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Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV. Prokaryotic Life Associated with Coal-Fire Gas Vents Revealed by Metagenomics. BIOLOGY 2023; 12:biology12050723. [PMID: 37237535 DOI: 10.3390/biology12050723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023]
Abstract
The natural combustion of underground coal seams leads to the formation of gas, which contains molecular hydrogen and carbon monoxide. In places where hot coal gases are released to the surface, specific thermal ecosystems are formed. Here, 16S rRNA gene profiling and shotgun metagenome sequencing were employed to characterize the taxonomic diversity and genetic potential of prokaryotic communities of the near-surface ground layer near hot gas vents in an open quarry heated by a subsurface coal fire. The communities were dominated by only a few groups of spore-forming Firmicutes, namely the aerobic heterotroph Candidatus Carbobacillus altaicus, the aerobic chemolitoautotrophs Kyrpidia tusciae and Hydrogenibacillus schlegelii, and the anaerobic chemolithoautotroph Brockia lithotrophica. Genome analysis predicted that these species can obtain energy from the oxidation of hydrogen and/or carbon monoxide in coal gases. We assembled the first complete closed genome of a member of uncultured class-level division DTU015 in the phylum Firmicutes. This bacterium, 'Candidatus Fermentithermobacillus carboniphilus' Bu02, was predicted to be rod-shaped and capable of flagellar motility and sporulation. Genome analysis showed the absence of aerobic and anaerobic respiration and suggested chemoheterotrophic lifestyle with the ability to ferment peptides, amino acids, N-acetylglucosamine, and tricarboxylic acid cycle intermediates. Bu02 bacterium probably plays the role of a scavenger, performing the fermentation of organics formed by autotrophic Firmicutes supported by coal gases. A comparative genome analysis of the DTU015 division revealed that most of its members have a similar lifestyle.
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Affiliation(s)
- Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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Feng G, Yong J, Liu Q, Chen H, Hu Y, Mao P. Remedial effect and operating status of a decommissioned uranium mill tailings (UMT) repository: A micro-ecological perspective based on bacterial community. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 340:117993. [PMID: 37094385 DOI: 10.1016/j.jenvman.2023.117993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/06/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
From a radioecological perspective, increasing attention has been paid to the long-term stabilisation of decommissioned uranium mill tailings (UMT) repositories. However, little is known about the evaluation of decommissioning and remedial effects of UMT repositories from a microecological perspective based on bacterial communities. Here, we analysed the distribution and structure of soil community assemblies along different vertical soil profiles in a decommissioned UMT repository and explored the impact of soil properties, including physicochemical parameters, metal(loid)s, and radionuclides, on the bacterial assemblage. We found that the α diversity of the bacterial community was unaffected by variations in different soil profiles and taxa were classified at the phylum level with small significant differences. In contrast, the bacterial community structure in and around the UMT repository showed significant differences; however, this difference was significantly affected by soil metal(loid)s and physicochemical properties rather than soil radionuclides. In addition, seven bacterial genera with significant differences between the inner and surrounding regions of the repository could be used as potential indicators to further investigate the remedial effects on soil environmental quality. These findings provide novel insights into the construction of an assessment system and in situ biomonitoring of UMT repositories from a microecological perspective based on bacterial communities.
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Affiliation(s)
- Guangwen Feng
- Research Center of Radiation Ecology and Ion Beam Biotechnology, College of Physics Science and Technology, Xinjiang University, Urumqi, Xinjiang, 830017, PR China.
