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Wu X, Chauhan A, Layton AC, Lau Vetter MCY, Stackhouse BT, Williams DE, Whyte L, Pfiffner SM, Onstott TC, Vishnivetskaya TA. Comparative Metagenomics of the Active Layer and Permafrost from Low-Carbon Soil in the Canadian High Arctic. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:12683-12693. [PMID: 34472853 DOI: 10.1021/acs.est.1c00802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Approximately 87% of the Arctic consists of low-organic carbon mineral soil, but knowledge of microbial activity in low-carbon permafrost (PF) and active layer soils remains limited. This study investigated the taxonomic composition and genetic potential of microbial communities at contrasting depths of the active layer (5, 35, and 65 cm below surface, bls) and PF (80 cm bls). We showed microbial communities in PF to be taxonomically and functionally different from those in the active layer. 16S rRNA gene sequence analysis revealed higher biodiversity in the active layer than in PF, and biodiversity decreased significantly with depth. The reconstructed 91 metagenome-assembled genomes showed that PF was dominated by heterotrophic, fermenting Bacteroidota using nitrite as their main electron acceptor. Prevalent microbes identified in the active layer belonged to bacterial taxa, gaining energy via aerobic respiration. Gene abundance in metagenomes revealed enrichment of genes encoding the plant-derived polysaccharide degradation and metabolism of nitrate and sulfate in PF, whereas genes encoding methane/ammonia oxidation, cold-shock protein, and two-component systems were generally more abundant in the active layer, particularly at 5 cm bls. The results of this study deepen our understanding of the low-carbon Arctic soil microbiome and improve prediction of the impacts of thawing PF.
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Affiliation(s)
- Xiaofen Wu
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Archana Chauhan
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Alice C Layton
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Maggie C Y Lau Vetter
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
| | - Brandon T Stackhouse
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
| | - Daniel E Williams
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
| | - Tatiana A Vishnivetskaya
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
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Li M, Wen J. Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments. Microb Cell Fact 2021; 20:178. [PMID: 34496835 PMCID: PMC8425152 DOI: 10.1186/s12934-021-01671-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/30/2021] [Indexed: 11/11/2022] Open
Abstract
Bio-mining microorganisms are a key factor affecting the metal recovery rate of bio-leaching, which inevitably produces an extremely acidic environment. As a powerful tool for exploring the adaptive mechanisms of microorganisms in extreme environments, omics technologies can greatly aid our understanding of bio-mining microorganisms and their communities on the gene, mRNA, and protein levels. These omics technologies have their own advantages in exploring microbial diversity, adaptive evolution, changes in metabolic characteristics, and resistance mechanisms of single strains or their communities to extreme environments. These technologies can also be used to discover potential new genes, enzymes, metabolites, metabolic pathways, and species. In addition, integrated multi-omics analysis can link information at different biomolecular levels, thereby obtaining more accurate and complete global adaptation mechanisms of bio-mining microorganisms. This review introduces the current status and future trends in the application of omics technologies in the study of bio-mining microorganisms and their communities in extreme environments.
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Affiliation(s)
- Min Li
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, China.,Frontier Science Center of Ministry of Education, Tianjin University, Tianjin, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, China. .,Frontier Science Center of Ministry of Education, Tianjin University, Tianjin, China.
