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Geng Y, Peng C, Zhou W, Huang S, Zhou P, Wang Z, Qin H, Li D. Gradient rise in seepage pollution levels in tailings ponds shapes closer linkages between phytoplankton and bacteria. JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129432. [PMID: 35753300 DOI: 10.1016/j.jhazmat.2022.129432] [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: 04/19/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 05/14/2023]
Abstract
A large number of tailings ponds formed by slag accumulation have become serious environmental hazards. Spatially high potential energy and long-term accumulation may result in gradient-changing seepage pollution. The assemblages of phytoplankton and bacteria are widely used as assessment indicators. In this study, we investigate the changes in phytoplankton and bacterial assemblages in tailing pollution. The results showed that there are temporal and spatial variabilities in seepage pollution. The abundance and diversity of phytoplankton and bacteria decreased with increasing pollution. However, Synedra acus (diatom) and Polynucleobacter (bacteria) were positively correlated with pollution levels (r = 0.37, P < 0.05; r = 0.24, P < 0.05). Heavy metals are the main contributors to bacterial changes (16.46%), while nutrients are for algae (13.24%). Tailings pond pollution reduced the number of phytoplankton and bacterial linkages. However, more pollution broke the originally independent modules of phytoplankton and bacteria, and they produced more positive correlations (79.39%; 87.68%). Microcystis sp. and Limnobacter were the key nodes of the co-occurrence network in the polluted areas. Exploring the interactions between bacteria and phytoplankton within different pollution levels could provide insights into biological interaction patterns and the bioremediation of tailings ponds.
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Affiliation(s)
- Yuchen Geng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengrong Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Weicheng Zhou
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shun Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Panpan Zhou
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhicong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Hongjie Qin
- Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Lab of Comprehensive Innovative Utilization of Ornamental Plant Germplasm, Guangzhou 510640, China
| | - Dunhai Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Genomic Insights into the Ecological Role and Evolution of a Novel Thermoplasmata Order, " Candidatus Sysuiplasmatales". Appl Environ Microbiol 2021; 87:e0106521. [PMID: 34524897 DOI: 10.1128/aem.01065-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent omics studies have provided invaluable insights into the metabolic potential, adaptation, and evolution of novel archaeal lineages from a variety of extreme environments. We utilized a genome-resolved metagenomic approach to recover eight medium- to high-quality metagenome-assembled genomes (MAGs) that likely represent a new order ("Candidatus Sysuiplasmatales") in the class Thermoplasmata from mine tailings and acid mine drainage (AMD) sediments sampled from two copper mines in South China. 16S rRNA gene-based analyses revealed a narrow habitat range for these uncultured archaea limited to AMD and hot spring-related environments. Metabolic reconstruction indicated a facultatively anaerobic heterotrophic lifestyle. This may allow the archaea to adapt to oxygen fluctuations and is thus in marked contrast to the majority of lineages in the domain Archaea, which typically show obligately anaerobic metabolisms. Notably, "Ca. Sysuiplasmatales" could conserve energy through degradation of fatty acids, amino acid metabolism, and oxidation of reduced inorganic sulfur compounds (RISCs), suggesting that they may contribute to acid generation in the extreme mine environments. Unlike the closely related orders Methanomassiliicoccales and "Candidatus Gimiplasmatales," "Ca. Sysuiplasmatales" lacks the capacity to perform methanogenesis and carbon fixation. Ancestral state reconstruction indicated that "Ca. Sysuiplasmatales," the closely related orders Methanomassiliicoccales and "Ca. Gimiplasmatales," and the orders SG8-5 and RBG-16-68-12 originated from a facultatively anaerobic ancestor capable of carbon fixation via the bacterial-type H4F Wood-Ljungdahl pathway (WLP). Their metabolic divergence might be attributed to different evolutionary paths. IMPORTANCE A wide array of archaea populate Earth's extreme environments; therefore, they may play important roles in mediating biogeochemical processes such as iron and sulfur cycling. However, our knowledge of archaeal biology and evolution is still limited, since the majority of the archaeal diversity is uncultured. For instance, most order-level lineages except Thermoplasmatales, Aciduliprofundales, and Methanomassiliicoccales within Thermoplasmata do not have cultured representatives. Here, we report the discovery and genomic characterization of a novel order, "Ca. Sysuiplasmatales," within Thermoplasmata in extremely acidic mine environments. "Ca. Sysuiplasmatales" are inferred to be facultatively anaerobic heterotrophs and likely contribute to acid generation through the oxidation of RISCs. The physiological divergence between "Ca. Sysuiplasmatales" and closely related Thermoplasmata lineages may be attributed to different evolutionary paths. These results expand our knowledge of archaea in the extreme mine ecosystem.
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Zhou WH, Wang YT, Lian ZH, Yang TT, Zeng QW, Feng SW, Fang Z, Shu WS, Huang LN, Ye ZH, Liao B, Li JT. Revegetation approach and plant identity unequally affect structure, ecological network and function of soil microbial community in a highly acidified mine tailings pond. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140793. [PMID: 32688002 DOI: 10.1016/j.scitotenv.2020.140793] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/12/2020] [Accepted: 07/05/2020] [Indexed: 05/22/2023]
Abstract
Owing to its sustainability and low cost, direct revegetation (DR) has been considered a promising alternative to capped revegetation (CR) for dealing with the serious environmental problem derived from various types of mine wastelands that are widespread in the world. However, a direct comparison of the performance of these two revegetation approaches for reclamation of extremely acidic mine wastelands and the underlying mechanisms is still lacking. To bridge this critical knowledge gap, we established 5000 m2 of vegetation on a highly acidified (pH < 3) Pb/Zn mine tailings pond employing both CR and DR schemes (2500 m2 for each scheme). We then profiled the structure, ecological network and function of soil microbial communities associated with two dominant plant species of the vegetations via high-throughput sequencing. Our results showed that CR and DR achieved a vegetation coverage of 59.7% and 90.5% within two years, respectively. This pattern was accompanied by higher concentrations of plant nutrients and lower acidification potentials in topsoils of the rhizospheres of the vegetation established by DR compared to those of CR. Revegetation approach, rather than plant identity, mostly affected the structure, ecological network and function of soil microbial community in the mine tailings pond. Rhizosphere soils of the vegetation established by DR generally had higher microbial diversity, higher relative abundances of dominant microbial phyla (e.g. Nitrospirae) that can aid plant uptake of nutrients, more complicated microbial interactive networks and more microbial genes responsible for nutrient cycling than those by CR. As the first report on a direct comparison of CR and DR schemes for reclamation of an extremely acidic mine wasteland, our study has important implications for not only the understanding of microbial ecology in revegetated mine wastelands but also the further development of sustainable revegetation schemes.
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Affiliation(s)
- Wen-Hua Zhou
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Yu-Tao Wang
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Zheng-Han Lian
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Tao-Tao Yang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Qing-Wei Zeng
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Shi-Wei Feng
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Zhou Fang
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Wen-Sheng Shu
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zhi-Hong Ye
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Bin Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China.
| | - Jin-Tian Li
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China.