| | - Jinlong Yong
- Research Center of Radiation Ecology and Ion Beam Biotechnology, College of Physics Science and Technology, Xinjiang University, Urumqi, Xinjiang, 830017, PR China
| | - Qian Liu
- School of Statistics and Data Science, Xinjiang University of Finance & Economics, Urumqi, Xinjiang, 830012, PR China
| | - Henglei Chen
- Research Center of Radiation Ecology and Ion Beam Biotechnology, College of Physics Science and Technology, Xinjiang University, Urumqi, Xinjiang, 830017, PR China
| | - Youhua Hu
- Radiation Environment Supervision Station of Xinjiang, Urumqi, Xinjiang, 830000, PR China
| | - Peihong Mao
- Research Center of Radiation Ecology and Ion Beam Biotechnology, College of Physics Science and Technology, Xinjiang University, Urumqi, Xinjiang, 830017, PR China
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Akimbekov NS, Digel I, Tastambek KT, Marat AK, Turaliyeva MA, Kaiyrmanova GK. Biotechnology of Microorganisms from Coal Environments: From Environmental Remediation to Energy Production. BIOLOGY 2022; 11:biology11091306. [PMID: 36138784 PMCID: PMC9495453 DOI: 10.3390/biology11091306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 11/22/2022]
Abstract
Simple Summary Despite the wide perception that coal environments are extreme habitats, they harbor resident microbial communities. Coal-associated habitats, such as coal mine areas/drainages, spoil heaps, and coalbeds, are defined as complex ecosystems with indigenous microbial groups and native microecological networks. Resident microorganisms possess rich functional potentials and profoundly shape a range of biotechnological processes in the coal industry, from production to remediation. Abstract It was generally believed that coal sources are not favorable as live-in habitats for microorganisms due to their recalcitrant chemical nature and negligible decomposition. However, accumulating evidence has revealed the presence of diverse microbial groups in coal environments and their significant metabolic role in coal biogeochemical dynamics and ecosystem functioning. The high oxygen content, organic fractions, and lignin-like structures of lower-rank coals may provide effective means for microbial attack, still representing a greatly unexplored frontier in microbiology. Coal degradation/conversion technology by native bacterial and fungal species has great potential in agricultural development, chemical industry production, and environmental rehabilitation. Furthermore, native microalgal species can offer a sustainable energy source and an excellent bioremediation strategy applicable to coal spill/seam waters. Additionally, the measures of the fate of the microbial community would serve as an indicator of restoration progress on post-coal-mining sites. This review puts forward a comprehensive vision of coal biodegradation and bioprocessing by microorganisms native to coal environments for determining their biotechnological potential and possible applications.
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Affiliation(s)
- Nuraly S. Akimbekov
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Correspondence:
| | - Ilya Digel
- Institute for Bioengineering, FH Aachen University of Applied Sciences, 52428 Jülich, Germany
| | - Kuanysh T. Tastambek
- Department of Fundamental Medicine, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Department of Applied Biology, M. Kh. Dulaty Taraz Regional University, Taraz 080012, Kazakhstan
- Ecology Research Institute, Khoja Akhmet Yassawi International Kazakh-Turkish University, Turkistan 161200, Kazakhstan
| | - Adel K. Marat
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Moldir A. Turaliyeva
- Department of Biotechnology, M. Auezov South Kazakhstan University, Shymkent 160012, Kazakhstan
| | - Gulzhan K. Kaiyrmanova
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
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Liu L, Lin W, Zhang L, Tang X, Liu Y, Lan S, Wang S, Zhou Y, Chen X, Wang L, Chen X, Guo L. Changes and Correlation Between Physiological Characteristics of Rhododendron simsii and Soil Microbial Communities Under Heat Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:950947. [PMID: 35937338 PMCID: PMC9355081 DOI: 10.3389/fpls.2022.950947] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
The relationship between Rhododendron simsii and its soil microbial community under heat stress was not clear. In this study, the effects of heat stress on the physiological characteristics, soil physicochemical properties and soil microbial community structure of R. simsii were investigated. The experimental control (CK) was set as day/night (14/10 h) 25/20°C and experimental treatments were set as light heat stress (LHS) 35/30°C and high heat stress (HHS) 40/35°C. Our results showed that, compared with CK, LHS treatment significantly increased malondialdehyde, hydrogen peroxide, proline and soluble sugar contents, as well as catalase and peroxidase activities, while HHS treatment significantly increased ascorbate peroxidase activity and decreased chlorophyll content. Compared with CK, LHS treatment significantly reduced soil ammonium-nitrogen and nitrate-nitrogen content, while HHS significantly increased soil ammonium-nitrogen content. Compared with CK, both treatments changed the soil microbial community structure. For bacterial community, LHS and HHS treatment resulting in the significant enrichment of Burkholderia-Caballeronia-Paraburkholderia and Occallatibacte, respectively. For fungal community, LHS treatment resulting in the significant enrichment of Candida, Mortierella and Boothiomyces. The redundancy analysis showed that plant physiological characteristics, soil ammonium-nitrogen content were significantly correlated with the soil microbial community. Therefore, heat stress altered the soil microbial community structure, and affected the availability of soil available nitrogen, which in turn affected the physiological characteristics of R. simsii. We suggest that soil microbial community may play an important role in plant resistance to heat stress, and its mechanism deserves further study.