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Asplund-Samuelsson J, Hudson EP. Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes. PLoS Comput Biol 2021; 17:e1008742. [PMID: 33556078 PMCID: PMC7895386 DOI: 10.1371/journal.pcbi.1008742] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/19/2021] [Accepted: 01/25/2021] [Indexed: 11/21/2022] Open
Abstract
Knowledge of the genetic basis for autotrophic metabolism is valuable since it relates to both the emergence of life and to the metabolic engineering challenge of incorporating CO2 as a potential substrate for biorefining. The most common CO2 fixation pathway is the Calvin cycle, which utilizes Rubisco and phosphoribulokinase enzymes. We searched thousands of microbial genomes and found that 6.0% contained the Calvin cycle. We then contrasted the genomes of Calvin cycle-positive, non-cyanobacterial microbes and their closest relatives by enrichment analysis, ancestral character estimation, and random forest machine learning, to explore genetic adaptations associated with acquisition of the Calvin cycle. The Calvin cycle overlaps with the pentose phosphate pathway and glycolysis, and we could confirm positive associations with fructose-1,6-bisphosphatase, aldolase, and transketolase, constituting a conserved operon, as well as ribulose-phosphate 3-epimerase, ribose-5-phosphate isomerase, and phosphoglycerate kinase. Additionally, carbohydrate storage enzymes, carboxysome proteins (that raise CO2 concentration around Rubisco), and Rubisco activases CbbQ and CbbX accompanied the Calvin cycle. Photorespiration did not appear to be adapted specifically for the Calvin cycle in the non-cyanobacterial microbes under study. Our results suggest that chemoautotrophy in Calvin cycle-positive organisms was commonly enabled by hydrogenase, and less commonly ammonia monooxygenase (nitrification). The enrichment of specific DNA-binding domains indicated Calvin-cycle associated genetic regulation. Metabolic regulatory adaptations were illustrated by negative correlation to AraC and the enzyme arabinose-5-phosphate isomerase, which suggests a downregulation of the metabolite arabinose-5-phosphate, which may interfere with the Calvin cycle through enzyme inhibition and substrate competition. Certain domains of unknown function that were found to be important in the analysis may indicate yet unknown regulatory mechanisms in Calvin cycle-utilizing microbes. Our gene ranking provides targets for experiments seeking to improve CO2 fixation, or engineer novel CO2-fixing organisms.
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Affiliation(s)
- Johannes Asplund-Samuelsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Elton P. Hudson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
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Acid Mine Drainage as Habitats for Distinct Microbiomes: Current Knowledge in the Era of Molecular and Omic Technologies. Curr Microbiol 2019; 77:657-674. [DOI: 10.1007/s00284-019-01771-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/09/2019] [Indexed: 11/27/2022]
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Esparza M, Jedlicki E, González C, Dopson M, Holmes DS. Effect of CO 2 Concentration on Uptake and Assimilation of Inorganic Carbon in the Extreme Acidophile Acidithiobacillus ferrooxidans. Front Microbiol 2019; 10:603. [PMID: 31019493 PMCID: PMC6458275 DOI: 10.3389/fmicb.2019.00603] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/11/2019] [Indexed: 02/01/2023] Open
Abstract
This study was motivated by surprising gaps in the current knowledge of microbial inorganic carbon (Ci) uptake and assimilation at acidic pH values (pH < 3). Particularly striking is the limited understanding of the differences between Ci uptake mechanisms in acidic versus circumneutral environments where the Ci predominantly occurs either as a dissolved gas (CO2) or as bicarbonate (HCO3 -), respectively. In order to gain initial traction on the problem, the relative abundance of transcripts encoding proteins involved in Ci uptake and assimilation was studied in the autotrophic, polyextreme acidophile Acidithiobacillus ferrooxidans whose optimum pH for growth is 2.5 using ferrous iron as an energy source, although they are able to grow at pH 5 when using sulfur as an energy source. The relative abundance of transcripts of five operons (cbb1-5) and one gene cluster (can-sulP) was monitored by RT-qPCR and, in selected cases, at the protein level by Western blotting, when cells were grown under different regimens of CO2 concentration in elemental sulfur. Of particular note was the absence of a classical bicarbonate uptake system in A. ferrooxidans. However, bioinformatic approaches predict that sulP, previously annotated as a sulfate transporter, is a novel type of bicarbonate transporter. A conceptual model of CO2 fixation was constructed from combined bioinformatic and experimental approaches that suggests strategies for providing ecological flexibility under changing concentrations of CO2 and provides a portal to elucidating Ci uptake and regulation in acidic conditions. The results could advance the understanding of industrial bioleaching processes to recover metals such as copper at acidic pH. In addition, they may also shed light on how chemolithoautotrophic acidophiles influence the nutrient and energy balance in naturally occurring low pH environments.
