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Nazina TN, Tourova TP, Grouzdev DS, Bidzhieva SK, Poltaraus AB. A Novel View on the Taxonomy of Sulfate-Reducing Bacterium ' Desulfotomaculum salinum' and a Description of a New Species Desulfofundulus salinus sp. nov. Microorganisms 2024; 12:1115. [PMID: 38930497 PMCID: PMC11206085 DOI: 10.3390/microorganisms12061115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Two thermophilic spore-forming sulfate-reducing strains, 435T and 781, were isolated from oil and gas reservoirs in Western Siberia (Russia) about 50 years ago. Both strains were found to be neutrophilic, chemoorganotrophic, anaerobic bacteria, growing at 45-70 °C (optimum, 55-60 °C) and with 0-4.5% (w/v) NaCl (optimum, 0.5-1% NaCl). The major fatty acids were iso-C15:0, iso-C17:0, C16:0, and C18:0. In sulfate-reducing conditions, the strains utilized H2/CO2, formate, lactate, pyruvate, malate, fumarate, succinate, methanol, ethanol, propanol, butanol, butyrate, valerate, and palmitate. In 2005, based on phenotypic characteristics and a 16S rRNA gene sequence analysis, the strains were described as 'Desulfotomaculum salinum' sp. nov. However, this species was not validly published because the type strain was not deposited in two culture collections. In this study, a genomic analysis of strain 435T was carried out to determine its taxonomic affiliation. The genome size of strain 435T was 2.886 Mb with a 55.1% genomic G + C content. The average nucleotide identity and digital DNA-DNA hybridization values were highest between strain 435T and members of the genus Desulfofundulus, 78.7-93.3% and 25.0-52.2%, respectively; these values were below the species delineation cut-offs (<95-96% and <70%). The cumulative phenotypic and phylogenetic data indicate that two strains represent a novel species within the genus Desulfofundulus, for which the name Desulfofundulus salinus sp. nov. is proposed. The type strain is 435T (=VKM B-1492T = DSM 23196T). A genome analysis of strain 435T revealed the genes for dissimilatory sulfate reduction, autotrophic carbon fixation via the Wood-Ljungdahl pathway, hydrogen utilization, methanol and organic acids metabolism, and sporulation, which were confirmed by cultivation studies.
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Affiliation(s)
- Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (T.P.T.); (S.K.B.)
| | - Tatyana P. Tourova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (T.P.T.); (S.K.B.)
| | | | - Salimat K. Bidzhieva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (T.P.T.); (S.K.B.)
| | - Andrey B. Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
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Frolov EN, Gololobova AV, Klyukina AA, Bonch-Osmolovskaya EA, Pimenov NV, Chernyh NA, Merkel AY. Diversity and Activity of Sulfate-Reducing Prokaryotes in Kamchatka Hot Springs. Microorganisms 2021; 9:2072. [PMID: 34683394 PMCID: PMC8539903 DOI: 10.3390/microorganisms9102072] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022] Open
Abstract
Microbial communities of the Kamchatka Peninsula terrestrial hot springs were studied using radioisotopic and cultural approaches, as well as by the amplification and sequencing of dsrB and 16S rRNA genes fragments. Radioisotopic experiments with 35S-labeled sulfate showed that microbial communities of the Kamchatka hot springs are actively reducing sulfate. Both the cultivation experiments and the results of dsrB and 16S rRNA genes fragments analyses indicated the presence of microorganisms participating in the reductive part of the sulfur cycle. It was found that sulfate-reducing prokaryotes (SRP) belonging to Desulfobacterota, Nitrospirota and Firmicutes phyla inhabited neutral and slightly acidic hot springs, while bacteria of phylum Thermodesulofobiota preferred moderately acidic hot springs. In high-temperature acidic springs sulfate reduction was mediated by archaea of the phylum Crenarchaeota, chemoorganoheterotrophic representatives of genus Vulcanisaeta being the most probable candidates. The 16S rRNA taxonomic profiling showed that in most of the studied communities SRP was present only as a minor component. Only in one microbial community, the representatives of genus Vulcanisaeta comprised a significant group. Thus, in spite of comparatively low sulfate concentrations in terrestrial hot springs of the Kamchatka, phylogenetically and metabolically diverse groups of sulfate-reducing prokaryotes are operating there coupling carbon and sulfur cycles in these habitats.
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Affiliation(s)
- Evgenii N. Frolov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
| | - Alexandra V. Gololobova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
| | - Elizaveta A. Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
| | - Nikolay V. Pimenov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
| | - Nikolay A. Chernyh
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
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3
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Thiel J, Spring S, Tindall BJ, Spröer C, Bunk B, Koeksoy E, Ngugi DK, Schink B, Pester M. Desulfolutivibrio sulfoxidireducens gen. nov., sp. nov., isolated from a pyrite-forming enrichment culture and reclassification of Desulfovibrio sulfodismutans as Desulfolutivibrio sulfodismutans comb. nov. Syst Appl Microbiol 2020; 43:126105. [DOI: 10.1016/j.syapm.2020.126105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 10/24/2022]
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Lukina AP, Frank YA, Ivasenko DA, Glukhova LB, Danilova EV, Avakyan MR, Karnachuk OV. Isolation of New Thermophilic Sulfidogens from Microbial Mat Associated with Groundwater Discharge in the Tunkin Valley. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719050096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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5
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Spring S, Sorokin DY, Verbarg S, Rohde M, Woyke T, Kyrpides NC. Sulfate-Reducing Bacteria That Produce Exopolymers Thrive in the Calcifying Zone of a Hypersaline Cyanobacterial Mat. Front Microbiol 2019; 10:862. [PMID: 31068923 PMCID: PMC6491731 DOI: 10.3389/fmicb.2019.00862] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/04/2019] [Indexed: 12/31/2022] Open
Abstract
Calcifying microbial mats in hypersaline environments are important model systems for the study of the earliest ecosystems on Earth that started to appear more than three billion years ago and have been preserved in the fossil record as laminated lithified structures known as stromatolites. It is believed that sulfate-reducing bacteria play a pivotal role in the lithification process by increasing the saturation index of calcium minerals within the mat. Strain L21-Syr-ABT was isolated from anoxic samples of a several centimeters-thick microbialite-forming cyanobacterial mat of a hypersaline lake on the Kiritimati Atoll (Kiribati, Central Pacific). The novel isolate was assigned to the family Desulfovibrionaceae within the Deltaproteobacteria. Available 16S rRNA-based population surveys obtained from discrete layers of the mat indicate that the occurrence of a species-level clade represented by strain L21-Syr-ABT is restricted to a specific layer of the suboxic zone, which is characterized by the presence of aragonitic spherulites. To elucidate a possible function of this sulfate-reducing bacterium in the mineral formation within the mat a comprehensive phenotypic characterization was combined with the results of a comparative genome analysis. Among the determined traits of strain L21-Syr-ABT, several features were identified that could play a role in the precipitation of calcium carbonate: (i) the potential deacetylation of polysaccharides and consumption of substrates such as lactate and sulfate could mobilize free calcium; (ii) under conditions that favor the utilization of formate and hydrogen, the alkalinity engine within the mat is stimulated, thereby increasing the availability of carbonate; (iii) the production of extracellular polysaccharides could provide nucleation sites for calcium mineralization. In addition, our data suggest the proposal of the novel species and genus Desulfohalovibrio reitneri represented by the type strain L21-Syr-ABT (=DSM 26903T = JCM 18662T).
