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Niu J, Wan Y, Ma Z, Wang Z, Dong W, Su X, Shen X, Zhai Y. Driving mechanism of different nutrient conditions on microbial mediated nitrate reduction in magnetite-present river infiltration zone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171963. [PMID: 38537835 DOI: 10.1016/j.scitotenv.2024.171963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/07/2024] [Accepted: 03/23/2024] [Indexed: 04/17/2024]
Abstract
Significant research is focused on the ability of riparian zones to reduce groundwater nitrate contamination. Owing to the extremely high redox activity of nitrate, naturally existing electron donors, such as organic matter and iron minerals, are crucial in facilitating nitrate reduction in the riparian zone. Here, we examined the coexistence of magnetite, an iron mineral, and nitrate, a frequently observed coexisting system in sediments, to investigate nitrate reduction features at various C/N ratios and evaluate the response of microbial communities to these settings. Additionally, we aimed to use this information as a foundation for examining the effect of nutritional conditions on the nitrate reduction process in magnetite-present environments. These results emphasise the significance of organic matter in enabling dissimilatory nitrate reduction to ammonium (DNRA) and enhancing the connection between nitrate reduction and iron in sedimentary environments. In the later phases of nitrate reduction, nitrogen fixation was the prevailing process in low-carbon environments, whereas high-carbon environments tended to facilitate the breakdown of organic nitrogen. High-throughput sequencing analysis revealed a robust association between C/N ratios and alterations in microbial community composition, providing insights into notable modifications in essential functioning microorganisms. The nitrogen-fixing bacterium Ralstonia is more abundant in ecosystems with scarce organic matter. In contrast, in settings rich in organic matter, microorganisms, such as Acinetobacter and Clostridia, which may produce ammonia, play crucial roles. Moreover, the population of iron bacteria grows in such an environment. Hence, this study proposes that C/N ratios can influence Fe(II)/Fe(III) conversions and simultaneously affect the process of nitrate reduction by shaping the composition of specific microbial communities.
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Affiliation(s)
- Jia Niu
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Yuyu Wan
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China.
| | - Zhe Ma
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Zhen Wang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Weihong Dong
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Xiaosi Su
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Xiaofang Shen
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, People's Republic of China; College of New Energy and Environment, Jilin University, Changchun 130021, People's Republic of China; Institute of Water Resources and Environment, Jilin University, Changchun 130021, People's Republic of China
| | - Yuanzheng Zhai
- College of Water Sciences, Beijing Normal University, Beijing 100875, People's Republic of China
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Khomyakova MA, Merkel AY, Segliuk VS, Slobodkin AI. Desulfatitalea alkaliphila sp. nov., an alkalipilic sulfate- and arsenate- reducing bacterium isolated from a terrestrial mud volcano. Extremophiles 2023; 27:12. [PMID: 37178152 DOI: 10.1007/s00792-023-01297-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
A novel alkaliphilic sulfate-reducing bacterium, strain M08butT, was isolated from a salsa lake of terrestrial mud volcano (Taman Peninsula, Russia). Cells were rod-shaped, motile and Gram-stain-negative. The temperature range for growth was 15-42 °C (optimum at 30 °C). The pH range for growth was 7.0-11.0, with an optimum at pH 8.5-9.0 Strain M08butT used sulfate, thiosulfate, sulfite, dimethyl sulfoxide and arsenate as electron acceptors. Acetate, formate, butyrate, fumarate, succinate, glycerol and pyruvate were utilized as electron donors with sulfate. Fermentative growth was observed with fumarate, pyruvate, crotonate. Strain M08butT grew chemolithoautotrophically with H2 and CO2. The G + C content of the genomic DNA was 60.1%. The fatty acid profile of strain M08butT was characterized by the presence of anteiso-C15:0 as the major component (68.8%). The closest phylogenetic relative of strain M08butT was Desulfatitalea tepidiphila (the order Desulfobacterales) with 96.3% 16S rRNA gene sequence similarity. Based on the phenotypic, genotypic and phylogenetic characteristics of the isolate, strain M08butT is considered to represent a novel species of the genus Desulfatitalea, with proposed name Desulfatitalea alkaliphila sp. nov. The type strain of Desulfatitalea alkaliphila is M08butT (= KCTC 25382T = VKM B-3560T = DSM 113909T = JCM 39202T = UQM 41473T).