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Affiliation(s)
- Mario Esparza
- Laboratorio de Biominería, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Eugenia Jedlicki
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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An integrated microbiological and electrochemical approach to determine distributions of Fe metabolism in acid mine drainage-induced "iron mound" sediments. PLoS One 2019; 14:e0213807. [PMID: 30913215 PMCID: PMC6435174 DOI: 10.1371/journal.pone.0213807] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/28/2019] [Indexed: 11/21/2022] Open
Abstract
Fe(III)-rich deposits referred to as “iron mounds” develop when Fe(II)-rich acid mine drainage (AMD) emerges at the terrestrial surface, and aeration of the fluids induces oxidation of Fe(II), with subsequent precipitation of Fe(III) phases. As Fe(III) phases accumulate in these systems, O2 gradients may develop in the sediments and influence the distributions and extents of aerobic and anaerobic microbiological Fe metabolism, and in turn the solubility of Fe. To determine how intrusion of O2 into iron mound sediments influences microbial community composition and Fe metabolism, we incubated samples of these sediments in a column format. O2 was only supplied through the top of the columns, and microbiological, geochemical, and electrochemical changes at discrete depths were determined with time. Despite the development of dramatic gradients in dissolved Fe(II) concentrations, indicating Fe(II) oxidation in shallower portions and Fe(III) reduction in the deeper portions, microbial communities varied little with depth, suggesting the metabolic versatility of organisms in the sediments with respect to Fe metabolism. Additionally, the availability of O2 in shallow portions of the sediments influenced Fe metabolism in deeper, O2-free sediments. Total potential (EH + self-potential) measurements at discrete depths in the columns indicated that Fe transformations and electron transfer processes were occurring through the sediments and could explain the impact of O2 on Fe metabolism past where it penetrates into the sediments. This work shows that O2 availability (or lack of it) minimally influences microbial communities, but influences microbial activities beyond its penetration depth in AMD-derived Fe(III) rich sediments. Our results indicate that O2 can modulate Fe redox state and solubility in larger volumes of iron mound sediments than only those directly exposed to O2.
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Bose H, Satyanarayana T. Microbial Carbonic Anhydrases in Biomimetic Carbon Sequestration for Mitigating Global Warming: Prospects and Perspectives. Front Microbiol 2017; 8:1615. [PMID: 28890712 PMCID: PMC5574912 DOI: 10.3389/fmicb.2017.01615] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/08/2017] [Indexed: 11/13/2022] Open
Abstract
All the leading cities in the world are slowly becoming inhospitable for human life with global warming playing havoc with the living conditions. Biomineralization of carbon dioxide using carbonic anhydrase (CA) is one of the most economical methods for mitigating global warming. The burning of fossil fuels results in the emission of large quantities of flue gas. The temperature of flue gas is quite high. Alkaline conditions are necessary for CaCO3 precipitation in the mineralization process. In order to use CAs for biomimetic carbon sequestration, thermo-alkali-stable CAs are, therefore, essential. CAs must be stable in the presence of various flue gas contaminants too. The extreme environments on earth harbor a variety of polyextremophilic microbes that are rich sources of thermo-alkali-stable CAs. CAs are the fastest among the known enzymes, which are of six basic types with no apparent sequence homology, thus represent an elegant example of convergent evolution. The current review focuses on the utility of thermo-alkali-stable CAs in biomineralization based strategies. A variety of roles that CAs play in various living organisms, the use of CA inhibitors as drug targets and strategies for overproduction of CAs to meet the demand are also briefly discussed.