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Susanne Verbarg
- Department Services Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, United States
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6
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Hanson CA, Müller AL, Loy A, Dona C, Appel R, Jørgensen BB, Hubert CRJ. Historical Factors Associated With Past Environments Influence the Biogeography of Thermophilic Endospores in Arctic Marine Sediments. Front Microbiol 2019; 10:245. [PMID: 30873129 PMCID: PMC6403435 DOI: 10.3389/fmicb.2019.00245] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/29/2019] [Indexed: 11/13/2022] Open
Abstract
Selection by the local, contemporary environment plays a prominent role in shaping the biogeography of microbes. However, the importance of historical factors in microbial biogeography is more debatable. Historical factors include past ecological and evolutionary circumstances that may have influenced present-day microbial diversity, such as dispersal and past environmental conditions. Diverse thermophilic sulfate-reducing Desulfotomaculum are present as dormant endospores in marine sediments worldwide where temperatures are too low to support their growth. Therefore, they are dispersed to here from elsewhere, presumably a hot, anoxic habitat. While dispersal through ocean currents must influence their distribution in cold marine sediments, it is not clear whether even earlier historical factors, related to the source habitat where these organisms were once active, also have an effect. We investigated whether these historical factors may have influenced the diversity and distribution of thermophilic endospores by comparing their diversity in 10 Arctic fjord surface sediments. Although community composition varied spatially, clear biogeographic patterns were only evident at a high level of taxonomic resolution (>97% sequence similarity of the 16S rRNA gene) achieved with oligotyping. In particular, the diversity and distribution of oligotypes differed for the two most prominent OTUs (defined using a standard 97% similarity cutoff). One OTU was dominated by a single ubiquitous oligotype, while the other OTU consisted of ten more spatially localized oligotypes that decreased in compositional similarity with geographic distance. These patterns are consistent with differences in historical factors that occurred when and where the taxa were once active, prior to sporulation. Further, the influence of history on biogeographic patterns was only revealed by analyzing microdiversity within OTUs, suggesting that populations within standard OTU-level groupings do not necessarily share a common ecological and evolutionary history.
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Affiliation(s)
- China A Hanson
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Albert L Müller
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.,Austrian Polar Research Institute, Vienna, Austria
| | - Clelia Dona
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ramona Appel
- Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Casey R J Hubert
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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7
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Spring S, Bunk B, Spröer C, Rohde M, Klenk H. Genome biology of a novel lineage of planctomycetes widespread in anoxic aquatic environments. Environ Microbiol 2018; 20:2438-2455. [DOI: 10.1111/1462-2920.14253] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Stefan Spring
- Department MicroorganismsLeibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweig Germany
| | - Boyke Bunk
- Department BioinformaticsLeibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweig Germany
| | - Cathrin Spröer
- Department Central ServicesLeibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweig Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection ResearchBraunschweig Germany
| | - Hans‐Peter Klenk
- Department MicroorganismsLeibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweig Germany
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8
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Watanabe M, Kojima H, Fukui M. Review of Desulfotomaculum species and proposal of the genera Desulfallas gen. nov., Desulfofundulus gen. nov., Desulfofarcimen gen. nov. and Desulfohalotomaculum gen. nov. Int J Syst Evol Microbiol 2018; 68:2891-2899. [PMID: 30028279 DOI: 10.1099/ijsem.0.002915] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Desulfotomaculumis a heterogeneous group of spore-forming sulfate-reducing bacteria. The type species of the genus is Desulfotomaculum nigrificans (Approved Lists 1980) emend. Visser et al. 2014. The results of phylogenetic analysis demonstrated that the genus Desulfotomaculum already has lost the clustering monophyly and was segregated into some distinct groups with low sequence similarity. Major features of the type strains in these groups were compared, and four novel genera, Desulfallas gen. nov., Desulfofundulus gen. nov., Desulfofarcimen gen. nov. and Desulfohalotomaculum gen. nov. were proposed to accommodate species transferred from the genus Desulfotomaculum.
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Affiliation(s)
- Miho Watanabe
- 2Postdoctoral Research Fellow of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-8471, Japan.,1The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Hisaya Kojima
- 1The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Manabu Fukui
- 1The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
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9
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Nancucheo I, Bitencourt JAP, Sahoo PK, Alves JO, Siqueira JO, Oliveira G. Recent Developments for Remediating Acidic Mine Waters Using Sulfidogenic Bacteria. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7256582. [PMID: 29119111 PMCID: PMC5651148 DOI: 10.1155/2017/7256582] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/31/2017] [Accepted: 08/23/2017] [Indexed: 11/24/2022]
Abstract
Acidic mine drainage (AMD) is regarded as a pollutant and considered as potential source of valuable metals. With diminishing metal resources and ever-increasing demand on industry, recovering AMD metals is a sustainable initiative, despite facing major challenges. AMD refers to effluents draining from abandoned mines and mine wastes usually highly acidic that contain a variety of dissolved metals (Fe, Mn, Cu, Ni, and Zn) in much greater concentration than what is found in natural water bodies. There are numerous remediation treatments including chemical (lime treatment) or biological methods (aerobic wetlands and compost bioreactors) used for metal precipitation and removal from AMD. However, controlled biomineralization and selective recovering of metals using sulfidogenic bacteria are advantageous, reducing costs and environmental risks of sludge disposal. The increased understanding of the microbiology of acid-tolerant sulfidogenic bacteria will lead to the development of novel approaches to AMD treatment. We present and discuss several important recent approaches using low sulfidogenic bioreactors to both remediate and selectively recover metal sulfides from AMD. This work also highlights the efficiency and drawbacks of these types of treatments for metal recovery and points to future research for enhancing the use of novel acidophilic and acid-tolerant sulfidogenic microorganisms in AMD treatment.
