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Park MJ, Kim YJ, Park M, Yu J, Namirimu T, Roh YR, Kwon KK. Establishment of Genome Based Criteria for Classification of the Family Desulfovibrionaceae and Proposal of Two Novel Genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov. Front Microbiol 2022; 13:738205. [PMID: 35694308 PMCID: PMC9174804 DOI: 10.3389/fmicb.2022.738205] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 04/11/2022] [Indexed: 01/14/2023] Open
Abstract
Bacteria in the Desulfovibrionaceae family, which contribute to S element turnover as sulfate-reducing bacteria (SRB) and disproportionation of partially oxidized sulfoxy anions, have been extensively investigated since the importance of the sulfur cycle emerged. Novel species belonging to this taxon are frequently reported, because they exist in various environments and are easy to culture using established methods. Due to the rapid expansion of the taxon, correction and reclassification have been conducted. The development of high-throughput sequencing facilitated rapid expansion of genome sequence database. Genome-based criteria, based on these databases, proved to be potential classification standard by overcoming the limitations of 16S rRNA-based phylogeny. Although standards methods for taxogenomics are being established, the addition of a novel genus requires extensive calculations with taxa, including many species, such as Desulfovibrionaceae. Thus, the genome-based criteria for classification of Desulfovibrionaceae were established and validated in this study. The average amino-acid identity (AAI) cut-off value, 63.43 ± 0.01, was calculated to be an appropriate criterion for genus delineation of the family Desulfovibrionaceae. By applying the AAI cut-off value, 88 genomes of the Desulfovibrionaceae were divided into 27 genera, which follows the core gene phylogeny results. In this process, two novel genera (Alkalidesulfovibrio and Salidesulfovibrio) and one former invalid genus (“Psychrodesulfovibrio”) were officially proposed. Further, by applying the 95–96% average nucleotide identity (ANI) standard and the 70% digital DNA–DNA hybridization standard values for species delineation of strains that were classified as the same species, five strains have the potential to be newly classified. After verifying that the classification was appropriately performed through relative synonymous codon usage analysis, common characteristics were listed by group. In addition, by detecting metal resistance related genes via in silico analysis, it was confirmed that most strains display metal tolerance.
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Affiliation(s)
- Mi-Jeong Park
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Yun Jae Kim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
| | - Myeongkyu Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Jihyun Yu
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Teddy Namirimu
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Yoo-Rim Roh
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
- *Correspondence: Kae Kyoung Kwon,
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Electrode Microbial Communities Associated with Electron Donor Source Types in a Bioelectrochemical System Treating Azo-Dye Wastewater. WATER 2022. [DOI: 10.3390/w14091505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Bioelectrochemical systems (BESs) have been acknowledged to be an efficient technology for refractory pollution treatment. An electron donor is as an indispensable element of BES, and domestic wastewater (DW) has been proved as a cost-efficient and accessible alternative option to expensive carbon sources (such as acetate and glucose), yet its effect on microbial community evolution has not been thoroughly revealed. In this study, the electrode microbial communities from BESs treating azo dye wastewater fed by DW (RDW), acetate (RAc), and glucose (RGlu) were systematically revealed based on 16S rRNA Illumina MiSeq sequencing platform. It was found that there were significant differences between three groups in microbial community structures. Desulfovibrio, Acinetobacter, and Klebsiella were identified as the predominant bacterial genera in RDW, RAc, and RGlu, respectively. Methanosaeta, the most enriched methanogen in all reactors, had a relative lower abundance in RDW. Microbial communities in RAc and RGlu were sensitive to electrode polarity while RDW was sensitive to electrode position. Compared with pure substrates, DW increased the diversity of microbial community and, thus, may enhance the stability of electrode biofilm. This study provides an insight into the microbial response mechanism to the electron donors and provides engineering implications for the development of BES.