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Zhang X, Liu X, Liang Y, Fan F, Zhang X, Yin H. Metabolic diversity and adaptive mechanisms of iron- and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:738-751. [PMID: 27337207 DOI: 10.1111/1758-2229.12435] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/30/2016] [Indexed: 06/06/2023]
Abstract
Many studies have investigated the mechanisms underlying the survival and growth of certain organisms in extremely acidic environments known to be harmful to most prokaryotes and eukaryotes. Acidithiobacillus and Leptospirillum spp. are dominant bioleaching bacteria widely used in bioleaching systems, which are characterized by extremely acidic environments. To survive and grow in such settings, these acidophiles utilize shared molecular mechanisms that allow life in extreme conditions. In this review, we have summarized the results of published genomic analyses, which underscore the ability of iron- and/or sulfur-oxidizing autotrophic acidophiles belonging to the genera Acidithiobacillus and Leptospirillum to adapt to acidic environmental conditions. Several lines of evidence point at the metabolic diversity and multiplicity of pathways involved in the survival of these organisms. The ability to thrive in adverse environments requires versatile activation of structural and functional adaptive responses, including bacterial adhesion, motility, and resistance to heavy metals. We have highlighted recent developments centered on the key survival mechanisms employed by dominant extremophiles, and have laid the foundation for future studies focused on the ability of acidophiles to thrive in extremely acidic environments.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Fenliang Fan
- Key Laboratory of Plant Nutrition and Fertilizer, Beijing, China
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Beijing, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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Xiao Y, Liu X, Liang Y, Niu J, Zhang X, Ma L, Hao X, Gu Y, Yin H. Insights into functional genes and taxonomical/phylogenetic diversity of microbial communities in biological heap leaching system and their correlation with functions. Appl Microbiol Biotechnol 2016; 100:9745-9756. [DOI: 10.1007/s00253-016-7819-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/11/2016] [Accepted: 08/15/2016] [Indexed: 01/17/2023]
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10
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Satagopan S, Tabita FR. RubisCO selection using the vigorously aerobic and metabolically versatile bacterium Ralstonia eutropha. FEBS J 2016; 283:2869-80. [PMID: 27261087 DOI: 10.1111/febs.13774] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/06/2016] [Accepted: 06/03/2016] [Indexed: 11/29/2022]
Abstract
UNLABELLED Recapturing atmospheric CO2 is key to reducing global warming and increasing biological carbon availability. Ralstonia eutropha is a biotechnologically useful aerobic bacterium that uses the Calvin-Benson-Bassham (CBB) cycle and the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) for CO2 utilization, suggesting that it may be a useful host to bioselect RubisCO molecules with improved CO2 -capture capabilities. A host strain of R. eutropha was constructed for this purpose after deleting endogenous genes encoding two related RubisCOs. This strain could be complemented for CO2 -dependent growth by introducing native or heterologous RubisCO genes. Mutagenesis and suppressor selection identified amino acid substitutions in a hydrophobic region that specifically influences RubisCO's interaction with its substrates, particularly O2 , which competes with CO2 at the active site. Unlike most RubisCOs, the R. eutropha enzyme has evolved to retain optimal CO2 -fixation rates in a fast-growing host, despite the presence of high levels of competing O2 . Yet its structure-function properties resemble those of several commonly found RubisCOs, including the higher plant enzymes, allowing strategies to engineer analogous enzymes. Because R. eutropha can be cultured rapidly under harsh environmental conditions (e.g., with toxic industrial flue gas), in the presence of near saturation levels of oxygen, artificial selection and directed evolution studies in this organism could potentially impact efforts toward improving RubisCO-dependent biological CO2 utilization in aerobic environments. ENZYMES d-ribulose 1,5-bisphosphate carboxylase/oxygenase, EC 4.1.1.39; phosphoribulokinase, EC 2.7.1.19.