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Affiliation(s)
- Ivan Nancucheo
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Lientur 1457, 4080871 Concepción, Chile
| | - José A. P. Bitencourt
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, 66055-090 Belém, PA, Brazil
| | - Prafulla K. Sahoo
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, 66055-090 Belém, PA, Brazil
| | - Joner Oliveira Alves
- SENAI Innovation Institute for Mineral Technologies, Av. Com. Brás de Aguiar 548, 66035-405 Belém, PA, Brazil
| | - José O. Siqueira
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, 66055-090 Belém, PA, Brazil
| | - Guilherme Oliveira
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, 66055-090 Belém, PA, Brazil
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Wang Y, Liu S, Su J, Zhang Y, Li J, Sui YQ, Li YY, Wang H, Li H. Three novel structural phenomena in the cellular ontogeny of Oenococcus oeni from northern China. Sci Rep 2017; 7:11265. [PMID: 28900232 PMCID: PMC5595991 DOI: 10.1038/s41598-017-09685-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/25/2017] [Indexed: 01/24/2023] Open
Abstract
Stress resistance and growth are important aspects to consider when engineering Oenococcus oeni strains for winemaking. We identified 3 previously unreported structural phenomena in the cell ontogeny of O. oeni sampled in northern China. We show that budding and binary fission (BBF) occur simultaneously in the growth process; that a novel ‘pomegranate-shaped structure’ (PSS) occurs mainly in the stationary and death phases; and that symbiosis and cyclical phenomena (SCP) occur throughout the various cell growth phases. These observations add to the current knowledge of the cell growth process of O. oeni. BBF, PSS, and SCP sufficiently describe the characteristics of the cellular ontogeny of O. oeni. We highlight a newly identified structure that explains the complex cell growth process. These findings will help understand the growth and development of O. oeni, supplementing the knowledge base of the established phases and providing new perspectives into its complex growth patterns.
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Affiliation(s)
- Yun Wang
- College of Enology, Northwest A&F University, Shaanxi, 712100, China
| | - Shuwen Liu
- College of Enology, Northwest A&F University, Shaanxi, 712100, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Shaanxi, 712100, China
| | - Jing Su
- College of Food Science and Engineering, Northwest A&F University, Shaanxi, 712100, China
| | - Yu Zhang
- College of Enology, Northwest A&F University, Shaanxi, 712100, China
| | - Jing Li
- College of Enology, Northwest A&F University, Shaanxi, 712100, China
| | - Yin-Qiang Sui
- College of Enology, Northwest A&F University, Shaanxi, 712100, China
| | - Ying-Ying Li
- College of Enology, Northwest A&F University, Shaanxi, 712100, China
| | - Hua Wang
- College of Enology, Northwest A&F University, Shaanxi, 712100, China.,Heyang Experimental and Demonstrational Stations for Grape, Shaanxi, 715300, China
| | - Hua Li
- College of Enology, Northwest A&F University, Shaanxi, 712100, China. .,Shaanxi Engineering Research Center for Viti-Viniculture, Shaanxi, 712100, China. .,Heyang Experimental and Demonstrational Stations for Grape, Shaanxi, 715300, China.
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11
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Ben Hania W, Joseph M, Bunk B, Spröer C, Klenk HP, Fardeau ML, Spring S. Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria. Environ Microbiol 2017; 19:1134-1148. [PMID: 27943642 DOI: 10.1111/1462-2920.13639] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/26/2016] [Accepted: 12/01/2016] [Indexed: 01/26/2023]
Abstract
The anaerobic, mesophilic and moderately halophilic strain L21-Spi-D4T was recently isolated from the suboxic zone of a hypersaline cyanobacterial mat using protein-rich extracts of Arthrospira (formerly Spirulina) platensis as substrate. Phylogenetic analyses based on 16S rRNA genes indicated an affiliation of the novel strain with the Bacteroidetes clade MgMjR-022, which is widely distributed and abundant in hypersaline microbial mats and heretofore comprised only sequences of uncultured bacteria. Analyses of the complete genome sequence of strain L21-Spi-D4T revealed a possible specialization on the degradation of cyanobacterial biomass. Besides genes for enzymes degrading specific cyanobacterial proteins a conspicuous transport complex for the polypeptide cyanophycin could be identified that is homologous to typical polysaccharide utilization loci of Bacteroidetes. A distinct and reproducible co-occurrence pattern of environmental 16S rRNA gene sequences of the MgMjR-022 clade and cyanobacteria in the suboxic zone of hypersaline mats points to a specific dependence of members of this clade on decaying cyanobacteria. Based on a comparative analysis of phenotypic, genomic and ecological characteristics we propose to establish the novel taxa Salinivirga cyanobacteriivorans gen. nov., sp. nov., represented by the type strain L21-Spi-D4T , and Salinivirgaceae fam. nov., comprising sequences of the MgMjR-022 clade.
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Affiliation(s)
- Wajdi Ben Hania
- Laboratoire de Microbiologie IRD, MIO, Aix Marseille Université, Marseille, France
| | - Manon Joseph
- Laboratoire de Microbiologie IRD, MIO, Aix Marseille Université, Marseille, France
| | - Boyke Bunk
- Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Marie-Laure Fardeau
- Laboratoire de Microbiologie IRD, MIO, Aix Marseille Université, Marseille, France
| | - Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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12
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Topçuoğlu BD, Stewart LC, Morrison HG, Butterfield DA, Huber JA, Holden JF. Hydrogen Limitation and Syntrophic Growth among Natural Assemblages of Thermophilic Methanogens at Deep-sea Hydrothermal Vents. Front Microbiol 2016; 7:1240. [PMID: 27547206 PMCID: PMC4974244 DOI: 10.3389/fmicb.2016.01240] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/26/2016] [Indexed: 11/13/2022] Open
Abstract
Thermophilic methanogens are common autotrophs at hydrothermal vents, but their growth constraints and dependence on H2 syntrophy in situ are poorly understood. Between 2012 and 2015, methanogens and H2-producing heterotrophs were detected by growth at 80°C and 55°C at most diffuse (7-40°C) hydrothermal vent sites at Axial Seamount. Microcosm incubations of diffuse hydrothermal fluids at 80°C and 55°C demonstrated that growth of thermophilic and hyperthermophilic methanogens is primarily limited by H2 availability. Amendment of microcosms with NH4 (+) generally had no effect on CH4 production. However, annual variations in abundance and CH4 production were observed in relation to the eruption cycle of the seamount. Microcosm incubations of hydrothermal fluids at 80°C and 55°C supplemented with tryptone and no added H2 showed CH4 production indicating the capacity in situ for methanogenic H2 syntrophy. 16S rRNA genes were found in 80°C microcosms from H2-producing archaea and H2-consuming methanogens, but not for any bacteria. In 55°C microcosms, sequences were found from H2-producing bacteria and H2-consuming methanogens and sulfate-reducing bacteria. A co-culture of representative organisms showed that Thermococcus paralvinellae supported the syntrophic growth of Methanocaldococcus bathoardescens at 82°C and Methanothermococcus sp. strain BW11 at 60°C. The results demonstrate that modeling of subseafloor methanogenesis should focus primarily on H2 availability and temperature, and that thermophilic H2 syntrophy can support methanogenesis within natural microbial assemblages and may be an important energy source for thermophilic autotrophs in marine geothermal environments.