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Affiliation(s)
- Lei Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/College of Forestry, Hainan University, Haikou, China
| | - Wei Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li Zhang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Xuexiao Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/College of Forestry, Hainan University, Haikou, China
| | - Yue Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/College of Forestry, Hainan University, Haikou, China
| | - Siren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shusheng Wang
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Lushan, China
| | - Yan Zhou
- Guizhou Botanical Garden, Guiyang, China
| | - Xiaochou Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ling Wang
- Fuzhou Qinting Lake Park Management Office, Fuzhou, China
| | - Xiang Chen
- Institute of Biology, Guizhou Academy of Sciences, Guiyang, China
| | - Lijin Guo
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/College of Forestry, Hainan University, Haikou, China
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Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV. Metagenomic Analysis of the Microbial Community in the Underground Coal Fire Area (Kemerovo Region, Russia) Revealed Predominance of Thermophilic Members of the Phyla Deinococcus-Thermus, Aquificae, and Firmicutes. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721050088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Abstract
Underground burning of coal seams accompanied by release of gases leads to development of local thermal ecosystems. We investigated the microbial community of the ground heated to 72°C in the release area of hot gases resulting from underground combustion of coal mining waste at the Bungurskiy-Severny coal deposit in the Kemerovo region of Russia. Analysis of the composition of the microbial community by 16S rRNA gene profiling revealed predominance of thermophilic bacteria of the phyla Deinococcus-Thermus, Aquificae, and Firmicutes. As a result of metagenomic analysis, 18 genomes of the main members of the microbial community were assembled, including the complete genomes of Hydrogenobacter thermophiles, a member of the candidate genus UBA11096 of the phylum Aquificae (RBS10-58), Thermoflexus hugenholtzii, and Thermus antranikianii. Analysis of the RBS10-58 genome indicates that this bacterium can autotrophically fix carbon in the reductive tricarboxylic acid cycle and obtain energy via oxidation of hydrogen and sulfur compounds with oxygen or nitrate as electron acceptors. Genome analysis of the two dominant Firmicutes species, Hydrogenibacillus schlegelii and an uncultured member of the class Thermaerobacteria, showed that these bacteria could grow aerobically by oxidizing hydrogen and carbon monoxide. Overall, the community was dominated by aerobic bacteria capable of growing autotrophically and obtaining energy via oxidation of the main components of coal gases, hydrogen and carbon monoxide. Thermus antranikianii, which makes up about a half of the microbial community, probably uses organic matter produced by autotrophic members of Firmicutes and Aquificae.