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Contributions of Microbial “Contact Leaching” to Pyrite Oxidation under Different Controlled Redox Potentials. MINERALS 2020. [DOI: 10.3390/min10100856] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The function of microbial contact leaching to pyrite oxidation was investigated by analyzing the differences of residue morphologies, leaching rates, surface products, and microbial consortia under different conditions in this study. This was achieved by novel equipment that can control the redox potential of the solution and isolate pyrite from microbial contact oxidation. The morphology of residues showed that the corrosions were a little bit severer in the presence of attached microbes under 750 mV and 850 mV (vs. SHE). At 650 mV, the oxidation of pyrite was undetectable even in the presence of attached microbes. The pyrite dissolution rate was higher with attached microbes than that without attached microbes at 750 mV and 850 mV. The elemental sulfur on the surface of pyrite residues with sessile microorganisms was much less than that without attached microbes at 750 mV and 850 mV, showing that sessile acidophiles may accelerate pyrite leaching by reducing the elemental sulfur inhibition. Many more sulfur-oxidizers were found in the sessile microbial consortium which also supported the idea. The results suggest that the microbial “contact leaching” to pyrite oxidation is limited and relies on the elimination of elemental sulfur passivation by attached sulfur-oxidizing microbes rather than the contact oxidation by EPS-Fe.
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Panyushkina A, Matyushkina D, Pobeguts O. Understanding Stress Response to High-Arsenic Gold-Bearing Sulfide Concentrate in Extremely Metal-Resistant Acidophile Sulfobacillus thermotolerans. Microorganisms 2020; 8:E1076. [PMID: 32707712 PMCID: PMC7409299 DOI: 10.3390/microorganisms8071076] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022] Open
Abstract
Biooxidation of gold-bearing arsenopyrite concentrates, using acidophilic microbial communities, is among the largest commercial biohydrometallurgical processes. However, molecular mechanisms of microbial responses to sulfide raw materials have not been widely studied. The goal of this research was to gain insight into the defense strategies of the acidophilic bacterium Sulfobacillus thermotolerans, which dominates microbial communities functioning in industrial biooxidation processes at >35 °C, against the toxic effect of the high-arsenic gold-bearing sulfide concentrate. In addition to extreme metal resistance, this acidophile proved to be one of the most As-tolerant microorganisms. Comparative proteomic analysis indicated that 30 out of 33 differentially expressed proteins were upregulated in response to the ore concentrate, while the synthesis level of the functional proteins required for cell survival was not negatively affected. Despite a high level of cellular metal(loid) accumulation, no specific metal(loid)-resistant systems were regulated. Instead, several proteins involved in the metabolic pathways and stress response, including MBL fold metallo-hydrolase, sulfide:quinone oxidoreductase, and GroEL chaperonin, may play crucial roles in resistance to the sulfide ore concentrate and arsenic, in particular. This study provides the first data on the microbial responses to sulfide ore concentrates and advances our understanding of defense mechanisms against toxic compounds in acidophiles.
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Affiliation(s)
- Anna Panyushkina
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., 33, bld. 2, Moscow 119071, Russia
| | - Daria Matyushkina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya, 1a, Moscow 119435, Russia; (D.M.); (O.P.)
| | - Olga Pobeguts
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya, 1a, Moscow 119435, Russia; (D.M.); (O.P.)
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Zhao X, Sun Y, Huang J, Wang H, Tang D. Effects of soil heavy metal pollution on microbial activities and community diversity in different land use types in mining areas. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:20215-20226. [PMID: 32239406 DOI: 10.1007/s11356-020-08538-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
Microbial activities and community structures play crucial roles in the soil environment and can be served as effective indicators to assess the ecological influence of heavy metal pollution in soil. This article selected soil samples from five land use types (mining area, mineral processing area, heap mining area, tailing area, and vegetable area) in the Shizishan mining area in Tongling, Anhui Province, China. The physicochemical properties, pollution characteristics, enzyme activities (catalase, urease, alkaline phosphatase, neutral phosphatase, cellulase, and sucrase), microbial biomass carbon (MBC), basal respiration (SBR), and metabolic entropy (qCO2) in soil were determined and compared, and the relationship between environmental factors and the microbial activities and community diversity was analyzed. The results showed that, according to the Nemerow's Pollution Index (PN), the values were the heap mining area (24.47) > mineral processing area (12.55) > mining area (9.81) > tailings area (6.02) > vegetable area (4.51). With the increase of heavy metal contamination in the sampling area, the six enzyme activities, MBC and SBR decreased, but the qCO2 increased. Principal coordinate analysis (PCoA) and canonical correlation analysis (CCA) showed that the land use types, soil moisture content (MC), heavy metal content, pH, MBC, SBR, and qCO2 were significantly affected by the microbial community. The most dominant phyla were Proteobacteria (34.73%), Bacteroidetes (9.25%), Acidobacteria (8.99%), and Chloroflexi (8.68%) at the phylum (0.01) level by a total of 18 phyla. It was also found that Firmicutes and Phormidium were more tolerant to heavy metals. These results contributed to an insight into key environmental variables shaping the microbial activities, community structure, and diversity under various land use types in mining area.
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Affiliation(s)
- Xingqing Zhao
- School of Environmental and Safety Engineering, Changzhou University, Gehu Middle Road 21, Changzhou, 213164, Jiangsu, People's Republic of China.
| | - Yu Sun
- School of Environmental and Safety Engineering, Changzhou University, Gehu Middle Road 21, Changzhou, 213164, Jiangsu, People's Republic of China
| | - Jian Huang
- School of Environmental and Safety Engineering, Changzhou University, Gehu Middle Road 21, Changzhou, 213164, Jiangsu, People's Republic of China
| | - Hui Wang
- School of Environmental and Safety Engineering, Changzhou University, Gehu Middle Road 21, Changzhou, 213164, Jiangsu, People's Republic of China
| | - Ding Tang
- School of Environmental and Safety Engineering, Changzhou University, Gehu Middle Road 21, Changzhou, 213164, Jiangsu, People's Republic of China
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Jia P, Liang J, Yang S, Zhang S, Liu J, Liang Z, Li F, Zeng Q, Fang Z, Liao B, Shu W, Cadotte MW, Li J. Plant diversity enhances the reclamation of degraded lands by stimulating plant–soil feedbacks. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13625] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pu Jia
- Institute of Ecological Science School of Life Sciences South China Normal University Guangzhou PR China
- Department of Biological Sciences University of Toronto‐Scarborough Toronto Canada
| | - Jie‐liang Liang
- Institute of Ecological Science School of Life Sciences South China Normal University Guangzhou PR China
| | - Sheng‐xiang Yang
- College of Resources and Environment Key Laboratory of Soil Resources and Environment in Qianbei of Guizhou Province Zunyi Normal College Zunyi PR China
| | | | - Jun Liu
- School of Life Sciences Sun Yat‐sen University Guangzhou PR China
| | - Zhi‐wei Liang
- School of Life Sciences Sun Yat‐sen University Guangzhou PR China
| | - Feng‐mei Li
- College of Bio‐Resources and Environmental Science Jishou University Jishou PR China
| | - Qing‐wei Zeng
- School of Life Sciences Sun Yat‐sen University Guangzhou PR China
| | - Zhou Fang
- Institute of Ecological Science School of Life Sciences South China Normal University Guangzhou PR China
| | - Bin Liao
- School of Life Sciences Sun Yat‐sen University Guangzhou PR China
| | - Wen‐sheng Shu
- Institute of Ecological Science School of Life Sciences South China Normal University Guangzhou PR China
| | - Marc W. Cadotte
- Department of Biological Sciences University of Toronto‐Scarborough Toronto Canada
| | - Jin‐tian Li
- Institute of Ecological Science School of Life Sciences South China Normal University Guangzhou PR China
- School of Life Sciences Sun Yat‐sen University Guangzhou PR China
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Performance of a Geosynthetic-Clay-Liner Cover System at a Cu/Zn Mine Tailings Impoundment. Appl Environ Microbiol 2020; 86:AEM.02846-19. [PMID: 32033946 DOI: 10.1128/aem.02846-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/29/2020] [Indexed: 12/18/2022] Open
Abstract
