Huo H, Liu Y, Zhao L, Wang E, Chen W, Wei G. Microbial communities in riparian soils of a settling pond for mine drainage treatment. WATER RESEARCH 2016; 96:198-207. [PMID: 27055175 DOI: 10.1016/j.watres.2016.03.061] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/12/2016] [Accepted: 03/25/2016] [Indexed: 06/05/2023]
Abstract
Mine drainage leads to serious contamination of soil. To assess the effects of mine drainage on microbial communities in riparian soils, we used an Illumina MiSeq platform to explore the soil microbial composition and diversity along a settling pond used for mine drainage treatment. Non-metric multidimensional scaling analysis showed that the microbial communities differed significantly among the four sampling zones (influent, upstream, downstream and effluent), but not seasonally. Constrained analysis of principal coordinates indicated heavy metals (zinc, lead and copper), total sulphur, pH and available potassium significantly influenced the microbial community compositions. Heavy metals were the key determinants separating the influent zone from the other three zones. Lower diversity indices were observed in the influent zone. However, more potential indicator species, related to sulphur and organic matter metabolism were found there, such as the sulphur-oxidizing genera Acidiferrobacter, Thermithiobacillus, Limnobacter, Thioprofundum and Thiovirga, and the sulphur-reducing genera Desulfotomaculum and Desulfobulbus; the organic matter degrading genera, Porphyrobacter and Paucimonas, were also identified. The results indicated that more microorganisms related to sulphur- and carbon-cycles may exist in soils heavily contaminated by mine drainage.
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Affiliation(s)
- Miaochun Fan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yanbing Lin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Haibo Huo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yang Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Liang Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D.F., Mexico
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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Yan X, Luo X, Zhao M. Metagenomic analysis of microbial community in uranium-contaminated soil. Appl Microbiol Biotechnol 2015; 100:299-310. [PMID: 26433967 DOI: 10.1007/s00253-015-7003-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/31/2015] [Accepted: 09/10/2015] [Indexed: 10/23/2022]
Abstract
Uranium tailing is a serious pollution challenge for the environment. Based on metagenomic sequencing analysis, we explored the functional and structural diversity of the microbial community in six soil samples taken at different soil depths from uranium-contaminated and uncontaminated areas. Kyoto Encyclopedia of Genes and Genomes Orthology (KO) groups were obtained using a Basic Local Alignment Search Tool search based on the universal protein resource database. The KO-pathway network was then constructed using the selected KOs. Finally, alpha and beta diversity analyses were performed to explore the differences in soil bacterial diversity between the radioactive soil and uncontaminated soil. In total, 30-68 million high-quality reads were obtained. Sequence assembly yielded 286,615 contigs; and these contigs mostly annotated to 1699 KOs. The KO distributions were similar among the six soil samples. Moreover, the proportion of the metabolism of other amino acids (e.g., beta-alanine, taurine, and hypotaurine) and signal transduction was significantly lower in radioactive soil than in uncontaminated soil, whereas the proportion of membrane transport and carbohydrate metabolism was higher. Additionally, KOs were mostly enriched in ATP-binding cassette transporters and two-component systems. According to diversity analyses, Actinobacteria and Proteobacteria were the dominant phyla in radioactive and uncontaminated soil, and Robiginitalea, Microlunatus, and Alicyclobacillus were the dominant genera in radioactive soil. Taken together, these results demonstrate that soil microbial community, structure, and functions show significant changes in uranium-contaminated soil. The dominant categories such as Actinobacteria and Proteobacteria may be applied in environmental governance for uranium-contaminated soil in southern China.
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Affiliation(s)
- Xun Yan
- Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, China.,College of Chemistry and Chemical Engineering, Qiqihar University Qiqihar, Heilongjiang, 161006, China
| | - Xuegang Luo
- Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, China.
| | - Min Zhao
- College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, 150040, China
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Delineating bacterial community structure of polluted soil samples collected from cancer prone belt of Punjab, India. 3 Biotech 2015; 5:727-734. [PMID: 28324527 PMCID: PMC4569629 DOI: 10.1007/s13205-014-0270-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/13/2014] [Indexed: 11/01/2022] Open
Abstract
16S rRNA gene analysis has emerged as one of the valuable tools that are being utilized in investigating the molecular phylogenetic structure of the particular environment. Here, we embarked upon understanding and delineating the molecular phylogeny structure of microbes in polluted soil samples from cancer prone belt of the Punjab, India, which is highly contaminated with herbicide, pesticide and heavy metals. To investigate the bacterial phylogeny structure, a high-molecular weight metagenomic DNA was extracted from the soil samples, followed by PCR amplification, cloning and analysis of the 16S rRNA genes. Study employing 16S rRNA profiling of the community DNA revealed the presence of two major phylums: the Proteobacteria (26.7 %), the Bacteroidetes (11.2 %), and several minor groups, i.e., Acidobacteria (4.2 %), Actinobacteria (4.2 %), Firmicutes (2.8 %), Verrucomicrobia (2.8 %), Gemmatimonadetes (1.4 %) and Chloroflexi (1.4 %). Among the Proteobacteria, we mainly observed the α-Proteobacteria (18.3 %). Nearly, 38 % of the recovered 16S rRNA gene sequences in this study do not share similarity with known culturable bacterial sequences reported in the genebank data base and hence considered to be novel. More interestingly, 16S rRNA gene sequences of archaeal origin (7.0 %) were also recovered that primarily indicate change in their evolution pattern. A phylogenetic tree constructed based on alignment-dependent method revealed the extent of similarity these clones shared with each other, followed by alignment-independent methods that statistically confirmed the sequence variation among the clones. Despite the high level of contamination in the study area, we observed remarkable microbial diversity that mainly includes the Gram-negative bacteria. The presence of more Gram-negative bacteria indicates that they have evolved a robust mechanism to resist and cope up with these pollutants compared to Gram-positive groups. Investigation of the polluted soil samples employing culture-independent approach revealed important bacterial groups which could be engineered for future bioremediation studies.
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Bacterial Community Structure from the Perspective of the Uranium Ore Deposits of Domiasiat in India. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s40011-013-0164-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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