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Affiliation(s)
- M A Khomyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, Bld. 2, 119071, Moscow, Russia.
| | - A Yu Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, Bld. 2, 119071, Moscow, Russia
| | - V S Segliuk
- Gubkin University, Leninskiy Prospect, 65/1, 119991, Moscow, Russia
| | - A I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, Bld. 2, 119071, Moscow, Russia
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Composition and Metabolic Potential of Fe(III)-Reducing Enrichment Cultures of Methanotrophic ANME-2a Archaea and Associated Bacteria. Microorganisms 2023; 11:microorganisms11030555. [PMID: 36985129 PMCID: PMC10052568 DOI: 10.3390/microorganisms11030555] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
The key microbial group involved in anaerobic methane oxidation is anaerobic methanotrophic archaea (ANME). From a terrestrial mud volcano, we enriched a microbial community containing ANME-2a, using methane as an electron donor, Fe(III) oxide (ferrihydrite) as an electron acceptor, and anthraquinone-2,6-disulfonate as an electron shuttle. Ferrihydrite reduction led to the formation of a black, highly magnetic precipitate. A significant relative abundance of ANME-2a in batch cultures was observed over five subsequent transfers. Phylogenetic analysis revealed that, in addition to ANME-2a, two bacterial taxa belonging to uncultured Desulfobulbaceae and Anaerolineaceae were constantly present in all enrichments. Metagenome-assembled genomes (MAGs) of ANME-2a contained a complete set of genes for methanogenesis and numerous genes of multiheme c-type cytochromes (MHC), indicating the capability of methanotrophs to transfer electrons to metal oxides or to a bacterial partner. One of the ANME MAGs encoded respiratory arsenate reductase (Arr), suggesting the potential for a direct coupling of methane oxidation with As(V) reduction in the single microorganism. The same MAG also encoded uptake [NiFe] hydrogenase, which is uncommon for ANME-2. The MAG of uncultured Desulfobulbaceae contained genes of dissimilatory sulfate reduction, a Wood–Ljungdahl pathway for autotrophic CO2 fixation, hydrogenases, and 43 MHC. We hypothesize that uncultured Desulfobulbaceae is a bacterial partner of ANME-2a, which mediates extracellular electron transfer to Fe(III) oxide.
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Dutra J, Gomes R, Yupanqui García GJ, Romero-Cale DX, Santos Cardoso M, Waldow V, Groposo C, Akamine RN, Sousa M, Figueiredo H, Azevedo V, Góes-Neto A. Corrosion-influencing microorganisms in petroliferous regions on a global scale: systematic review, analysis, and scientific synthesis of 16S amplicon metagenomic studies. PeerJ 2023; 11:e14642. [PMID: 36655046 PMCID: PMC9841911 DOI: 10.7717/peerj.14642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/05/2022] [Indexed: 01/15/2023] Open
Abstract
The objective of the current systematic review was to evaluate the taxonomic composition and relative abundance of bacteria and archaea associated with the microbiologically influenced corrosion (MIC), and the prediction of their metabolic functions in different sample types from oil production and transport structures worldwide. To accomplish this goal, a total of 552 published studies on the diversity of microbial communities using 16S amplicon metagenomics in oil and gas industry facilities indexed in Scopus, Web of Science, PubMed and OnePetro databases were analyzed on 10th May 2021. The selection of articles was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Only studies that performed amplicon metagenomics to obtain the microbial composition of samples from oil fields were included. Studies that evaluated oil refineries, carried out amplicon metagenomics directly from cultures, and those that used DGGE analysis were removed. Data were thoroughly investigated using multivariate statistics by ordination analysis, bivariate statistics by correlation, and microorganisms' shareability and uniqueness analysis. Additionally, the full deposited databases of 16S rDNA sequences were obtained to perform functional prediction. A total of 69 eligible articles was included for data analysis. The results showed that the sulfidogenic, methanogenic, acid-producing, and nitrate-reducing functional groups were the most expressive, all of which can be directly involved in MIC processes. There were significant positive correlations between microorganisms in the injection water (IW), produced water (PW), and solid deposits (SD) samples, and negative correlations in the PW and SD samples. Only the PW and SD samples displayed genera common to all petroliferous regions, Desulfotomaculum and Thermovirga (PW), and Marinobacter (SD). There was an inferred high microbial activity in the oil fields, with the highest abundances of (i) cofactor, (ii) carrier, and (iii) vitamin biosynthesis, associated with survival metabolism. Additionally, there was the presence of secondary metabolic pathways and defense mechanisms in extreme conditions. Competitive or inhibitory relationships and metabolic patterns were influenced by the physicochemical characteristics of the environments (mainly sulfate concentration) and by human interference (application of biocides and nutrients). Our worldwide baseline study of microbial communities associated with environments of the oil and gas industry will greatly facilitate the establishment of standardized approaches to control MIC.