The abandoned Kam Kotia Mine (Canada) is undergoing remediation. A geosynthetic-clay-liner (GCL) cover system was installed in the Northern Impounded Tailings (NIT) area in 2008 to isolate acid-generating tailings from water and oxygen and to mitigate sulfide oxidation. The cover system includes a vegetated uppermost soil layer underlain by a granular protective layer (sand), a clay moisture-retaining layer, a GCL, a granular capillary-break material (cushion sand), and a crushed waste rock-capillary break layer installed above the tailings. The goal of this study was to characterize the microbiology of the covered tailings to assess the performance of the cover system for mitigating sulfide bio-oxidation. Tailings beneath the GCL were characterized by high sulfur and low carbon content. The bulk pH of the tailings pore water was circumneutral (∼5.5 to 7.3). Total genomic DNA was extracted from 36 samples recovered from the constituent layers of the cover system and the underlying tailings and was analyzed in triplicates using high-throughput amplicon sequencing of 16S rRNA genes. Iron-oxidizing, sulfur-oxidizing, sulfate-reducing, and aerobic heterotrophic microorganisms were enumerated by use of most probable number enumeration, which identified heterotrophs as the most numerous group of culturable microorganisms throughout the depth profile. Low relative abundances and viable counts of microorganisms that catalyze transformations of iron and sulfur in the covered tailings, compared to previous studies on unreclaimed tailings, indicate that sulfide oxidation rates have decreased due to the presence of the GCL. Characterization of the microbial community can provide a sensitive indicator for assessing the performance of remediation systems.IMPORTANCE Mining activities are accompanied by significant environmental and financial liabilities, including the release of acid mine drainage (AMD). AMD is caused by accelerated chemical and biological oxidation of sulfide minerals in mine wastes and is characterized by low pH and high concentrations of sulfate and metal(loid)s. Microorganisms assume important roles in the catalysis of redox reactions. Our research elucidates linkages among the biogeochemistry of mine wastes and remediation systems and microbial community and activity. This study assesses the performance and utility of geosynthetic-clay-liner cover systems for management of acid-generating mine wastes. Analyses of the microbial communities in tailings isolated beneath an engineered cover system provide a better understanding of the complex biogeochemical processes involved in the redox cycling of key elements, contribute to the remediation of mine wastes, and provide a valuable tool for assessment of the effectiveness of the remediation system.
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Panyushkina AE. Metabolic Potential of Sulfobacillus thermotolerans: Pathways for Assimilation of Nitrogen Compounds and the Possibility of Lithotrophic Growth in the Presence of Molecular Hydrogen. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261719060134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Acidithiobacillus ferrianus sp. nov.: an ancestral extremely acidophilic and facultatively anaerobic chemolithoautotroph. Extremophiles 2020; 24:329-337. [PMID: 31980944 PMCID: PMC7040056 DOI: 10.1007/s00792-020-01157-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/10/2020] [Indexed: 01/21/2023]
Abstract
Strain MG, isolated from an acidic pond sediment on the island of Milos (Greece), is proposed as a novel species of ferrous iron- and sulfur-oxidizing Acidithiobacillus. Currently, four of the eight validated species of this genus oxidize ferrous iron, and strain MG shares many key characteristics with these four, including the capacities for catalyzing the oxidative dissolution of pyrite and for anaerobic growth via ferric iron respiration. Strain MG also grows aerobically on hydrogen and anaerobically on hydrogen coupled to ferric iron reduction. While the 16S rRNA genes of the iron-oxidizing Acidi-thiobacillus species (and strain MG) are located in a distinct phylogenetic clade and are closely related (98–99% 16S rRNA gene identity), genomic relatedness indexes (ANI/dDDH) revealed strong genomic divergence between strain MG and all sequenced type strains of the taxon, and placed MG as the first cultured representative of an ancestral phylotype of iron oxidizing acidithiobacilli. Strain MG is proposed as a novel species, Acidithiobacillus ferrianus sp. nov. The type strain is MGT (= DSM 107098T = JCM 33084T). Similar strains have been found as isolates or indicated by cloned 16S rRNA genes from several mineral sulfide mine sites.
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Panyushkina AE, Babenko VV, Nikitina AS, Selezneva OV, Tsaplina IA, Letarova MA, Kostryukova ES, Letarov AV. Sulfobacillus thermotolerans: new insights into resistance and metabolic capacities of acidophilic chemolithotrophs. Sci Rep 2019; 9:15069. [PMID: 31636299 PMCID: PMC6803676 DOI: 10.1038/s41598-019-51486-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 09/23/2019] [Indexed: 11/09/2022] Open
Abstract
The first complete genome of the biotechnologically important species Sulfobacillus thermotolerans has been sequenced. Its 3 317 203-bp chromosome contains an 83 269-bp plasmid-like region, which carries heavy metal resistance determinants and the rusticyanin gene. Plasmid-mediated metal resistance is unusual for acidophilic chemolithotrophs. Moreover, most of their plasmids are cryptic and do not contribute to the phenotype of the host cells. A polyphosphate-based mechanism of metal resistance, which has been previously unknown in the genus Sulfobacillus or other Gram-positive chemolithotrophs, potentially operates in two Sulfobacillus species. The methylcitrate cycle typical for pathogens and identified in the genus Sulfobacillus for the first time can fulfill the energy and/or protective function in S. thermotolerans Kr1 and two other Sulfobacillus species, which have incomplete glyoxylate cycles. It is notable that the TCA cycle, disrupted in all Sulfobacillus isolates under optimal growth conditions, proved to be complete in the cells enduring temperature stress. An efficient antioxidant defense system gives S. thermotolerans another competitive advantage in the microbial communities inhabiting acidic metal-rich environments. The genomic comparisons revealed 80 unique genes in the strain Kr1, including those involved in lactose/galactose catabolism. The results provide new insights into metabolism and resistance mechanisms in the Sulfobacillus genus and other acidophiles.
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Affiliation(s)
- Anna E Panyushkina
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia.
| | - Vladislav V Babenko
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Anastasia S Nikitina
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Oksana V Selezneva
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Iraida A Tsaplina
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
| | - Maria A Letarova
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
| | - Elena S Kostryukova
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Andrey V Letarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
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Zhao X, Huang J, Lu J, Sun Y. Study on the influence of soil microbial community on the long-term heavy metal pollution of different land use types and depth layers in mine. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 170:218-226. [PMID: 30529916 DOI: 10.1016/j.ecoenv.2018.11.136] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 05/27/2023]
Abstract
To understand the importance of the response of soil microbial communities to the stress of heavy metals around mining areas by assessing the feedback of soil ecosystems in different soil habitats, this article selected different land use types (Mining area, Dressing area, Heap mine area, Tailings area and Vegetable field) and surface soil samples of different depths (0-10 cm, 10-20 cm, 20-30 cm) as the variables related to the mining activities in the Shizishan mining area in Tongling, Anhui Province, China. Soil physicochemical properties and heavy metal concentrations of the different land use types and soil depths were compared. Illumina MiSeq. 2500 Sequencing Technology was used to analyze the abundance and structural diversity of the microbial community in soil samples. The relationship between mine soil pollution characteristics and microbial community were investigated. The results showed that soil physicochemical properties and heavy metals significantly affected the microbial community. The microbial community structure was significantly variable in vertical soil depth-layer habitats. The relative abundance (1%) of the soil microbial community at the phylum level was represented by a total of 14 phyla, where the two most dominant phyla were Proteobacteria (41.71%) and Firmicutes (20.44%). The two bacteria were positively related with Cu, Zn, Pb, and pH but negatively associated with soil organic matter (SOM), available potassium (AK), and moisture content (MC). Therefore, Proteobacteria and Firmicutes were highly resistant to heavy metals. These results increased our understanding of microbial variation and assembly pattern under different land use types in heavy metals contaminated mining soils.