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Affiliation(s)
| | - Lucy C. Stewart
- Department of Microbiology, University of Massachusetts, AmherstMA, USA
| | - Hilary G. Morrison
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods HoleMA, USA
| | - David A. Butterfield
- Joint Institute for the Study of Atmosphere and Ocean, University of Washington, SeattleWA, USA
- Pacific Marine Environmental Laboratory, National Oceanic and Atmospheric Administration, SeattleWA, USA
| | - Julie A. Huber
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods HoleMA, USA
| | - James F. Holden
- Department of Microbiology, University of Massachusetts, AmherstMA, USA
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Yang G, Guo J, Zhuang L, Yuan Y, Zhou S. Desulfotomaculum ferrireducens sp. nov., a moderately thermophilic sulfate-reducing and dissimilatory Fe(III)-reducing bacterium isolated from compost. Int J Syst Evol Microbiol 2016; 66:3022-3028. [DOI: 10.1099/ijsem.0.001139] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Guiqin Yang
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Junhui Guo
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China
| | - Li Zhuang
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China
| | - Yong Yuan
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China
| | - Shungui Zhou
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China
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Berlendis S, Ranchou-Peyruse M, Fardeau ML, Lascourrèges JF, Joseph M, Ollivier B, Aüllo T, Dequidt D, Magot M, Ranchou-Peyruse A. Desulfotomaculum aquiferis sp. nov. and Desulfotomaculum profundi sp. nov., isolated from a deep natural gas storage aquifer. Int J Syst Evol Microbiol 2016; 66:4329-4338. [PMID: 27473224 DOI: 10.1099/ijsem.0.001352] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Two novel strictly anaerobic bacteria, strains Bs105T and Bs107T, were isolated from a deep aquifer-derived hydrocarbonoclastic community. The cells were rod-shaped, not motile and had terminal spores. Phylogenetic affiliation and physiological properties revealed that these isolates belong to two novel species of the genus Desulfotomaculum. Optimal growth temperatures for strains Bs105T and Bs107T were 42 and 45 °C, respectively. The estimated G+C content of the genomic DNA was 42.9 and 48.7 mol%. For both strains, the major cellular fatty acid was palmitate (C16 : 0). Specific carbon fatty acid signatures of Gram-positive bacteria (iso-C17 : 0) and sulfate-reducing bacteria (C17 : 0cyc) were also detected. An insertion was revealed in one of the two 16S rRNA gene copies harboured by strain Bs107T. Similar insertions have previously been highlighted among moderately thermophilic species of the genus Desulfotomaculum. Both strains shared the ability to oxidize aromatic acids (Bs105T: hydroquinone, acetophenone, para-toluic acid, 2-phenylethanol, trans-cinnamic acid, 4-hydroxybenzaldehyde, benzyl alcohol, benzoic acid 4-hydroxybutyl ester; Bs107T: ortho-toluic acid, benzoic acid 4-hydroxybutyl ester). The names Desulfotomaculum aquiferis sp. nov. and Desulfotomaculum profundi sp. nov. are proposed for the type strains Bs105T (=DSM 24088T=JCM 31386T) and Bs107T (=DSM 24093T=JCM 31387T).
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Affiliation(s)
- Sabrina Berlendis
- Université de Pau et des Pays de l'Adour, CNRS, IPREM UMR 5254, Equipe Environnement et Microbiologie, Pau 64013, France.,School of Earth and Ocean Sciences, Main building, Park Place, Cardiff University, Cardiff CF10 3AT, UK
| | - Magali Ranchou-Peyruse
- Université de Pau et des Pays de l'Adour, CNRS, IPREM UMR 5254, Equipe Environnement et Microbiologie, Pau 64013, France
| | - Marie-Laure Fardeau
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288 Marseille Cedex 09, France
| | | | - Manon Joseph
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288 Marseille Cedex 09, France
| | - Bernard Ollivier
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288 Marseille Cedex 09, France
| | - Thomas Aüllo
- TIGF - Transport et Infrastructures Gaz France, 40 Avenue de l'Europe, CS20522, Pau 64000, France
| | - David Dequidt
- Storengy - Geosciences Department, Bois-Colombes, France
| | - Michel Magot
- Université de Pau et des Pays de l'Adour, CNRS, IPREM UMR 5254, Equipe Environnement et Microbiologie, Pau 64013, France
| | - Anthony Ranchou-Peyruse
- Université de Pau et des Pays de l'Adour, CNRS, IPREM UMR 5254, Equipe Environnement et Microbiologie, Pau 64013, France
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15
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Spring S, Bunk B, Spröer C, Schumann P, Rohde M, Tindall BJ, Klenk HP. Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum. ISME JOURNAL 2016; 10:2801-2816. [PMID: 27300277 PMCID: PMC5148204 DOI: 10.1038/ismej.2016.84] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 04/15/2016] [Accepted: 04/21/2016] [Indexed: 12/29/2022]
Abstract
The recently isolated strain L21-Fru-ABT represents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. Phylogenetic analyses based on 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-ABT represents a novel species and genus affiliated with a distinct phylum-level lineage originally designated Verrucomicrobia subdivision 5. A survey of environmental 16S rRNA gene sequences revealed that members of this newly recognized phylum are wide-spread and ecologically important in various anoxic environments ranging from hypersaline sediments to wastewater and the intestine of animals. Characteristic phenotypic traits of the novel strain included the formation of extracellular polymeric substances, a Gram-negative cell wall containing peptidoglycan and the absence of odd-numbered cellular fatty acids. Unusual metabolic features deduced from analysis of the genome sequence were the production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking pyruvate kinase and the synthesis of isoprenoids via mevalonate. On the basis of the analyses of phenotypic, genomic and environmental data, it is proposed that strain L21-Fru-ABT and related bacteria are specifically adapted to the utilization of sulfated glycopolymers produced in microbial mats or biofilms.