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Affiliation(s)
- Sriram Satagopan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - F Robert Tabita
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
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Sun W, Xiao E, Krumins V, Dong Y, Xiao T, Ning Z, Chen H, Xiao Q. Characterization of the microbial community composition and the distribution of Fe-metabolizing bacteria in a creek contaminated by acid mine drainage. Appl Microbiol Biotechnol 2016; 100:8523-35. [PMID: 27277134 DOI: 10.1007/s00253-016-7653-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 05/23/2016] [Accepted: 05/26/2016] [Indexed: 01/09/2023]
Abstract
A small watershed heavily contaminated by long-term acid mine drainage (AMD) from an upstream abandoned coal mine was selected to study the microbial community developed in such extreme system. The watershed consists of AMD-contaminated creek, adjacent contaminated soils, and a small cascade aeration unit constructed downstream, which provide an excellent contaminated site to study the microbial response in diverse extreme AMD-polluted environments. The results showed that the innate microbial communities were dominated by acidophilic bacteria, especially acidophilic Fe-metabolizing bacteria, suggesting that Fe and pH are the primary environmental factors in governing the indigenous microbial communities. The distribution of Fe-metabolizing bacteria showed distinct site-specific patterns. A pronounced shift from diverse communities in the upstream to Proteobacteria-dominated communities in the downstream was observed in the ecosystem. This location-specific trend was more apparent at genus level. In the upstream samples (sampling sites just below the coal mining adit), a number of Fe(II)-oxidizing bacteria such as Alicyclobacillus spp., Metallibacterium spp., and Acidithrix spp. were dominant, while Halomonas spp. were the major Fe(II)-oxidizing bacteria observed in downstream samples. Additionally, Acidiphilium, an Fe(III)-reducing bacterium, was enriched in the upstream samples, while Shewanella spp. were the dominant Fe(III)-reducing bacteria in downstream samples. Further investigation using linear discriminant analysis (LDA) effect size (LEfSe), principal coordinate analysis (PCoA), and unweighted pair group method with arithmetic mean (UPGMA) clustering confirmed the difference of microbial communities between upstream and downstream samples. Canonical correspondence analysis (CCA) and Spearman's rank correlation indicate that total organic carbon (TOC) content is the primary environmental parameter in structuring the indigenous microbial communities, suggesting that the microbial communities are shaped by three major environmental parameters (i.e., Fe, pH, and TOC). These findings were beneficial to a better understanding of natural attenuation of AMD.
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Affiliation(s)
- Weimin Sun
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA.,Guangdong Institute of Eco-environment and Soil Sciences, Guangzhou, 510650, China
| | - Enzong Xiao
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Yiran Dong
- Department of Geology, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA
| | - Tangfu Xiao
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China. .,Innovation Center and Key Laboratory of Waters Safety & Protection in the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China
| | - Haiyan Chen
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingxiang Xiao
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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12
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Varaljay VA, Satagopan S, North JA, Witte B, Dourado MN, Anantharaman K, Arbing MA, McCann SH, Oremland RS, Banfield JF, Wrighton KC, Tabita FR. Functional metagenomic selection of ribulose 1, 5-bisphosphate carboxylase/oxygenase from uncultivated bacteria. Environ Microbiol 2016; 18:1187-99. [PMID: 26617072 PMCID: PMC10035430 DOI: 10.1111/1462-2920.13138] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/17/2015] [Accepted: 11/17/2015] [Indexed: 01/29/2023]
Abstract
Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a critical yet severely inefficient enzyme that catalyses the fixation of virtually all of the carbon found on Earth. Here, we report a functional metagenomic selection that recovers physiologically active RubisCO molecules directly from uncultivated and largely unknown members of natural microbial communities. Selection is based on CO2 -dependent growth in a host strain capable of expressing environmental deoxyribonucleic acid (DNA), precluding the need for pure cultures or screening of recombinant clones for enzymatic activity. Seventeen functional RubisCO-encoded sequences were selected using DNA extracted from soil and river autotrophic enrichments, a photosynthetic biofilm and a subsurface groundwater aquifer. Notably, three related form II RubisCOs were recovered which share high sequence similarity with metagenomic scaffolds from uncultivated members of the Gallionellaceae family. One of the Gallionellaceae RubisCOs was purified and shown to possess CO2 /O2 specificity typical of form II enzymes. X-ray crystallography determined that this enzyme is a hexamer, only the second form II multimer ever solved and the first RubisCO structure obtained from an uncultivated bacterium. Functional metagenomic selection leverages natural biological diversity and billions of years of evolution inherent in environmental communities, providing a new window into the discovery of CO2 -fixing enzymes not previously characterized.