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Affiliation(s)
- Xingqing Zhao
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, PR China.
| | - Jian Huang
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, PR China
| | - Jin Lu
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, PR China
| | - Yu Sun
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, PR China
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Korzhenkov AA, Toshchakov SV, Bargiela R, Gibbard H, Ferrer M, Teplyuk AV, Jones DL, Kublanov IV, Golyshin PN, Golyshina OV. Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity. MICROBIOME 2019; 7:11. [PMID: 30691532 PMCID: PMC6350386 DOI: 10.1186/s40168-019-0623-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/10/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND The current view suggests that in low-temperature acidic environments, archaea are significantly less abundant than bacteria. Thus, this study of the microbiome of Parys Mountain (Anglesey, UK) sheds light on the generality of this current assumption. Parys Mountain is a historically important copper mine and its acid mine drainage (AMD) water streams are characterised by constant moderate temperatures (8-18 °C), extremely low pH (1.7) and high concentrations of soluble iron and other metal cations. RESULTS Metagenomic and SSU rRNA amplicon sequencing of DNA from Parys Mountain revealed a significant proportion of archaea affiliated with Euryarchaeota, which accounted for ca. 67% of the community. Within this phylum, potentially new clades of Thermoplasmata were overrepresented (58%), with the most predominant group being "E-plasma", alongside low-abundant Cuniculiplasmataceae, 'Ca. Micrarchaeota' and 'Terrestrial Miscellaneous Euryarchaeal Group' (TMEG) archaea, which were phylogenetically close to Methanomassilicoccales and clustered with counterparts from acidic/moderately acidic settings. In the sediment, archaea and Thermoplasmata contributed the highest numbers in V3-V4 amplicon reads, in contrast with the water body community, where Proteobacteria, Nitrospirae, Acidobacteria and Actinobacteria outnumbered archaea. Cultivation efforts revealed the abundance of archaeal sequences closely related to Cuniculiplasma divulgatum in an enrichment culture established from the filterable fraction of the water sample. Enrichment cultures with unfiltered samples showed the presence of Ferrimicrobium acidiphilum, C. divulgatum, 'Ca. Mancarchaeum acidiphilum Mia14', 'Ca. Micrarchaeota'-related and diverse minor (< 2%) bacterial metagenomic reads. CONCLUSION Contrary to expectation, our study showed a high abundance of archaea in this extremely acidic mine-impacted environment. Further, archaeal populations were dominated by one particular group, suggesting that they are functionally important. The prevalence of archaea over bacteria in these microbiomes and their spatial distribution patterns represents a novel and important advance in our understanding of acidophile ecology. We also demonstrated a procedure for the specific enrichment of cell wall-deficient members of the archaeal component of this community, although the large fraction of archaeal taxa remained unculturable. Lastly, we identified a separate clustering of globally occurring acidophilic members of TMEG that collectively belong to a distinct order within Thermoplasmata with yet unclear functional roles in the ecosystem.
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Affiliation(s)
- Aleksei A. Korzhenkov
- National Research Center “Kurchatov Institute”, Akademika Kurchatova sq., 1, Moscow, 123182 Russia
| | - Stepan V. Toshchakov
- Winogradsky Institute of Microbiology, Federal Research Center for Biotechnology, Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, Moscow, 117312 Russia
| | - Rafael Bargiela
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
| | - Huw Gibbard
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
| | | | - Alina V. Teplyuk
- National Research Center “Kurchatov Institute”, Akademika Kurchatova sq., 1, Moscow, 123182 Russia
| | - David L. Jones
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
- UWA School of Agriculture and Environment, University of Western Australia, Crawley, WA 6009 Australia
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center for Biotechnology, Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, Moscow, 117312 Russia
| | - Peter N. Golyshin
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
- Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
| | - Olga V. Golyshina
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
- Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
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Abinandan S, Subashchandrabose SR, Venkateswarlu K, Megharaj M. Microalgae-bacteria biofilms: a sustainable synergistic approach in remediation of acid mine drainage. Appl Microbiol Biotechnol 2018; 102:1131-1144. [PMID: 29260261 DOI: 10.1007/s00253-017-8693-] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 05/28/2023]
Abstract
Microalgae and bacteria offer a huge potential in delving interest to study and explore various mechanisms under extreme environments. Acid mine drainage (AMD) is one such environment which is extremely acidic containing copious amounts of heavy metals and poses a major threat to the ecosystem. Despite its extreme conditions, AMD is the habitat for several microbes and their activities. The use of various chemicals in prevention of AMD formation and conventional treatment in a larger scale is not feasible under different geological conditions. It implies that microbe-mediated approach is a viable and sustainable alternative technology for AMD remediation. Microalgae in biofilms play a pivotal role in such bioremediation as they maintain mutualism with heterotrophic bacteria. Synergistic approach of using microalgae-bacteria biofilms provides supportive metabolites from algal biomass for growth of bacteria and mediates remediation of AMD. However, by virtue of their physiology and capabilities of metal removal, non-acidophilic microalgae can be acclimated for use in AMD remediation. A combination of selective acidophilic and non-acidophilic microalgae together with bacteria, all in the form of biofilms, may be very effective for bioremediation of metal-contaminated waters. The present review critically examines the nature of mutualistic interactions established between microalgae and bacteria in biofilms and their role in removal of metals from AMDs, and consequent biomass production for the yield of biofuel. Integration of microalgal-bacterial consortia in fuel cells would be an attractive emerging approach of microbial biotechnology for AMD remediation.
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Affiliation(s)
- Sudharsanam Abinandan
- Global Centre for Environmental Remediation (GCER), Faculty of Science, University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia
| | - Suresh R Subashchandrabose
- Global Centre for Environmental Remediation (GCER), Faculty of Science, University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapur, 515055, India
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), Faculty of Science, University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia.
- Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia.
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15
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Microalgae-bacteria biofilms: a sustainable synergistic approach in remediation of acid mine drainage. Appl Microbiol Biotechnol 2017; 102:1131-1144. [PMID: 29260261 DOI: 10.1007/s00253-017-8693-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 10/18/2022]
Abstract
Microalgae and bacteria offer a huge potential in delving interest to study and explore various mechanisms under extreme environments. Acid mine drainage (AMD) is one such environment which is extremely acidic containing copious amounts of heavy metals and poses a major threat to the ecosystem. Despite its extreme conditions, AMD is the habitat for several microbes and their activities. The use of various chemicals in prevention of AMD formation and conventional treatment in a larger scale is not feasible under different geological conditions. It implies that microbe-mediated approach is a viable and sustainable alternative technology for AMD remediation. Microalgae in biofilms play a pivotal role in such bioremediation as they maintain mutualism with heterotrophic bacteria. Synergistic approach of using microalgae-bacteria biofilms provides supportive metabolites from algal biomass for growth of bacteria and mediates remediation of AMD. However, by virtue of their physiology and capabilities of metal removal, non-acidophilic microalgae can be acclimated for use in AMD remediation. A combination of selective acidophilic and non-acidophilic microalgae together with bacteria, all in the form of biofilms, may be very effective for bioremediation of metal-contaminated waters. The present review critically examines the nature of mutualistic interactions established between microalgae and bacteria in biofilms and their role in removal of metals from AMDs, and consequent biomass production for the yield of biofuel. Integration of microalgal-bacterial consortia in fuel cells would be an attractive emerging approach of microbial biotechnology for AMD remediation.