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Ueno A, Tamazawa S, Tamamura S, Murakami T, Kiyama T, Inomata H, Amano Y, Miyakawa K, Tamaki H, Naganuma T, Kaneko K. Desulfovibrio subterraneus sp. nov., a mesophilic sulfate-reducing deltaproteobacterium isolated from a deep siliceous mudstone formation. Int J Syst Evol Microbiol 2021; 71. [PMID: 33588983 DOI: 10.1099/ijsem.0.004683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel mesophilic sulfate-reducing bacterium, strain HN2T, was isolated from groundwater sampled from the subsurface siliceous mudstone of the Wakkanai Formation located in Horonobe, Hokkaido, Japan. The bacterium was Gram-negative and vibrio-shaped, and its motility was conferred by a single polar flagellum. Cells had desulfoviridin. Catalase and oxidase activities were not detected. It grew in the temperature range of 25-40 °C (optimum, 35 °C) and pH range of 6.3-8.1 (optimum, pH 7.2-7.6). It used sulfate, thiosulfate, dimethyl sulfoxide, anthraquinone-2,6-disulfonate, Fe3+, and manganese oxide, but not elemental sulfur, nitrite, nitrate, or fumarate as electron acceptors. The strain showed weak growth with sulfite as the electron acceptor. Fermentative growth with pyruvate, lactate and cysteine was observed in the absence of sulfate, but not with malate or fumarate. NaCl was not required, but the strain tolerated up to 40 g l-1. Strain HN2T did not require vitamins. The major cellular fatty acids were iso-C15 : 0 (23.8 %), C18 : 1 ω9t (18.4 %), C18 : 0 (15.0 %), C16 : 0 (14.5 %), and anteiso-C17 :0 (10.1 %). The major respiratory quinone was menaquinone MK-6(H2). The G+C content of the genomic DNA was 56.7 mol%. Based on 16S rRNA gene sequence analysis, the closest phylogenetic relative of strain HN2T is Desulfovibrio psychrotolerans JS1T (97.0 %). Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of the strains HN2T and D. psychrotolerans JS1T were 22.2 and 79.8 %, respectively. Based on the phenotypic and molecular genetic evidence, we propose a novel species, D. subterraneus sp. nov. with the type strain HN2T (=DSM 101010T=NBRC 112213T).
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Affiliation(s)
- Akio Ueno
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Satoshi Tamazawa
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Shuji Tamamura
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Takuma Murakami
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Tamotsu Kiyama
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Hidenori Inomata
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Yuki Amano
- Horonobe Underground Research Center, Japan Atomic Energy Agency (JAEA), Hokushin 432-2, Horonobe-cho, Hokkaido 098-3224, Japan
| | - Kazuya Miyakawa
- Horonobe Underground Research Center, Japan Atomic Energy Agency (JAEA), Hokushin 432-2, Horonobe-cho, Hokkaido 098-3224, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba 305-856, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Katsuhiko Kaneko
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
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Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol 2020; 70:5972-6016. [DOI: 10.1099/ijsem.0.004213] [Citation(s) in RCA: 696] [Impact Index Per Article: 174.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class
Deltaproteobacteria
comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum
Proteobacteria
, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class
Deltaproteobacteria
encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the
Oligoflexia
. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes
Deltaproteobacteria
and
Oligoflexia
in the phylum
Proteobacteria
. Instead, the great majority of currently recognized members of the class
Deltaproteobacteria
are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class
Oligoflexia
represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum
Thermodesulfobacteria
, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the
Thermodesulfobacteria
rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.