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Affiliation(s)
- Vanessa A. Varaljay
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Sriram Satagopan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Justin A. North
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Brian Witte
- The Botanical Research Institute of Texas, Fort Worth, TX 76107, USA
| | | | - Karthik Anantharaman
- Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA
| | - Mark A. Arbing
- Protein Expression Technology Center, UCLA-DOE Institute, University of California, Los Angeles, CA 90095, USA
| | | | | | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA
| | - Kelly C. Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - F. Robert Tabita
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- For correspondence. ; Tel. +1 614 292 4297; Fax: +1 614 292 6337
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Zhang X, Niu J, Liang Y, Liu X, Yin H. Metagenome-scale analysis yields insights into the structure and function of microbial communities in a copper bioleaching heap. BMC Genet 2016; 17:21. [PMID: 26781463 PMCID: PMC4717592 DOI: 10.1186/s12863-016-0330-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 01/13/2016] [Indexed: 01/18/2023] Open
Abstract
Background Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. Here, shotgun metagenome sequencing was used to investigate microbial communities from the surface layer of low grade copper tailings that were industrially bioleached at the Dexing Copper Mine, China. A bioinformatics analysis was further performed to elucidate structural and functional properties of the microbial communities in a copper bioleaching heap. Results Taxonomic analysis revealed unexpectedly high microbial biodiversity of this extremely acidic environment, as most sequences were phylogenetically assigned to Proteobacteria, while Euryarchaeota-related sequences occupied little proportion in this system, assuming that Archaea probably played little role in the bioleaching systems. At the genus level, the microbial community in mineral surface-layer was dominated by the sulfur- and iron-oxidizing acidophiles such as Acidithiobacillus-like populations, most of which were A. ferrivorans-like and A. ferrooxidans-like groups. In addition, Caudovirales were the dominant viral type observed in this extremely environment. Functional analysis illustrated that the principal participants related to the key metabolic pathways (carbon fixation, nitrogen metabolism, Fe(II) oxidation and sulfur metabolism) were mainly identified to be Acidithiobacillus-like, Thiobacillus-like and Leptospirillum-like microorganisms, indicating their vital roles. Also, microbial community harbored certain adaptive mechanisms (heavy metal resistance, low pH adaption, organic solvents tolerance and detoxification of hydroxyl radicals) as they performed their functions in the bioleaching system. Conclusion Our study provides several valuable datasets for understanding the microbial community composition and function in the surface-layer of copper bioleaching heap. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0330-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
| | - Jiaojiao Niu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
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14
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Contemporary molecular tools in microbial ecology and their application to advancing biotechnology. Biotechnol Adv 2015; 33:1755-73. [DOI: 10.1016/j.biotechadv.2015.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 09/19/2015] [Accepted: 09/20/2015] [Indexed: 12/30/2022]
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15
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Metal resistance in acidophilic microorganisms and its significance for biotechnologies. Appl Microbiol Biotechnol 2014; 98:8133-44. [PMID: 25104030 DOI: 10.1007/s00253-014-5982-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 10/24/2022]
Abstract
Extremely acidophilic microorganisms have an optimal pH of <3 and are found in all three domains of life. As metals are more soluble at acid pH, acidophiles are often challenged by very high metal concentrations. Acidophiles are metal-tolerant by both intrinsic, passive mechanisms as well as active systems. Passive mechanisms include an internal positive membrane potential that creates a chemiosmotic gradient against which metal cations must move, as well as the formation of metal sulfate complexes reducing the concentration of the free metal ion. Active systems include efflux proteins that pump metals out of the cytoplasm and conversion of the metal to a less toxic form. Acidophiles are exploited in a number of biotechnologies including biomining for sulfide mineral dissolution, biosulfidogenesis to produce sulfide that can selectively precipitate metals from process streams, treatment of acid mine drainage, and bioremediation of acidic metal-contaminated milieux. This review describes how acidophilic microorganisms tolerate extremely high metal concentrations in biotechnological processes and identifies areas of future work that hold promise for improving the efficiency of these applications.