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Affiliation(s)
- Joyce Dutra
- Graduate Program in Microbiology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rosimeire Gomes
- Graduate Program in Microbiology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Glen Jasper Yupanqui García
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Mariana Santos Cardoso
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vinicius Waldow
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Rubens N. Akamine
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maira Sousa
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Henrique Figueiredo
- Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Allioux M, Yvenou S, Godfroy A, Shao Z, Jebbar M, Alain K. Genome analysis of a new sulphur disproportionating species Thermosulfurimonas strain F29 and comparative genomics of sulfur-disproportionating bacteria from marine hydrothermal vents. Microb Genom 2022; 8. [PMID: 36136081 DOI: 10.1099/mgen.0.000865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This paper reports on the genome analysis of strain F29 representing a new species of the genus Thermosulfurimonas. This strain, isolated from the Lucky Strike hydrothermal vent field on the Mid-Atlantic Ridge, is able to grow by disproportionation of S0 with CO2 as a carbon source. Strain F29 possesses a genome of 2,345,565 bp, with a G+C content of 58.09%, and at least one plasmid. The genome analysis revealed complete sets of genes for CO2 fixation via the Wood-Ljungdahl pathway, for sulphate-reduction and for hydrogen oxidation, suggesting the involvement of the strain into carbon, sulphur, and hydrogen cycles of deep-sea hydrothermal vents. Strain F29 genome encodes also several CRISPR sequences, suggesting that the strain may be subjected to viral attacks. Comparative genomics was carried out to decipher sulphur disproportionation pathways. Genomes of sulphur-disproportionating bacteria from marine hydrothermal vents were compared to the genomes of non-sulphur-disproportionating bacteria. This analysis revealed the ubiquitous presence in these genomes of a molybdopterin protein consisting of a large and a small subunit, and an associated chaperone. We hypothesize that these proteins may be involved in the process of elemental sulphur disproportionation.