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16
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Quatrini R, Escudero LV, Moya-Beltrán A, Galleguillos PA, Issotta F, Acosta M, Cárdenas JP, Nuñez H, Salinas K, Holmes DS, Demergasso C. Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile. Stand Genomic Sci 2017; 12:84. [PMID: 29270251 PMCID: PMC5735861 DOI: 10.1186/s40793-017-0305-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/06/2017] [Indexed: 01/16/2023] Open
Abstract
10.1601/nm.2199 CLST is an extremely acidophilic gamma-proteobacteria that was isolated from the Gorbea salt flat, an acidic hypersaline environment in northern Chile. This kind of environment is considered a terrestrial analog of ancient Martian terrains and a source of new material for biotechnological applications. 10.1601/nm.2199 plays a key role in industrial bioleaching; it has the capacity of generating and maintaining acidic conditions by producing sulfuric acid and it can also remove sulfur layers from the surface of minerals, which are detrimental for their dissolution. CLST is a strain of 10.1601/nm.2199 able to tolerate moderate chloride concentrations (up to 15 g L-1 Cl-), a feature that is quite unusual in extreme acidophilic microorganisms. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 3,974,949 bp draft genome is arranged into 40 scaffolds of 389 contigs containing 3866 protein-coding genes and 75 RNAs encoding genes. This is the first draft genome of a halotolerant 10.1601/nm.2199 strain. The release of the genome sequence of this strain improves representation of these extreme acidophilic Gram negative bacteria in public databases and strengthens the framework for further investigation of the physiological diversity and ecological function of 10.1601/nm.2199 populations.
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Affiliation(s)
- Raquel Quatrini
- Fundación Ciencia & Vida, Av. Zañartu 1482, 7780272 Santiago, Chile
| | - Lorena V. Escudero
- Centro de Biotecnología “Profesor Alberto Ruiz”, Universidad Católica del Norte, 1270709 Antofagasta, Chile
- Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
| | - Ana Moya-Beltrán
- Fundación Ciencia & Vida, Av. Zañartu 1482, 7780272 Santiago, Chile
| | - Pedro A. Galleguillos
- Centro de Biotecnología “Profesor Alberto Ruiz”, Universidad Católica del Norte, 1270709 Antofagasta, Chile
- Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
| | | | - Mauricio Acosta
- Centro de Biotecnología “Profesor Alberto Ruiz”, Universidad Católica del Norte, 1270709 Antofagasta, Chile
| | | | - Harold Nuñez
- Fundación Ciencia & Vida, Av. Zañartu 1482, 7780272 Santiago, Chile
| | | | - David S. Holmes
- Fundación Ciencia & Vida, Av. Zañartu 1482, 7780272 Santiago, Chile
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Cecilia Demergasso
- Centro de Biotecnología “Profesor Alberto Ruiz”, Universidad Católica del Norte, 1270709 Antofagasta, Chile
- Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
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17
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Sheeba VA, Abdulaziz A, Gireeshkumar TR, Ram A, Rakesh PS, Jasmin C, Parameswaran PS. Role of heavy metals in structuring the microbial community associated with particulate matter in a tropical estuary. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:589-600. [PMID: 28843898 DOI: 10.1016/j.envpol.2017.08.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 08/11/2017] [Accepted: 08/13/2017] [Indexed: 05/20/2023]
Abstract
Particulate matter (PM), which are chemically and biochemically complicated particles, accommodate a plethora of microorganisms. In the present study, we report the influence of heavy metal pollution on the abundance and community structure of archaea and bacteria associated with PM samples collected from polluted and non-polluted regions of Cochin Estuary (CE), Southwest coast of India. We observed an accumulation of heavy metals in PM collected from CE, and their concentrations were in the order Fe > Zn > Mn > Cr > Pb > Cu > Cd > Co > Ni. Zinc was a major pollutant in the water (4.36-130.50 μgL-1) and in the particulate matter (765.5-8451.28 μgg-1). Heavy metals, Cd, Co, and Pb were recorded in the particulate matter, although they were below detectable limits in the water column. Statistical analysis showed a positive influence of particulate organic carbon, nitrogen, PM-Pb, PM-Zn and PM-Fe on the abundance of PM-archaea and PM-bacteria. The abundance of archaea and bacteria were ten times less in PM compared with planktonic ones. The abundance of PM-archaea ranged between 4.27 and 9.50 × 107and 2.73 to 3.85 × 107 cellsL-1 respectively for the wet and dry season, while that of PM-bacteria was between 1.14 and 6.72 × 108 cellsL-1 for both seasons. Community structure of PM-bacteria varied between polluted and non-polluted stations, while their abundance does not show a drastic difference. This could be attributed to the selective enrichment of bacteria by heavy metals in PM. Such enrichment may only promote the growth of metal resistant archaea and bacteria, which may not participate in the processing of PM. In such cases, the PM may remain without remineralization in the system arresting the food web dynamics and biogeochemical cycles.
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Affiliation(s)
- V A Sheeba
- CSIR -National Institute of Oceanography, Regional Centre, Cochin, 682018, India
| | - Anas Abdulaziz
- CSIR -National Institute of Oceanography, Regional Centre, Cochin, 682018, India.
| | - T R Gireeshkumar
- CSIR -National Institute of Oceanography, Regional Centre, Cochin, 682018, India
| | - Anirudh Ram
- CSIR -National Institute of Oceanography, Regional Centre, Mumbai, 400 053, India
| | - P S Rakesh
- CSIR -National Institute of Oceanography, Regional Centre, Mumbai, 400 053, India
| | - C Jasmin
- CSIR -National Institute of Oceanography, Regional Centre, Cochin, 682018, India
| | - P S Parameswaran
- CSIR -National Institute of Oceanography, Regional Centre, Cochin, 682018, India
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18
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Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage. MINERALS 2017. [DOI: 10.3390/min7060106] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microorganisms play an important role in weathering sulfide minerals worldwide and thrive in metal-rich and extremely acidic environments in acid mine drainage (AMD). Advanced molecular methods provide in-depth information on the microbial diversity and community dynamics in the AMD-generating environment. Although the diversity is relatively low and in general inversely correlated with the acidity, a considerable number of microbial species have been detected and described in AMD ecosystems. The acidophilic microbial communities dominated by iron/sulfur-oxidizing microbes vary widely in their composition and structure across diverse environmental gradients. Environmental conditions affect the microbial community assembly via direct and indirect interactions with microbes, resulting in an environmentally dependent biogeographic pattern. This article summarizes the latest studies to provide a better understanding of the microbial biodiversity and community assembly in AMD environments.