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16
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Brantner JS, Senko JM. Response of soil-associated microbial communities to intrusion of coal mine-derived acid mine drainage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:8556-8563. [PMID: 24971467 DOI: 10.1021/es502261u] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A system has been identified in which coal mine-derived acid mine drainage (AMD) flows as a 0.5-cm-deep sheet over the terrestrial surface. This flow regime enhances the activities of Fe(II) oxidizing bacteria, which catalyze the oxidative precipitation of Fe from AMD. These activities give rise to Fe(III) (hydr)oxide-rich deposits (referred to as an iron mound) overlying formerly pristine soil. This iron mound has developed with no human intervention, indicating that microbiological activities associated with iron mounds may be exploited as an inexpensive and sustainable approach to remove Fe(II) from AMD. To evaluate the changes in microbial activities and communities that occur when AMD infiltrates initially pristine soil, we incubated AMD-unimpacted soil with site AMD. Continuous exposure of soil to AMD induced progressively greater rates of Fe(II) biooxidation. The development of Fe(II) oxidizing activities was enhanced by inoculation of soil with microorganisms associated with mature iron mound sediment. Evaluation of pyrosequencing-derived 16S rRNA gene sequences recovered from incubations revealed the development of microbial community characteristics that were similar to those of the mature iron mound sediment. Our results indicate that upon mixing of AMD with pristine soil, microbial communities develop that mediate rapid oxidative precipitation of Fe from AMD.
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Affiliation(s)
- Justin S Brantner
- Department of Biology, ‡Integrated Biosciences Program, and §Department of Geosciences, The University of Akron , Akron, Ohio 44325, United States
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17
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Brantner JS, Haake ZJ, Burwick JE, Menge CM, Hotchkiss ST, Senko JM. Depth-dependent geochemical and microbiological gradients in Fe(III) deposits resulting from coal mine-derived acid mine drainage. Front Microbiol 2014; 5:215. [PMID: 24860562 PMCID: PMC4030175 DOI: 10.3389/fmicb.2014.00215] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/23/2014] [Indexed: 02/01/2023] Open
Abstract
We evaluated the depth-dependent geochemistry and microbiology of sediments that have developed via the microbially-mediated oxidation of Fe(II) dissolved in acid mine drainage (AMD), giving rise to a 8–10 cm deep “iron mound” that is composed primarily of Fe(III) (hydr)oxide phases. Chemical analyses of iron mound sediments indicated a zone of maximal Fe(III) reducing bacterial activity at a depth of approximately 2.5 cm despite the availability of dissolved O2 at this depth. Subsequently, Fe(II) was depleted at depths within the iron mound sediments that did not contain abundant O2. Evaluations of microbial communities at 1 cm depth intervals within the iron mound sediments using “next generation” nucleic acid sequencing approaches revealed an abundance of phylotypes attributable to acidophilic Fe(II) oxidizing Betaproteobacteria and the chloroplasts of photosynthetic microeukaryotic organisms in the upper 4 cm of the iron mound sediments. While we observed a depth-dependent transition in microbial community structure within the iron mound sediments, phylotypes attributable to Gammaproteobacterial lineages capable of both Fe(II) oxidation and Fe(III) reduction were abundant in sequence libraries (comprising ≥20% of sequences) from all depths. Similarly, abundances of total cells and culturable Fe(II) oxidizing bacteria were uniform throughout the iron mound sediments. Our results indicate that O2 and Fe(III) reduction co-occur in AMD-induced iron mound sediments, but that Fe(II)-oxidizing activity may be sustained in regions of the sediments that are depleted in O2.
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Affiliation(s)
- Justin S Brantner
- Department of Biology, The University of Akron Akron, OH, USA ; Integrated Bioscience Program, The University of Akron Akron, OH, USA
| | - Zachary J Haake
- Department of Geosciences, The University of Akron Akron, OH, USA
| | - John E Burwick
- Department of Geosciences, The University of Akron Akron, OH, USA
| | | | | | - John M Senko
- Department of Biology, The University of Akron Akron, OH, USA ; Integrated Bioscience Program, The University of Akron Akron, OH, USA ; Department of Geosciences, The University of Akron Akron, OH, USA
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18
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Dai Z, Guo X, Yin H, Liang Y, Cong J, Liu X. Identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage. PLoS One 2014; 9:e87976. [PMID: 24498417 PMCID: PMC3912193 DOI: 10.1371/journal.pone.0087976] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 01/02/2014] [Indexed: 11/19/2022] Open
Abstract
Biological nitrogen fixation is an essential function of acid mine drainage (AMD) microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community.
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Affiliation(s)
- Zhimin Dai
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
| | - Xue Guo
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
| | - Jing Cong
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
- * E-mail:
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