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Affiliation(s)
- David W Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Maria Chuvochina
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Claus Pelikan
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | | | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Alexander Loy
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | | | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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Paradesulfovibrio onnuriensis gen. nov., sp. nov., a chemolithoautotrophic sulfate-reducing bacterium isolated from the Onnuri vent field of the Indian Ocean and reclassification of Desulfovibrio senegalensis as Paradesulfovibrio senegalensis comb. nov. J Microbiol 2020; 58:252-259. [DOI: 10.1007/s12275-020-9376-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/31/2019] [Accepted: 01/21/2020] [Indexed: 10/24/2022]
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Baltic Sea methanogens compete with acetogens for electrons from metallic iron. ISME JOURNAL 2019; 13:3011-3023. [PMID: 31444483 PMCID: PMC6864099 DOI: 10.1038/s41396-019-0490-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 07/17/2019] [Accepted: 08/02/2019] [Indexed: 01/05/2023]
Abstract
Microbially induced corrosion of metallic iron (Fe0)-containing structures is an environmental and economic hazard. Methanogens are abundant in low-sulfide environments and yet their specific role in Fe0 corrosion is poorly understood. In this study, Sporomusa and Methanosarcina dominated enrichments from Baltic Sea methanogenic sediments that were established with Fe0 as the sole electron donor and CO2 as the electron acceptor. The Baltic-Sporomusa was phylogenetically affiliated to the electroactive acetogen S. silvacetica. Baltic-Sporomusa adjusted rapidly to growth on H2. On Fe0, spent filtrate enhanced growth of this acetogen suggesting that it was using endogenous enzymes to retrieve electrons and produce acetate. Previous studies have proposed that acetate produced by acetogens can feed commensal acetoclastic methanogens such as Methanosarcina. However, Baltic-methanogens could not generate methane from acetate, plus the decrease or absence of acetogens stimulated their growth. The decrease in numbers of Sporomusa was concurrent with an upsurge in Methanosarcina and increased methane production, suggesting that methanogens compete with acetogens for electrons from Fe0. Furthermore, Baltic-methanogens were unable to use H2 (1.5 atm) for methanogenesis and were inhibited by spent filtrate additions, indicating that enzymatically produced H2 is not a favorable electron donor. We hypothesize that Baltic-methanogens retrieve electrons from Fe0 via a yet enigmatic direct electron uptake mechanism.
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7
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Zavarzina DG, Gavrilov SN, Zhilina TN. Direct Fe(III) Reduction from Synthetic Ferrihydrite by Haloalkaliphilic Lithotrophic Sulfidogens. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718020170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Martinez CM, Alvarez LH, Celis LB, Cervantes FJ. Humus-reducing microorganisms and their valuable contribution in environmental processes. Appl Microbiol Biotechnol 2013; 97:10293-308. [PMID: 24220793 DOI: 10.1007/s00253-013-5350-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/17/2013] [Accepted: 10/19/2013] [Indexed: 02/08/2023]
Abstract
Humus constitutes a very abundant class of organic compounds that are chemically heterogeneous and widely distributed in terrestrial and aquatic environments. Evidence accumulated during the last decades indicating that humic substances play relevant roles on the transport, fate, and redox conversion of organic and inorganic compounds both in chemically and microbially driven reactions. The present review underlines the contribution of humus-reducing microorganisms in relevant environmental processes such as biodegradation of recalcitrant pollutants and mitigation of greenhouse gases emission in anoxic ecosystems, redox conversion of industrial contaminants in anaerobic wastewater treatment systems, and on the microbial production of nanocatalysts and alternative energy sources.
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Affiliation(s)
- Claudia M Martinez
- División de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), Camino a la Presa San José 2055, Col. Lomas 4a Sección, San Luis Potosí, SLP, 78216, Mexico
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Bolan NS, Choppala G, Kunhikrishnan A, Park J, Naidu R. Microbial transformation of trace elements in soils in relation to bioavailability and remediation. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2013; 225:1-56. [PMID: 23494555 DOI: 10.1007/978-1-4614-6470-9_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- Nanthi S Bolan
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, SA, Australia,
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Pecheritsyna SA, Rivkina EM, Akimov VN, Shcherbakova VA. Desulfovibrio arcticus sp. nov., a psychrotolerant sulfate-reducing bacterium from a cryopeg. Int J Syst Evol Microbiol 2012; 62:33-37. [DOI: 10.1099/ijs.0.021451-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A psychrotolerant sulfate-reducing bacterium, designated B15T, was isolated from supercooled water brine from within permafrost of the Varandey Peninsula, on the southern coast of the Barents Sea. Cells were Gram-negative, motile vibrions (3.0–4.0×0.4–0.5 µm) with a single polar flagellum. The isolate was positive for desulfoviridin as a bisulfite reductase. Strain B15T grew at −2 to 28 °C (optimum 24 °C) and with 0–2.0 % NaCl (optimum 0.2 %). The isolate used H2 plus acetate, formate, ethanol, lactate, pyruvate and choline as electron donors and used sulfate, sulfite, thiosulfate, elemental sulfur, DMSO and Fe3+ as electron acceptors. Pyruvate and lactate were not fermented in the absence of sulfate. The G+C content of genomic DNA was 55.2 mol%. Analysis of the 16S rRNA gene sequence showed that the isolate belonged to the genus Desulfovibrio. Its closest relatives were Desulfovibrio idahonensis CY1T (98.8 % 16S rRNA gene sequence similarity) and Desulfovibrio mexicanus Lup1T (96.5 %). On the basis of genotypic, phenotypic and phylogenetic characteristics, the isolate represents a novel species, for which the name Desulfovibrio arcticus sp. nov. is proposed; the type strain is B15T ( = VKM B-2367T = DSM 21064T).