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Peter Schumann
- Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz-Centre of Infection Research, Braunschweig, Germany
| | - Brian J Tindall
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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16
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Ben Hania W, Joseph M, Schumann P, Bunk B, Fiebig A, Spröer C, Klenk HP, Fardeau ML, Spring S. Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat. Stand Genomic Sci 2015. [PMID: 26203324 PMCID: PMC4511686 DOI: 10.1186/1944-3277-10-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
During a study of the anaerobic microbial community of a lithifying hypersaline microbial mat of Lake 21 on the Kiritimati atoll (Kiribati Republic, Central Pacific) strain L21-RPul-D2T was isolated. The closest phylogenetic neighbor was Spirochaeta africana Z-7692T that shared a 16S rRNA gene sequence identity value of 90% with the novel strain and thus was only distantly related. A comprehensive polyphasic study including determination of the complete genome sequence was initiated to characterize the novel isolate. Cells of strain L21-RPul-D2T had a size of 0.2 – 0.25 × 8–9 μm, were helical, motile, stained Gram-negative and produced an orange carotenoid-like pigment. Optimal conditions for growth were 35°C, a salinity of 50 g/l NaCl and a pH around 7.0. Preferred substrates for growth were carbohydrates and a few carboxylic acids. The novel strain had an obligate fermentative metabolism and produced ethanol, acetate, lactate, hydrogen and carbon dioxide during growth on glucose. Strain L21-RPul-D2T was aerotolerant, but oxygen did not stimulate growth. Major cellular fatty acids were C14:0, iso-C15:0, C16:0 and C18:0. The major polar lipids were an unidentified aminolipid, phosphatidylglycerol, an unidentified phospholipid and two unidentified glycolipids. Whole-cell hydrolysates contained L-ornithine as diagnostic diamino acid of the cell wall peptidoglycan. The complete genome sequence was determined and annotated. The genome comprised one circular chromosome with a size of 3.78 Mbp that contained 3450 protein-coding genes and 50 RNA genes, including 2 operons of ribosomal RNA genes. The DNA G + C content was determined from the genome sequence as 51.9 mol%. There were no predicted genes encoding cytochromes or enzymes responsible for the biosynthesis of respiratory lipoquinones. Based on significant differences to the uncultured type species of the genus Spirochaeta, S. plicatilis, as well as to any other phylogenetically related cultured species it is suggested to place strain L21-RPul-D2T (=DSM 27196T = JCM 18663T) in a novel species and genus, for which the name Salinispira pacifica gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Wajdi Ben Hania
- Laboratoire de Microbiologie IRD, MIO, Aix Marseille Université, Marseille, France
| | - Manon Joseph
- Laboratoire de Microbiologie IRD, MIO, Aix Marseille Université, Marseille, France
| | - Peter Schumann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anne Fiebig
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany ; Current address: Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany ; Current address: School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Marie-Laure Fardeau
- Laboratoire de Microbiologie IRD, MIO, Aix Marseille Université, Marseille, France
| | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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17
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Hao TW, Xiang PY, Mackey HR, Chi K, Lu H, Chui HK, van Loosdrecht MCM, Chen GH. A review of biological sulfate conversions in wastewater treatment. WATER RESEARCH 2014; 65:1-21. [PMID: 25086411 DOI: 10.1016/j.watres.2014.06.043] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/26/2014] [Accepted: 06/30/2014] [Indexed: 06/03/2023]
Abstract
Treatment of waters contaminated with sulfur containing compounds (S) resulting from seawater intrusion, the use of seawater (e.g. seawater flushing, cooling) and industrial processes has become a challenging issue since around two thirds of the world's population live within 150 km of the coast. In the past, research has produced a number of bioengineered systems for remediation of industrial sulfate containing sewage and sulfur contaminated groundwater utilizing sulfate reducing bacteria (SRB). The majority of these studies are specific with SRB only or focusing on the microbiology rather than the engineered application. In this review, existing sulfate based biotechnologies and new approaches for sulfate contaminated waters treatment are discussed. The sulfur cycle connects with carbon, nitrogen and phosphorus cycles, thus a new platform of sulfur based biotechnologies incorporating sulfur cycle with other cycles can be developed, for the removal of sulfate and other pollutants (e.g. carbon, nitrogen, phosphorus and metal) from wastewaters. All possible electron donors for sulfate reduction are summarized for further understanding of the S related biotechnologies including rates and benefits/drawbacks of each electron donor. A review of known SRB and their environmental preferences with regard to bioreactor operational parameters (e.g. pH, temperature, salinity etc.) shed light on the optimization of sulfur conversion-based biotechnologies. This review not only summarizes information from the current sulfur conversion-based biotechnologies for further optimization and understanding, but also offers new directions for sulfur related biotechnology development.
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Affiliation(s)
- Tian-wei Hao
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Peng-yu Xiang
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hamish R Mackey
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Kun Chi
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hui Lu
- SYSU-HKUST Joint Research Centre for Innovative Environmental Technology, Sun Yat-sen University, Guangzhou, China
| | - Ho-kwong Chui
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Guang-Hao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; SYSU-HKUST Joint Research Centre for Innovative Environmental Technology, Sun Yat-sen University, Guangzhou, China.
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18
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Cha IT, Roh SW, Kim SJ, Hong HJ, Lee HW, Lim WT, Rhee SK. Desulfotomaculum tongense sp. nov., a moderately thermophilic sulfate-reducing bacterium isolated from a hydrothermal vent sediment collected from the Tofua Arc in the Tonga Trench. Antonie van Leeuwenhoek 2014; 104:1185-92. [PMID: 24078017 DOI: 10.1007/s10482-013-0040-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/18/2013] [Indexed: 11/28/2022]
Abstract
A novel, strictly anaerobic, moderately thermophilic, endospore-forming, sulfate-reducing bacterium, designated TGB60-1T, was isolated from a hydrothermal sediment vent collected from the Tofua Arc in the Tonga Trench. The strain was characterized phenotypically and phylogenetically. The isolated strain was observed to be Gram-positive, with slightly curved rod-shaped cells and a polar flagellum. Strain TGB60-1T was found to grow anaerobically at 37–60 °C (optimum, 50 °C), at pH 6.0–8.5 (optimum, pH 7.0) and with 1.0–4.0 % (w/v) NaCl (optimum, 3.0 %). The electron acceptors utilised were determined to be sulfate, sulfite, and thiosulfate. Strain TGB60-1T was found to utilise pyruvate and H2 as electron donors. Strain TGB60-1T was determined to be related to representatives of the genus Desulfotomaculum and the closest relatives within this genus were identified as Desulfotomaculum halophilum SEBR 3139T, Desulfotomaculum alkaliphilum S1T and Desulfotomaculum peckii LINDBHT1T (92.7, 92.1, and 91.8 % 16S rRNA gene sequence similarity, respectively). The major fatty acids (>20 %) were identified as C16:0 and C18:1 ω7c. The G+C content of the genomic DNA of this novel bacterium was determined to be 53.9 mol%. Based on this polyphasic taxonomic study, strain TGB60-1T is considered to represent a novel species in the genus Desulfotomaculum, for which the name Desulfotomaculum tongense sp. nov. is proposed. The type strain of D. tongense is strain TGB60-1T (= KTCT 4534T = JCM 18733T).