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Affiliation(s)
- Maxime Allioux
- Univ Brest, CNRS, Ifremer, Unité Biologie et Ecologie des Ecosystèmes marins Profonds BEEP, UMR 6197, IRP 1211 MicrobSea, IUEM, Rue Dumont d'Urville, F-29280 Plouzané, France
| | - Stéven Yvenou
- Univ Brest, CNRS, Ifremer, Unité Biologie et Ecologie des Ecosystèmes marins Profonds BEEP, UMR 6197, IRP 1211 MicrobSea, IUEM, Rue Dumont d'Urville, F-29280 Plouzané, France
| | - Anne Godfroy
- Univ Brest, CNRS, Ifremer, Unité Biologie et Ecologie des Ecosystèmes marins Profonds BEEP, UMR 6197, IRP 1211 MicrobSea, IUEM, Rue Dumont d'Urville, F-29280 Plouzané, France
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China
| | - Mohamed Jebbar
- Univ Brest, CNRS, Ifremer, Unité Biologie et Ecologie des Ecosystèmes marins Profonds BEEP, UMR 6197, IRP 1211 MicrobSea, IUEM, Rue Dumont d'Urville, F-29280 Plouzané, France
| | - Karine Alain
- Univ Brest, CNRS, Ifremer, Unité Biologie et Ecologie des Ecosystèmes marins Profonds BEEP, UMR 6197, IRP 1211 MicrobSea, IUEM, Rue Dumont d'Urville, F-29280 Plouzané, France
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Nixon SL, Bonsall E, Cockell CS. Limitations of microbial iron reduction under extreme conditions. FEMS Microbiol Rev 2022; 46:6645348. [PMID: 35849069 PMCID: PMC9629499 DOI: 10.1093/femsre/fuac033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/23/2022] [Accepted: 07/15/2022] [Indexed: 01/09/2023] Open
Abstract
Microbial iron reduction is a widespread and ancient metabolism on Earth, and may plausibly support microbial life on Mars and beyond. Yet, the extreme limits of this metabolism are yet to be defined. To investigate this, we surveyed the recorded limits to microbial iron reduction in a wide range of characterized iron-reducing microorganisms (n = 141), with a focus on pH and temperature. We then calculated Gibbs free energy of common microbially mediated iron reduction reactions across the pH-temperature habitability space to identify thermodynamic limits. Comparing predicted and observed limits, we show that microbial iron reduction is generally reported at extremes of pH or temperature alone, but not when these extremes are combined (with the exception of a small number of acidophilic hyperthermophiles). These patterns leave thermodynamically favourable combinations of pH and temperature apparently unoccupied. The empty spaces could be explained by experimental bias, but they could also be explained by energetic and biochemical limits to iron reduction at combined extremes. Our data allow for a review of our current understanding of the limits to microbial iron reduction at extremes and provide a basis to test more general hypotheses about the extent to which biochemistry establishes the limits to life.
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Affiliation(s)
- Sophie L Nixon
- Corresponding author: Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. E-mail:
| | - Emily Bonsall
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, United Kingdom
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Kochetkova TV, Podosokorskaya OA, Elcheninov AG, Kublanov IV. Diversity of Thermophilic Prokaryotes Inhabiting Russian Natural Hot Springs. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Pseudodesulfovibrio alkaliphilus, sp. nov., an alkaliphilic sulfate-reducing bacterium isolated from a terrestrial mud volcano. Antonie van Leeuwenhoek 2021; 114:1387-1397. [PMID: 34212258 DOI: 10.1007/s10482-021-01608-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/23/2021] [Indexed: 10/21/2022]
Abstract
The diversity of anaerobic microorganisms in terrestrial mud volcanoes is largely unexplored. Here we report the isolation of a novel sulfate-reducing alkaliphilic bacterium (strain F-1T) from a terrestrial mud volcano located at the Taman peninsula, Russia. Cells of strain F-1T were Gram-negative motile vibrios with a single polar flagellum; 2.0-4.0 µm in length and 0.5 µm in diameter. The temperature range for growth was 6-37 °C, with an optimum at 24 °C. The pH range for growth was 7.0-10.5, with an optimum at pH 9.5. Strain F-1T utilized lactate, pyruvate, and molecular hydrogen as electron donors and sulfate, sulfite, thiosulfate, elemental sulfur, fumarate or arsenate as electron acceptors. In the presence of sulfate, the end products of lactate oxidation were acetate, H2S and CO2. Lactate and pyruvate could also be fermented. The major product of lactate fermentation was acetate. The main cellular fatty acids were anteiso-C15:0, C16:0, C18:0, and iso-C17:1ω8. Phylogenetic analysis revealed that strain F-1T was most closely related to Pseudodesulfovibrio aespoeensis (98.05% similarity). The total size of the genome of the novel isolate was 3.23 Mb and the genomic DNA G + C content was 61.93 mol%. The genome contained all genes essential for dissimilatory sulfate reduction. We propose to assign strain F-1T to the genus Pseudodesulfovibrio, as a new species, Pseudodesulfovibrio alkaliphilus sp. nov. The type strain is F-1T (= KCTC 15918T = VKM B-3405T).