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Affiliation(s)
- Svetlana A. Pecheritsyna
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Elizaveta M. Rivkina
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Vladimir N. Akimov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Viktoria A. Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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Rastogi G, Barua S, Sani RK, Peyton BM. Investigation of microbial populations in the extremely metal-contaminated Coeur d'Alene River sediments. MICROBIAL ECOLOGY 2011; 62:1-13. [PMID: 21331609 DOI: 10.1007/s00248-011-9810-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Accepted: 01/17/2011] [Indexed: 05/30/2023]
Abstract
The deposition of mine tailings generated from 125 years of sulfidic ore mining resulted in the enrichment of Coeur d'Alene River (CdAR) sediments with significant amounts of toxic heavy metals. A review of literature suggests that microbial populations play a pivotal role in the biogeochemical cycling of elements in such mining-impacted sedimentary environments. To assess the indigenous microbial communities associated with metal-enriched sediments of the CdAR, high-density 16S microarray (PhyloChip) and clone libraries specific to bacteria (16S rRNA), ammonia oxidizers (amoA), and methanogens (mcrA) were analyzed. PhyloChip analysis provided a comprehensive assessment of bacterial populations and detected the largest number of phylotypes in Proteobacteria followed by Firmicutes and Actinobacteria. Furthermore, PhyloChip and clone libraries displayed considerable metabolic diversity in indigenous microbial populations by capturing several chemolithotrophic groups such as ammonia oxidizers, iron-reducers and -oxidizers, methanogens, and sulfate-reducers in the CdAR sediments. Twenty-two phylotypes detected on PhyloChip could not be classified even at phylum level thus suggesting the presence of novel microbial populations in the CdAR sediments. Clone libraries demonstrated very limited diversity of ammonia oxidizers and methanogens in the CdAR sediments as evidenced by the fact that only Nitrosospira- and Methanosarcina-related phylotypes were retrieved in amoA and mcrA clone libraries, respectively.
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Affiliation(s)
- Gurdeep Rastogi
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
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Ramamoorthy S, Piotrowski JS, Langner HW, Holben WE, Morra MJ, Rosenzweig RF. Ecology of sulfate-reducing bacteria in an iron-dominated, mining-impacted freshwater sediment. JOURNAL OF ENVIRONMENTAL QUALITY 2009; 38:675-684. [PMID: 19244488 DOI: 10.2134/jeq2007.0577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A legacy of lead and silver mining in its headwaters left Lake Coeur d'Alene, Idaho with a sediment body that is highly reduced and contains up to 100 g kg(-1) iron and a smaller fraction of chemically active sulfide phases. The dynamic character of these sulfides and their importance for the sequestering of contaminating trace elements prompted this study of the sulfate-reducing bacteria (SRB) involved in their production. We estimated parameters indicative of the distribution and activity of SRB in relation to season, site, and depth. Most probable number estimates and quantitative PCR assays of an SRB-specific functional gene, alpha-adenosine 5'-phosphosulfate reductase, indicated 10(3) to 10(6) cultivable cells and 10(5) to 10(7) gene copy numbers g(-1) dry wt sediment, respectively. Although culture-based estimates of SRB abundance correlated poorly with site, season, depth, total S, or pore water SO(4), non-culture-based estimates of SRB abundance were markedly higher at contaminated sites and positively correlated with pore water SO(4). Ex situ estimates of (35)SO(4) respiration and acid volatile sulfides abundance also showed strong among-site effects, indicating elevated sulfidogenesis at contaminated sites. These observations support the view that biogenic sulfides may act in concert with reduced iron to retain soluble metal(loid)s in the solid phase.
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