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19
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Slobodkin AI, Slobodkina GB. Thermophilic prokaryotes from deep subterranean habitats. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714030151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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20
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Aüllo T, Ranchou-Peyruse A, Ollivier B, Magot M. Desulfotomaculum spp. and related gram-positive sulfate-reducing bacteria in deep subsurface environments. Front Microbiol 2013; 4:362. [PMID: 24348471 PMCID: PMC3844878 DOI: 10.3389/fmicb.2013.00362] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 11/14/2013] [Indexed: 11/25/2022] Open
Abstract
Gram-positive spore-forming sulfate reducers and particularly members of the genus Desulfotomaculum are commonly found in the subsurface biosphere by culture based and molecular approaches. Due to their metabolic versatility and their ability to persist as endospores. Desulfotomaculum spp. are well-adapted for colonizing environments through a slow sedimentation process. Because of their ability to grow autotrophically (H2/CO2) and produce sulfide or acetate, these microorganisms may play key roles in deep lithoautotrophic microbial communities. Available data about Desulfotomaculum spp. and related species from studies carried out from deep freshwater lakes, marine sediments, oligotrophic and organic rich deep geological settings are discussed in this review.
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Affiliation(s)
- Thomas Aüllo
- Equipe Environnement et Microbiologie, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM UMR 5254), Université de Pau et des Pays de l'AdourPau, France
| | - Anthony Ranchou-Peyruse
- Equipe Environnement et Microbiologie, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM UMR 5254), Université de Pau et des Pays de l'AdourPau, France
| | - Bernard Ollivier
- Mediterranean Institute of Oceanology (MIO), Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, UM 110Marseille, France
| | - Michel Magot
- Equipe Environnement et Microbiologie, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM UMR 5254), Université de Pau et des Pays de l'AdourPau, France
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21
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Spring S, Riedel T, Spröer C, Yan S, Harder J, Fuchs BM. Taxonomy and evolution of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria: description of Luminiphilus syltensis gen. nov., sp. nov., reclassification of Haliea rubra as Pseudohaliea rubra gen. nov., comb. nov., and emendation of Chromatocurvus halotolerans. BMC Microbiol 2013; 13:118. [PMID: 23705883 PMCID: PMC3679898 DOI: 10.1186/1471-2180-13-118] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/16/2013] [Indexed: 12/27/2022] Open
Abstract
Background Aerobic gammaproteobacteria affiliated to the OM60/NOR5 clade are widespread in saline environments and of ecological importance in several marine ecosystems, especially the euphotic zone of coastal areas. Within this group a close relationship between aerobic anoxygenic photoheterotrophs and non-phototrophic members has been found. Results Several strains of aerobic red-pigmented bacteria affiliated to the OM60/NOR5 clade were obtained from tidal flat sediment samples at the island of Sylt (North Sea, Germany). Two of the novel isolates, Rap1red and Ivo14T, were chosen for an analysis in detail. Strain Rap1red shared a 16S rRNA sequence identity of 99% with the type strain of Congregibacter litoralis and was genome-sequenced to reveal the extent of genetic microheterogeneity among closely related strains within this clade. In addition, a draft genome sequence was obtained from the isolate Ivo14T, which belongs to the environmental important NOR5-1 lineage that contains so far no cultured representative with a comprehensive description. Strain Ivo14T was characterized using a polyphasic approach and compared with other red-pigmented members of the OM60/NOR5 clade, including Congregibacter litoralis DSM 17192T, Haliea rubra DSM 19751T and Chromatocurvus halotolerans DSM 23344T. All analyzed strains contained bacteriochlorophyll a and spirilloxanthin as photosynthetic pigments. Besides a detailed phenotypic characterization including physiological and chemotaxonomic traits, sequence information based on protein-coding genes and a comparison of draft genome data sets were used to identify possible features characteristic for distinct taxa within this clade. Conclusions Comparative sequence analyses of the pufLM genes of genome-sequenced representatives of the OM60/NOR5 clade indicated that the photosynthetic apparatus of these species was derived from a common ancestor and not acquired by multiple horizontal gene transfer from phylogenetically distant species. An affiliation of the characterized bacteriochlorophyll a-containing strains to different genera was indicated by significant phenotypic differences and pufLM nucleotide sequence identity values below 82%. The revealed high genotypic and phenotypic diversity of closely related strains within this phylogenetic group reflects a rapid evolution and frequent niche separation in the OM60/NOR5 clade, which is possibly driven by the necessities of an adaptation to oligotrophic marine habitats.
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Affiliation(s)
- Stefan Spring
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstr 7B, Braunschweig 38124, Germany.
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Klein R, Tischler JS, Mühling M, Schlömann M. Bioremediation of mine water. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 141:109-72. [PMID: 24357145 DOI: 10.1007/10_2013_265] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Caused by the oxidative dissolution of sulfide minerals, mine waters are often acidic and contaminated with high concentrations of sulfates, metals, and metalloids. Because the so-called acid mine drainage (AMD) affects the environment or poses severe problems for later use, treatment of these waters is required. Therefore, various remediation strategies have been developed to remove soluble metals and sulfates through immobilization using physical, chemical, and biological approaches. Conventionally, iron and sulfate-the main pollutants in mine waters-are removed by addition of neutralization reagents and subsequent chemical iron oxidation and sulfate mineral precipitation. Biological treatment strategies take advantage of the ability of microorganisms that occur in mine waters to metabolize iron and sulfate. As a rule, these can be grouped into oxidative and reductive processes, reflecting the redox state of mobilized iron (reduced form) and sulfur (oxidized form) in AMD. Changing the redox states of iron and sulfur results in iron and sulfur compounds with low solubility, thus leading to their precipitation and removal. Various techniques have been developed to enhance the efficacy of these microbial processes, as outlined in this review.