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19
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Wegner CE, Liesack W. Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags. Front Microbiol 2017; 8:1023. [PMID: 28642744 PMCID: PMC5462947 DOI: 10.3389/fmicb.2017.01023] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/22/2017] [Indexed: 11/19/2022] Open
Abstract
Acid mine drainage (AMD) and mine tailing environments are well-characterized ecosystems known to be dominated by organisms involved in iron- and sulfur-cycling. Here we examined the microbiology of industrial soft coal slags that originate from alum leaching, an ecosystem distantly related to AMD environments. Our study involved geochemical analyses, bacterial community profiling, and shotgun metagenomics. The slags still contained high amounts of alum constituents (aluminum, sulfur), which mediated direct and indirect effects on bacterial community structure. Bacterial groups typically found in AMD systems and mine tailings were not present. Instead, the soft coal slags were dominated by uncharacterized groups of Acidobacteria (DA052 [subdivision 2], KF-JG30-18 [subdivision 13]), Actinobacteria (TM214), Alphaproteobacteria (DA111), and Chloroflexi (JG37-AG-4), which have previously been detected primarily in peatlands and uranium waste piles. Shotgun metagenomics allowed us to reconstruct 13 high-quality Acidobacteria draft genomes, of which two genomes could be directly linked to dominating groups (DA052, KF-JG30-18) by recovered 16S rRNA gene sequences. Comparative genomics revealed broad carbon utilization capabilities for these two groups of elusive Acidobacteria, including polysaccharide breakdown (cellulose, xylan) and the competence to metabolize C1 compounds (ribulose monophosphate pathway) and lignin derivatives (dye-decolorizing peroxidases). Equipped with a broad range of efflux systems for metal cations and xenobiotics, DA052 and KF-JG30-18 may have a competitive advantage over other bacterial groups in this unique habitat.
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Affiliation(s)
- Carl-Eric Wegner
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany
| | - Werner Liesack
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
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20
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Gupta A, Dutta A, Sarkar J, Paul D, Panigrahi MK, Sar P. Metagenomic exploration of microbial community in mine tailings of Malanjkhand copper project, India. GENOMICS DATA 2017; 12:11-13. [PMID: 28239550 PMCID: PMC5315440 DOI: 10.1016/j.gdata.2017.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 02/03/2017] [Indexed: 11/25/2022]
Abstract
Mine tailings from copper mines are considered as one of the sources of highly hazardous acid mine drainage (AMD) due to bio-oxidation of its sulfidic constituents. This study was designed to understand microbial community composition and potential for acid generation using samples from mine tailings of Malanjkhand copper project (MCP), India through 16S rRNA gene based amplicon sequencing approach (targeting V4 region). Three tailings samples (T1, T2 and T3) with varied physiochemical properties selected for the study revealed distinct microbial assemblages. Sample (T3) with most extreme nature (pH < 2.0) harbored Proteobacteria, Actinobacteria, Chloroflexi while the samples (T1 and T3) with slightly moderate nature (pH < 4.0 and > 3.0) exhibited abundance of Proteobacteria, Fimicutes, Actinobacteria and/or Nitrospirae. Metagenomic sequences are available under the BioProject ID PRJNA361456.
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Affiliation(s)
- Abhishek Gupta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Avishek Dutta
- School of Bioscience, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Jayeeta Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Dhiraj Paul
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Mruganka Kumar Panigrahi
- Department of Geology and Geophysics, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal 721302, India
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21
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Bruneel O, Mghazli N, Hakkou R, Dahmani I, Filali Maltouf A, Sbabou L. In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco). Extremophiles 2017; 21:671-685. [PMID: 28447266 DOI: 10.1007/s00792-017-0933-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 04/17/2017] [Indexed: 01/28/2023]
Abstract
In Morocco, pollution caused by closed mines continues to be a serious threat to the environment, like the generation of acid mine drainage. Mine drainage is produced by environmental and microbial oxidation of sulfur minerals originating from mine wastes. The fundamental role of microbial communities is well known, like implication of Fe-oxidizing and to a lesser extent S-oxidizing microorganism in bioleaching. However, the structure of the microbial communities varies a lot from one site to another, like diversity depends on many factors such as mineralogy, concentration of metals and metalloids or pH, etc. In this study, prokaryotic communities in the pyrrhotite-rich tailings of Kettara mine were characterized using the Illumina sequencing. In-depth phylogenetic analysis revealed a total of 12 phyla of bacteria and 1 phyla of Archaea. The majority of sequences belonged to the phylum of Proteobacteria and Firmicutes with a predominance of Bacillus, Pseudomonas or Corynebacterium genera. Many microbial populations are implicated in the iron, sulfur and arsenic cycles, like Acidiferrobacter, Leptospirillum, or Alicyclobacillus in Fe; Acidiferrobacter and Sulfobacillus in S; and Bacillus or Pseudomonas in As. This is one of the first description of prokaryotic communities in pyrrhotite-rich mine tailings using high-throughput sequencing.
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Affiliation(s)
- Odile Bruneel
- Laboratoire de Microbiologie et Biologie Moléculaire, LMBM, Faculté des Sciences, Université Mohammed V, Av Ibn Batouta, BP1014, Rabat, Morocco.
- Laboratoire HydroSciences Montpellier, UMR5569 (CNRS/IRD/UM), Université de Montpellier, CC0057 (MSE), 16, rue Auguste Broussonet, 34090, Montpellier, France.
| | - N Mghazli
- Laboratoire de Microbiologie et Biologie Moléculaire, LMBM, Faculté des Sciences, Université Mohammed V, Av Ibn Batouta, BP1014, Rabat, Morocco
| | - R Hakkou
- Laboratoire de Chimie des Matériaux et de l'Environnement (LCME), Faculté des Sciences et Technique Guéliz, Université de Cadi Ayyad, Avenue Abdelkarim Elkhattabi, Gueliz, P.O. Box 549, Marrakech, Morocco
| | - I Dahmani
- Laboratoire de Microbiologie et Biologie Moléculaire, LMBM, Faculté des Sciences, Université Mohammed V, Av Ibn Batouta, BP1014, Rabat, Morocco
| | - A Filali Maltouf
- Laboratoire de Microbiologie et Biologie Moléculaire, LMBM, Faculté des Sciences, Université Mohammed V, Av Ibn Batouta, BP1014, Rabat, Morocco
| | - L Sbabou
- Laboratoire de Microbiologie et Biologie Moléculaire, LMBM, Faculté des Sciences, Université Mohammed V, Av Ibn Batouta, BP1014, Rabat, Morocco
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22
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Review of Biohydrometallurgical Metals Extraction from Polymetallic Mineral Resources. MINERALS 2014. [DOI: 10.3390/min5010001] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Valentín-Vargas A, Root RA, Neilson JW, Chorover J, Maier RM. Environmental factors influencing the structural dynamics of soil microbial communities during assisted phytostabilization of acid-generating mine tailings: a mesocosm experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 500-501:314-24. [PMID: 25237788 PMCID: PMC4253589 DOI: 10.1016/j.scitotenv.2014.08.107] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/27/2014] [Accepted: 08/27/2014] [Indexed: 04/13/2023]
Abstract
Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost-amended, metalliferous mine tailings.
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Affiliation(s)
- Alexis Valentín-Vargas
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA.
| | - Robert A Root
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA.
| | - Julia W Neilson
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA.
| | - Jon Chorover
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA.
| | - Raina M Maier
- Department of Soil, Water and Environmental Science, 429 Shantz Bldg. #38, 1177 E. Fourth Street, University of Arizona, Tucson, AZ 85721-0038, USA.