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Kadnikov VV, Mardanov AV, Beletsky AV, Grigoriev MA, Karnachuk OV, Ravin NV. Thermophilic Chloroflexi Dominate in the Microbial Community Associated with Coal-Fire Gas Vents in the Kuznetsk Coal Basin, Russia. Microorganisms 2021; 9:microorganisms9050948. [PMID: 33924824 PMCID: PMC8146126 DOI: 10.3390/microorganisms9050948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 01/12/2023] Open
Abstract
Thermal ecosystems associated with areas of underground burning coal seams are rare and poorly understood in comparison with geothermal objects. We studied the microbial communities associated with gas vents from the coal-fire in the mining wastes in the Kemerovo region of the Russian Federation. The temperature of the ground heated by the hot coal gases and steam coming out to the surface was 58 °C. Analysis of the composition of microbial communities revealed the dominance of Ktedonobacteria (the phylum Chloroflexi), known to be capable of oxidizing hydrogen and carbon monoxide. Thermophilic hydrogenotrophic Firmicutes constituted a minor part of the community. Among the well-known thermophiles, members of the phyla Aquificae, Deinococcus-Thermus and Bacteroidetes were also found. In the upper ground layer, Acidobacteria, Verrucomicrobia, Actinobacteria, Planctomycetes, as well as Proteobacteria of the alpha and gamma classes, typical of soils, were detected; their relative abundancies decreased with depth. The phylum Verrucomicrobia was dominated by Candidatus Udaeobacter, aerobic heterotrophs capable of generating energy through the oxidation of hydrogen present in the atmosphere in trace amounts. Archaea made up a small part of the communities and were represented by thermophilic ammonium-oxidizers. Overall, the community was dominated by bacteria, whose cultivated relatives are able to obtain energy through the oxidation of the main components of coal gases, hydrogen and carbon monoxide, under aerobic conditions.
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Affiliation(s)
- Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (A.V.M.); (A.V.B.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (A.V.M.); (A.V.B.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (A.V.M.); (A.V.B.)
| | - Mikhail A. Grigoriev
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia; (M.A.G.); (O.V.K.)
| | - Olga V. Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia; (M.A.G.); (O.V.K.)
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (A.V.M.); (A.V.B.)
- Correspondence:
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Kadnikov VV, Mardanov AV, Ivasenko DA, Antsiferov DV, Beletsky AV, Karnachuk OV, Ravin NV. Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen-driven thermophilic microbial community. Sci Rep 2018; 8:6730. [PMID: 29712968 PMCID: PMC5928048 DOI: 10.1038/s41598-018-25146-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 04/17/2018] [Indexed: 12/05/2022] Open
Abstract
Thermal ecosystems associated with underground coal combustion sites are rare and less studied than geothermal features. Here we analysed microbial communities of near-surface ground layer and bituminous substance in an open quarry heated by subsurface coal fire by metagenomic DNA sequencing. Taxonomic classification revealed dominance of only a few groups of Firmicutes. Near-complete genomes of three most abundant species, ‘Candidatus Carbobacillus altaicus’ AL32, Brockia lithotrophica AL31, and Hydrogenibacillus schlegelii AL33, were assembled. According to the genomic data, Ca. Carbobacillus altaicus AL32 is an aerobic heterotroph, while B. lithotrophica AL31 is a chemolithotrophic anaerobe assimilating CO2 via the Calvin cycle. H. schlegelii AL33 is an aerobe capable of both growth on organic compounds and carrying out CO2 fixation via the Calvin cycle. Phylogenetic analysis of the large subunit of RuBisCO of B. lithotrophica AL31 and H. schlegelii AL33 showed that it belongs to the type 1-E. All three Firmicutes species can gain energy from aerobic or anaerobic oxidation of molecular hydrogen, produced as a result of underground coal combustion along with other coal gases. We propose that thermophilic Firmicutes, whose spores can spread from their original geothermal habitats over long distances, are the first colonizers of this recently formed thermal ecosystem.
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Affiliation(s)
- Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Denis A Ivasenko
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050, Tomsk, Russia
| | - Dmitry V Antsiferov
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050, Tomsk, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050, Tomsk, Russia
| | - Nikolay V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.
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