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Affiliation(s)
- Robert Klein
- Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
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23
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Abstract
Sulfur is central to the metabolisms of many organisms that inhabit extreme environments. While biotic and abiotic cycling of organic sulfur compounds has been well documented in low-temperature anaerobic environments, cycling of organic sulfur in hydrothermal environments has received less attention. Recently published thermodynamic data have been used to estimate aqueous alkyl thiol and sulfide activities in deep-sea hydrothermal systems. Here we use geochemical mixing models to predict fluid compositions that result from mixing end-member hydrothermal fluid from the East Pacific Rise with bottom seawater. These fluid compositions are combined with estimates of methanethiol and dimethylsulfide activities to evaluate energy yields for potential organic sulfur-based metabolisms under hydrothermal conditions. Aerobic respiration has the highest energy yields (over -240 kJ/mol e⁻) at lower temperature; however, oxygen is unlikely to persist at high temperatures, restricting aerobic respiration to mesophilic communities. Nitrite reduction to N₂ has the highest energy yields at higher temperatures (greater than ∼40 °C). Nitrate and nitrite reduction to ammonium also yield significant energy (up to -70 kJ/mol e⁻). Much lower, but still feasible energy yields are calculated for sulfate reduction, disproportionation, and reduction with H₂. Organic compound family and the activity of methanethiol and dimethylsulfide were less important than metabolic strategy in determining overall energy yields. All metabolic strategies considered were exergonic within some portion of the mixing regime suggesting that organic sulfur-based metabolisms may be prevalent within deep-sea hydrothermal vent microbial communities.
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Affiliation(s)
- Karyn L Rogers
- Department of Geological Sciences, University of Missouri, Columbia, MO 65203, USA.
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24
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Spring S, Lünsdorf H, Fuchs BM, Tindall BJ. The photosynthetic apparatus and its regulation in the aerobic gammaproteobacterium Congregibacter litoralis gen. nov., sp. nov. PLoS One 2009; 4:e4866. [PMID: 19287491 PMCID: PMC2654016 DOI: 10.1371/journal.pone.0004866] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Accepted: 02/16/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND There is accumulating evidence that in some marine environments aerobic bacteriochlorophyll a-producing bacteria represent a significant part of the microbial population. The interaction of photosynthesis and carbon metabolism in these interesting bacteria is still largely unknown and requires further investigation in order to estimate their contribution to the marine carbon cycle. METHODOLOGY/PRINCIPAL FINDINGS Here, we analyzed the structure, composition and regulation of the photosynthetic apparatus in the obligately aerobic marine gammaproteobacterium KT71(T). Photoheterotrophically grown cells were characterized by a poorly developed lamellar intracytoplasmic membrane system, a type 1 light-harvesting antenna complex and a photosynthetic reaction center associated with a tetraheme cytochrome c. The only photosynthetic pigments produced were bacteriochlorophyll a and spirilloxanthin. Under semiaerobic conditions KT71(T) cells expressing a photosynthetic apparatus showed a light-dependent increase of growth yield in the range of 1.3-2.5 fold. The expression level of the photosynthetic apparatus depended largely on the utilized substrate, the intermediary carbon metabolism and oxygen tension. In addition, pigment synthesis was strongly influenced by light, with blue light exerting the most significant effect, implicating that proteins containing a BLUF domain may be involved in regulation of the photosynthetic apparatus. Several phenotypic traits in KT71(T) could be identified that correlated with the assumed redox state of growing cells and thus could be used to monitor the cellular redox state under various incubation conditions. CONCLUSIONS/SIGNIFICANCE In a hypothetical model that explains the regulation of the photosynthetic apparatus in strain KT71(T) we propose that the expression of photosynthesis genes depends on the cellular redox state and is maximal under conditions that allow a balanced membrane redox state. So far, bacteria capable of an obligately aerobic, photosynthetic metabolism constitute a unique phenotype within the class Gammaproteobacteria, so that it is justified to propose a new genus and species, Congregibacter litoralis gen. nov, sp. nov., represented by the type strain KT71(T) ( = DSM 17192(T) = NBRC 104960(T)).
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Affiliation(s)
- Stefan Spring
- Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.
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van Houten BHGW, Meulepas RJW, van Doesburg W, Smidt H, Muyzer G, Stams AJM. Desulfovibrio paquesii sp. nov., a hydrogenotrophic sulfate-reducing bacterium isolated from a synthesis-gas-fed bioreactor treating zinc- and sulfate-rich wastewater. Int J Syst Evol Microbiol 2009; 59:229-33. [DOI: 10.1099/ijs.0.65616-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Selesi D, Meckenstock RU. Anaerobic degradation of the aromatic hydrocarbon biphenyl by a sulfate-reducing enrichment culture. FEMS Microbiol Ecol 2009; 68:86-93. [PMID: 19187215 DOI: 10.1111/j.1574-6941.2009.00652.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The aromatic hydrocarbon biphenyl is a widely distributed environmental pollutant. Whereas the aerobic degradation of biphenyl has been extensively studied, knowledge of the anaerobic biphenyl-oxidizing bacteria and their biochemical degradation pathway is scarce. Here, we report on an enrichment culture that oxidized biphenyl completely to carbon dioxide under sulfate-reducing conditions. The biphenyl-degrading culture was dominated by two distinct bacterial species distantly affiliated with the Gram-positive genus Desulfotomaculum. Moreover, the enrichment culture has the ability to grow with benzene and a mixture of anthracene and phenanthrene as the sole source of carbon, but here the microbial community composition differed substantially from the biphenyl-grown culture. Biphenyl-4-carboxylic acid was identified as an intermediate in the biphenyl-degrading culture. Moreover, 4-fluorobiphenyl was converted cometabolically with biphenyl because in addition to the biphenyl-4-carboxylic acid, a compound identified as its fluorinated analog was observed. These findings are consistent with the general pattern in the anaerobic catabolism of many aromatic hydrocarbons where carboxylic acids are found to be central metabolites.