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Korehi H, Blöthe M, Schippers A. Microbial diversity at the moderate acidic stage in three different sulfidic mine tailings dumps generating acid mine drainage. Res Microbiol 2014; 165:713-8. [PMID: 25205555 DOI: 10.1016/j.resmic.2014.08.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 08/25/2014] [Accepted: 08/30/2014] [Indexed: 10/24/2022]
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Liu J, Hua ZS, Chen LX, Kuang JL, Li SJ, Shu WS, Huang LN. Correlating microbial diversity patterns with geochemistry in an extreme and heterogeneous environment of mine tailings. Appl Environ Microbiol 2014; 80:3677-86. [PMID: 24727268 PMCID: PMC4054149 DOI: 10.1128/aem.00294-14] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 04/02/2014] [Indexed: 11/20/2022] Open
Abstract
Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.
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Chen YT, Li JT, Chen LX, Hua ZS, Huang LN, Liu J, Xu BB, Liao B, Shu WS. Biogeochemical processes governing natural pyrite oxidation and release of acid metalliferous drainage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:5537-5545. [PMID: 24730689 DOI: 10.1021/es500154z] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The oxidative dissolution of sulfide minerals (principally pyrite) is responsible for the majority of acid metalliferous drainage from mine sites, which represents a significant environmental problem worldwide. Understanding the complex biogeochemical processes governing natural pyrite oxidation is critical not only for solving this problem but also for understanding the industrial bioleaching of sulfide minerals. To this end, we conducted a simulated experiment of natural pyrite oxidative dissolution. Pyrosequencing analysis of the microbial community revealed a distinct succession across three stages. At the early stage, a newly proposed genus, Tumebacillus (which can use sodium thiosulfate and sulfite as the sole electron donors), dominated the microbial community. At the midstage, Alicyclobacillus (the fifth most abundant genus at the early stage) became the most dominant genus, whereas Tumebacillus was still ranked as the second most abundant. At the final stage, the microbial community was dominated by Ferroplasma (the tenth most abundant genus at the early stage). Our geochemical and mineralogical analyses indicated that exchangeable heavy metals increased as the oxidation progressed and that some secondary sulfate minerals (including jarosite and magnesiocopiapite) were formed at the final stage of the oxidation sequence. Additionally, we propose a comprehensive model of biogeochemical processes governing the oxidation of sulfide minerals.
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Affiliation(s)
- Ya-ting Chen
- State Key Laboratory of Biocontrol and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University , Guangzhou 510275, PR China
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Chen LX, Li JT, Chen YT, Huang LN, Hua ZS, Hu M, Shu WS. Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings. Environ Microbiol 2013; 15:2431-44. [PMID: 23574280 DOI: 10.1111/1462-2920.12114] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 02/20/2013] [Indexed: 11/29/2022]
Abstract
In an attempt to link the microbial community composition and function in mine tailings to the generation of acid mine drainage, we simultaneously explored the geochemistry and microbiology of six tailings collected from a lead/zinc mine, i.e. primary tailings (T1), slightly acidic tailings (T2), extremely acidic tailings (T3, T4 and T5) and orange-coloured oxidized tailings (T6). Geochemical results showed that the six tailings (from T1 to T6) likely represented sequential stages of the acidification process of the mine tailings. 16S rRNA pyrosequencing revealed a contrasting microbial composition between the six tailings: Proteobacteria-related sequences dominated T1-T3 with relative abundance ranging from 56 to 93%, whereas Ferroplasma-related sequences dominated T4-T6 with relative abundance ranging from 28 to 58%. Furthermore, metagenomic analysis of the microbial communities of T2 and T6 indicated that the genes encoding key enzymes for microbial carbon fixation, nitrogen fixation and sulfur oxidation in T2 were largely from Thiobacillus and Acidithiobacillus, Methylococcus capsulatus, and Thiobacillus denitrificans respectively; while those in T6 were mostly identified in Acidithiobacillus and Leptospirillum, Acidithiobacillus and Leptospirillum, and Acidithiobacillus respectively. The microbial communities in T2 and T6 harboured more genes suggesting diverse metabolic capacities for sulfur oxidation/heavy metal detoxification and tolerating low pH respectively.
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Affiliation(s)
- Lin-Xing Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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Justice NB, Pan C, Mueller R, Spaulding SE, Shah V, Sun CL, Yelton AP, Miller CS, Thomas BC, Shah M, VerBerkmoes N, Hettich R, Banfield JF. Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities. Appl Environ Microbiol 2012; 78:8321-30. [PMID: 23001646 PMCID: PMC3497393 DOI: 10.1128/aem.01938-12] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 09/13/2012] [Indexed: 11/20/2022] Open
Abstract
Archaea are widely distributed and yet are most often not the most abundant members of microbial communities. Here, we document a transition from Bacteria- to Archaea-dominated communities in microbial biofilms sampled from the Richmond Mine acid mine drainage (AMD) system (∼pH 1.0, ∼38°C) and in laboratory-cultivated biofilms. This transition occurs when chemoautotrophic microbial communities that develop at the air-solution interface sink to the sediment-solution interface and degrade under microaerobic and anaerobic conditions. The archaea identified in these sunken biofilms are from the class Thermoplasmata, and in some cases, the highly divergent ARMAN nanoarchaeal lineage. In several of the sunken biofilms, nanoarchaea comprise 10 to 25% of the community, based on fluorescent in situ hybridization and metagenomic analyses. Comparative community proteomic analyses show a persistence of bacterial proteins in sunken biofilms, but there is clear evidence for amino acid modifications due to acid hydrolysis. Given the low representation of bacterial cells in sunken biofilms based on microscopy, we infer that hydrolysis reflects proteins derived from lysed cells. For archaea, we detected ∼2,400 distinct proteins, including a subset involved in proteolysis and peptide uptake. Laboratory cultivation experiments using complex carbon substrates demonstrated anaerobic enrichment of Ferroplasma and Aplasma coupled to the reduction of ferric iron. These findings indicate dominance of acidophilic archaea in degrading biofilms and suggest that they play roles in anaerobic nutrient cycling at low pH.
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Affiliation(s)
| | - Chongle Pan
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Ryan Mueller
- University of California–Berkeley, Berkeley, California, USA
| | | | - Vega Shah
- University of California–Berkeley, Berkeley, California, USA
| | | | | | | | - Brian C. Thomas
- University of California–Berkeley, Berkeley, California, USA
| | - Manesh Shah
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Robert Hettich
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Delavat F, Lett MC, Lièvremont D. Novel and unexpected bacterial diversity in an arsenic-rich ecosystem revealed by culture-dependent approaches. Biol Direct 2012; 7:28. [PMID: 22963335 PMCID: PMC3443666 DOI: 10.1186/1745-6150-7-28] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 07/17/2012] [Indexed: 11/17/2022] Open
Abstract
Background Acid Mine Drainages (AMDs) are extreme environments characterized by very acid conditions and heavy metal contaminations. In these ecosystems, the bacterial diversity is considered to be low. Previous culture-independent approaches performed in the AMD of Carnoulès (France) confirmed this low species richness. However, very little is known about the cultured bacteria in this ecosystem. The aims of the study were firstly to apply novel culture methods in order to access to the largest cultured bacterial diversity, and secondly to better define the robustness of the community for 3 important functions: As(III) oxidation, cellulose degradation and cobalamine biosynthesis. Results Despite the oligotrophic and acidic conditions found in AMDs, the newly designed media covered a large range of nutrient concentrations and a pH range from 3.5 to 9.8, in order to target also non-acidophilic bacteria. These approaches generated 49 isolates representing 19 genera belonging to 4 different phyla. Importantly, overall diversity gained 16 extra genera never detected in Carnoulès. Among the 19 genera, 3 were previously uncultured, one of them being novel in databases. This strategy increased the overall diversity in the Carnoulès sediment by 70% when compared with previous culture-independent approaches, as specific phylogenetic groups (e.g. the subclass Actinobacteridae or the order Rhizobiales) were only detected by culture. Cobalamin auxotrophy, cellulose degradation and As(III)-oxidation are 3 crucial functions in this ecosystem, and a previous meta- and proteo-genomic work attributed each function to only one taxon. Here, we demonstrate that other members of this community can also assume these functions, thus increasing the overall community robustness. Conclusions This work highlights that bacterial diversity in AMDs is much higher than previously envisaged, thus pointing out that the AMD system is functionally more robust than expected. The isolated bacteria may be part of the rare biosphere which remained previously undetected due to molecular biases. No matter their current ecological relevance, the exploration of the full diversity remains crucial to decipher the function and dynamic of any community. This work also underlines the importance to associate culture-dependent and -independent approaches to gain an integrative view of the community function. Reviewers This paper was reviewed by Sándor Pongor, Eugene V. Koonin and Brett Baker (nominated by Purificacion Lopez-Garcia).