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Zeng X, Alain K, Shao Z. Microorganisms from deep-sea hydrothermal vents. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:204-230. [PMID: 37073341 PMCID: PMC10077256 DOI: 10.1007/s42995-020-00086-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/17/2020] [Indexed: 05/03/2023]
Abstract
With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-020-00086-4.
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Affiliation(s)
- Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E UMR6197, Univ Brest, CNRS, IFREMER, F-29280 Plouzané, France
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
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Magalhães CP, Ribeiro JA, Guedes AP, Arantes AL, Sousa DZ, Stams AJM, Alves MM, Cavaleiro AJ. Co-cultivation of Thermoanaerobacter strains with a methanogenic partner enhances glycerol conversion. Microb Biotechnol 2020; 13:962-973. [PMID: 32154666 PMCID: PMC7264899 DOI: 10.1111/1751-7915.13506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/07/2019] [Accepted: 10/13/2019] [Indexed: 11/30/2022] Open
Abstract
Glycerol-rich waste streams produced by the biodiesel, bioethanol and oleochemical industries can be treated and valorized by anaerobic microbial communities to produce methane. As current knowledge of the microorganisms involved in thermophilic glycerol conversion to methane is scarce, thermophilic glycerol-degrading methanogenic communities were enriched. A co-culture of Thermoanaerobacter and Methanothermobacter species was obtained, pointing to a non-obligately syntrophic glycerol degradation. This hypothesis was further studied by incubating Thermoanaerobacter brockii subsp. finnii and T. wiegelii with glycerol (10 mM) in pure culture and with different hydrogenotrophic methanogens. The presence of the methanogen accelerated glycerol fermentation by the two Thermoanaerobacter strains up to 3.3 mM day-1 , corresponding to 12 times higher volumetric glycerol depletion rates in the methanogenic co-cultures than in the pure bacterial cultures. The catabolic pathways of glycerol conversion were identified by genome analysis of the two Thermoanaerobacter strains. NADH and reduced ferredoxin formed in the pathway are linked to proton reduction, which becomes thermodynamically favourable when the hydrogen partial pressure is kept low by the hydrogenotrophic methanogenic partner.
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Affiliation(s)
| | - Joaquim A. Ribeiro
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
- Present address:
Optimizer ‐ Serviços e Consultadoria Informática Lda.PortoPortugal
| | - Ana P. Guedes
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
- Present address:
Agricultural Superior School of Ponte de LimaPolytechnic Institute of Viana do CasteloViana do CasteloPortugal
| | - Ana L. Arantes
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
| | - Diana Z. Sousa
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
- Laboratory of MicrobiologyWageningen University and ResearchWageningenThe Netherlands
| | - Alfons J. M. Stams
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
- Laboratory of MicrobiologyWageningen University and ResearchWageningenThe Netherlands
| | - Maria M. Alves
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
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Sun Y, Liu Y, Pan J, Wang F, Li M. Perspectives on Cultivation Strategies of Archaea. MICROBIAL ECOLOGY 2020; 79:770-784. [PMID: 31432245 DOI: 10.1007/s00248-019-01422-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Archaea have been recognized as a major domain of life since the 1970s and occupy a key position in the tree of life. Recent advances in culture-independent approaches have greatly accelerated the research son Archaea. However, many hypotheses concerning the diversity, physiology, and evolution of archaea are waiting to be confirmed by culture-base experiments. Consequently, archaeal isolates are in great demand. On the other hand, traditional approaches of archaeal cultivation are rarely successful and require urgent improvement. Here, we review the current practices and applicable microbial cultivation techniques, to inform on potential strategies that could improve archaeal cultivation in the future. We first summarize the current knowledge on archaeal diversity, with an emphasis on cultivated and uncultivated lineages pertinent to future research. Possible causes for the low success rate of the current cultivation practices are then discussed to propose future improvements. Finally, innovative insights for archaeal cultivation are described, including (1) medium refinement for selective cultivation based on the genetic and transcriptional information; (2) consideration of the up-to-date archaeal culturing skills; and (3) application of multiple cultivation techniques, such as co-culture, direct interspecies electron transfer (DIET), single-cell isolation, high-throughput culturing (HTC), and simulation of the natural habitat. Improved cultivation efforts should allow successful isolation of as yet uncultured archaea, contributing to the much-needed physiological investigation of archaea.