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Affiliation(s)
- Drazenka Selesi
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
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27
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Desulfonauticus autotrophicus sp. nov., a novel thermophilic sulfate-reducing bacterium isolated from oil-production water and emended description of the genus Desulfonauticus. Extremophiles 2008; 13:247-55. [DOI: 10.1007/s00792-008-0212-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 11/10/2008] [Indexed: 10/21/2022]
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Abstract
Thermophilic anaerobes are Archaea and Bacteria that grow optimally at temperatures of 50 degrees C or higher and do not require the use of O(2) as a terminal electron acceptor for growth. The prokaryotes with this type of physiology are studied for a variety of reasons, including (a) to understand how life can thrive under extreme conditions, (b) for their biotechnological potential, and (c) because anaerobic thermophiles are thought to share characteristics with the early evolutionary life forms on Earth. Over 300 species of thermophilic anaerobes have been described; most have been isolated from thermal environments, but some are from mesobiotic environments, and others are from environments with temperatures below 0 degrees C. In this overview, the authors outline the phylogenetic and physiological diversity of thermophilic anaerobes as currently known. The purpose of this overview is to convey the incredible diversity and breadth of metabolism within this subset of anaerobic microorganisms.
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Affiliation(s)
- Isaac D Wagner
- 212 Biological Sciences Building, 1000 Cedar Street, University of Georgia, Athens, GA 30602-2605, USA
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Kaksonen AH, Spring S, Schumann P, Kroppenstedt RM, Puhakka JA. Desulfotomaculum alcoholivorax sp. nov., a moderately thermophilic, spore-forming, sulfate-reducer isolated from a fluidized-bed reactor treating acidic metal- and sulfate-containing wastewater. Int J Syst Evol Microbiol 2008; 58:833-8. [DOI: 10.1099/ijs.0.65025-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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30
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Kaksonen AH, Spring S, Schumann P, Kroppenstedt RM, Puhakka JA. Desulfurispora thermophila gen. nov., sp. nov., a thermophilic, spore-forming sulfate-reducer isolated from a sulfidogenic fluidized-bed reactor. Int J Syst Evol Microbiol 2007; 57:1089-1094. [PMID: 17473265 DOI: 10.1099/ijs.0.64593-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterium was isolated from a sulfidogenic fluidized-bed reactor treating acidic metal- and sulfate-containing water. The strain, designated RA50E1T, was rod-shaped and motile. The strain grew at 40–67 °C (optimum growth at 59–61 °C) and pH 6.4–7.9 (optimum growth at pH 7.0–7.3). The strain tolerated up to 1 % NaCl. Sulfate, sulfite, thiosulfate and elemental sulfur were used as electron acceptors, but not nitrate, nitrite or iron(III). Electron donors utilized were H2/CO2 (80 : 20, v/v), alcohols, various carboxylic acids and some sugars. Fermentative growth occurred on lactate and pyruvate. The cell wall contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone MK-7. Major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 0. Strain RA50E1T was distantly related to representatives of the genera Desulfotomaculum, Pelotomaculum, Sporotomaculum and Cryptanaerobacter. On the basis of 16S rRNA gene sequence data, the strain cannot be assigned to any known genus. Based on the phenotypic and phylogenetic features of strain RA50E1T, it is proposed that the strain represents a novel species in a new genus, for which the name Desulfurispora thermophila gen. nov., sp. nov. is proposed. The type strain of Desulfurispora thermophila is RA50E1T (=DSM 16022T=JCM 14018T).
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MESH Headings
- Alcohols/metabolism
- Bacterial Typing Techniques
- Carbohydrate Metabolism
- Carbon Dioxide/metabolism
- Carboxylic Acids/metabolism
- Cell Wall/chemistry
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Diaminopimelic Acid/isolation & purification
- Fatty Acids/analysis
- Genes, rRNA
- Gram-Positive Endospore-Forming Rods/chemistry
- Gram-Positive Endospore-Forming Rods/classification
- Gram-Positive Endospore-Forming Rods/genetics
- Gram-Positive Endospore-Forming Rods/isolation & purification
- Gram-Positive Endospore-Forming Rods/metabolism
- Hydrogen/metabolism
- Hydrogen-Ion Concentration
- Microscopy, Phase-Contrast
- Molecular Sequence Data
- Movement
- Oxidation-Reduction
- Phylogeny
- Quinones/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/metabolism
- Sulfates/metabolism
- Sulfites/metabolism
- Sulfur/metabolism
- Temperature
- Thiosulfates/metabolism
- Water Microbiology
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Affiliation(s)
- Anna H Kaksonen
- Institute of Environmental Engineering and Biotechnology, Tampere University of Technology, Tampere, Finland
| | - Stefan Spring
- DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Peter Schumann
- DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Jaakko A Puhakka
- Institute of Environmental Engineering and Biotechnology, Tampere University of Technology, Tampere, Finland
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Kaksonen AH, Spring S, Schumann P, Kroppenstedt RM, Puhakka JA. Desulfovirgula thermocuniculi gen. nov., sp. nov., a thermophilic sulfate-reducer isolated from a geothermal underground mine in Japan. Int J Syst Evol Microbiol 2007; 57:98-102. [PMID: 17220449 DOI: 10.1099/ijs.0.64655-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterial strain, designated RL80JIVT, was isolated from a geothermally active underground mine in Japan. Cells were rod-shaped and motile. The temperature and pH ranges for growth were 61–80 °C (optimum at 69–72 °C) and pH 6.4–7.9 (optimum at pH 6.8–7.3), and the strain tolerated up to 0.5 % NaCl. Strain RL80JIVT utilized sulfate, sulfite, thiosulfate and elemental sulfur as electron acceptors. Electron donors utilized were H2 in the presence of CO2, and carboxylic acids. Fermentative growth occurred on lactate and pyruvate. The cell wall contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone MK-7. Major whole-cell fatty acids were iso-C15 : 0, iso-C17 : 0 and C16 : 0. Strain RL80JIVT was found to be affiliated with the thiosulfate-reducer Thermanaeromonas toyohensis DSM 14490T (90.9 % 16S rRNA gene sequence similarity) and with the sulfate-reducer Desulfotomaculum thermocisternum DSM 10259T (90.0 % similarity). Strain RL80JIVT is therefore considered to represent a novel species of a new genus, for which the name Desulfovirgula thermocuniculi gen. nov., sp. nov. is proposed. The type strain of Desulfovirgula thermocuniculi is RL80JIVT (=DSM 16036T=JCM 13928T).
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Affiliation(s)
- Anna H Kaksonen
- Institute of Environmental Engineering and Biotechnology, Tampere University of Technology, Tampere, Finland
| | - Stefan Spring
- DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Peter Schumann
- DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Jaakko A Puhakka
- Institute of Environmental Engineering and Biotechnology, Tampere University of Technology, Tampere, Finland
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