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Affiliation(s)
- François Delavat
- UMR7156 Université de Strasbourg/CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
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Urbieta MS, González Toril E, Aguilera A, Giaveno MA, Donati E. First prokaryotic biodiversity assessment using molecular techniques of an acidic river in Neuquén, Argentina. MICROBIAL ECOLOGY 2012; 64:91-104. [PMID: 22214994 DOI: 10.1007/s00248-011-9997-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 12/13/2011] [Indexed: 05/25/2023]
Abstract
Two acidic hot springs close to the crater of Copahue Volcano (Neuquén, Argentina) are the source of the Río Agrio. The river runs several kilometres before flowing into Caviahue Lake. Along the river, temperature, iron, other metal and proton concentrations decrease gradually with distance downstream. From the source to the lake and depending on the season, pH can rise from 1.0 (or even less) to about 4.0, while temperature values decrease from 70°C to 15°C. Water samples were taken from different stations on the river selected according to their physicochemical parameters. In order to assess prokaryotic biodiversity throughout the water column, different and complementary molecular biology techniques were used, mainly in situ hybridisation and 16S rRNA gene cloning and sequencing. All microorganisms found are typical of acidic environments. Sulphur-oxidizing bacteria like Acidithiobacillus thiooxidans and Acidithiobacillus albertensis were detected in every station. Moderately thermophile iron- and sulphur-oxidizing bacteria like members of Alicyclobacillus and Sulfobacillus genera were also ubiquitous. Strict iron-oxidizing bacteria like Leptospirillum and Ferrimicrobium were present at the source of the river, but disappeared downstream where iron concentrations were much lower. Iron-oxidizing, mesophilic Ferroplasma spp. were the main archaea found. The data presented in this work represent the first molecular assessment of this rare natural acidic environment.
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Affiliation(s)
- M Sofía Urbieta
- CINDEFI (CONICET-UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.
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Spatial and temporal analysis of the microbial community in the tailings of a Pb-Zn mine generating acidic drainage. Appl Environ Microbiol 2011; 77:5540-4. [PMID: 21705549 DOI: 10.1128/aem.02458-10] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of spatial and temporal variations in the microbial community in the abandoned tailings impoundment of a Pb-Zn mine revealed distinct microbial populations associated with the different oxidation stages of the tailings. Although Acidithiobacillus ferrooxidans and Leptospirillum spp. were consistently present in the acidic tailings, acidophilic archaea, mostly Ferroplasma acidiphilum, were predominant in the oxidized zones and the oxidation front, indicating their importance to generation of acid mine drainage.
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Environmental, biogeographic, and biochemical patterns of archaea of the family Ferroplasmaceae. Appl Environ Microbiol 2011; 77:5071-8. [PMID: 21685165 DOI: 10.1128/aem.00726-11] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
About 10 years ago, a new family of cell wall-deficient, iron-oxidizing archaea, Ferroplasmaceae, within the large archaeal phylum Euryarchaeota, was described. In this minireview, I summarize the research progress achieved since then and report on the current status of taxonomy, biogeography, physiological diversity, biochemistry, and other research areas involving this exciting group of acidophilic archaea.
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Automatic extraction of microorganisms and their habitats from free text using text mining workflows. J Integr Bioinform 2011. [DOI: 10.1515/jib-2011-184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Summary In this paper we illustrate the usage of text mining workflows to automatically extract instances of microorganisms and their habitats from free text; these entries can then be curated and added to different databases. To this end, we use a Conditional Random Field (CRF) based classifier, as part of the workflows, to extract the mention of microorganisms, habitats and the inter-relation between organisms and their habitats.Results indicate a good performance for extraction of microorganisms and the relation extraction aspects of the task (with a precision of over 80%), while habitat recognition is only moderate (a precision of about 65%). We also conjecture that pdf-to-text conversion can be quite noisy and this implicitly affects any sentence-based relation extraction algorithms.
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Watlinga HR, Watkinb ELJ, Ralphe DE. The resilience and versatility of acidophiles that contribute to the bio-assisted extraction of metals from mineral sulphides. ENVIRONMENTAL TECHNOLOGY 2010; 31:915-933. [PMID: 20662381 DOI: 10.1080/09593331003646646] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this paper, a brief outline is presented on acidic ferric ion oxidation of mineral sulphides for the extraction of metals in both stirred tank reactors for mineral concentrates and heaps for low-grade ores. The identities and capabilities of the relatively few acidophiles that assist the oxidative processes are summarized and their responses to selected extremes in their growth environments described. Individually, the organisms adapt to the presence of high concentrations of heavy metals and other elements in the bioleaching environment, tolerate a wide range of acidities and can recover from prolonged exposure to temperatures significantly above their preferred temperatures for growth. However, the presence of chloride in their acidic environment presents a significant physiological challenge. Species that exhibit a chemotactic response and attachment to sulphide surfaces, where they can create their own micro-environments, would be favoured in both heap bioreactors with low availability of energy substrates and physically aggressive, agitated continuous stirred-tank reactor environments treating concentrates.
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Affiliation(s)
- H R Watlinga
- Parker Centre for Integrated Hydrometallurgy Solutions: CSIRO Minerals Down Under Flagship, P.O. Box 7229, Karawara, Western Australia 6152, Australia.
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Abstract
We are becoming increasingly aware of the role played by archaea in the biogeochemical cycling of the elements. Metabolism of metals is linked to fundamental metabolic functions, including nitrogen fixation, energy production, and cellular processes based on oxidoreductions. Comparative genomic analyses have shown that genes for metabolism, resistance, and detoxification of metals are widespread throughout the archaeal domain. Archaea share with other organisms strategies allowing them to utilize essential metals and maintain metal ions within a physiological range, although comparative proteomics show, in a few cases, preferences for specific genetic traits related to metals. A more in-depth understanding of the physiology of acidophilic archaea might lead to the development of new strategies for the bioremediation of metal-polluted sites and other applications, such as biomining.
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Affiliation(s)
- Elisabetta Bini
- Department of Biochemistry and Microbiology, Rutgers-The State University of New Jersey, New Brunswick, NJ, USA.
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Tan GL, Shu WS, Zhou WH, Li XL, Lan CY, Huang LN. Seasonal and spatial variations in microbial community structure and diversity in the acid stream draining across an ongoing surface mining site. FEMS Microbiol Ecol 2009; 70:121-9. [DOI: 10.1111/j.1574-6941.2009.00744.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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