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Affiliation(s)
- Yihua Sun
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China.
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Pelomicrobium methylotrophicum gen. nov., sp. nov. a moderately thermophilic, facultatively anaerobic, lithoautotrophic and methylotrophic bacterium isolated from a terrestrial mud volcano. Extremophiles 2019; 24:177-185. [PMID: 31705207 DOI: 10.1007/s00792-019-01145-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
Abstract
A novel moderately thermophilic, bacterium, strain SM250T, was isolated from a terrestrial mud volcano, Taman peninsula, Krasnodar region, Russia. Cells of strain SM250T were Gram-negative non-spore forming motile straight rods. Growth was observed at temperatures 30-63 °C (optimum at 50 °C), pH 6.5-10.0 (optimum at pH 8.5) and NaCl concentrations 0-4.5% (w/v) (optimum at 1.0-1.5% (w/v)). The novel isolate grows by aerobic respiration or anaerobic respiration with nitrate as the terminal electron acceptor. Strain SM250T grows by the utilization of methanol, formate and a number of other organic compounds or lithoautotrophically with hydrogen, elemental sulfur or thiosulfate as electron donors. The total size of the genome of the novel isolate was 3,327,116 bp and a genomic DNA G + C content was 64.8 mol%. Analysis of the 16S rRNA gene sequences revealed that strain SM250T belongs to the class Hydrogenophilia within the phylum Proteobacteria, with less than 91% of 16S rRNA gene sequence similarity to any species with validly published name. We propose to assign strain SM250T to a new species of a novel genus Pelomicrobium methylotrophicum gen. nov., sp. nov. The type strain is SM250T (= KCTC 62861T = VKM B-3274T).
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Branched-chain amino acid catabolism of Thermoanaerobacter strain AK85 and the influence of culture conditions on branched-chain alcohol formation. Amino Acids 2019; 51:1039-1054. [PMID: 31134352 DOI: 10.1007/s00726-019-02744-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/08/2019] [Indexed: 10/26/2022]
Abstract
The bioprocessing of amino acids to branched-chain fatty acids and alcohols is described using Thermoanaerobacter strain AK85. The amino acid utilization profile was evaluated without an electron scavenger, with thiosulfate, and in a co-culture with a methanogen. There was an emphasis on the production of branched-chain alcohols and fatty acids from the branched-chain amino acids, particularly the influence of culture conditions which was investigated using isoleucine, which revealed that the concentration of thiosulfate was of great importance for the branched-chain alcohols/fatty acid ratio produced. Kinetic studies show that branched-chain amino acid fermentation is relatively slow as compared to glucose metabolism with the concentrations of the branched-chain alcohol increasing over time. To understand the flow of electrons and to investigate if the branched-chain fatty acid was being converted to branched-chain alcohol, enzyme assays and fermentation studies using 13C-labeled leucine and 3-methyl-1-butyrate were performed which indeed suggest that carboxylic acid reduction is a source of branched-chain alcohols when Thermoanaerobacter strain AK85 was cultivated with thiosulfate as an electron scavenger.
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14
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A review of the mechanisms of mineral-based metabolism in early Earth analog rock-hosted hydrothermal ecosystems. World J Microbiol Biotechnol 2019; 35:29. [PMID: 30689069 DOI: 10.1007/s11274-019-2604-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 01/20/2019] [Indexed: 10/27/2022]
Abstract
Prior to the advent of oxygenic photosynthesis ~ 2.8-3.2 Ga, life was dependent on chemical energy captured from oxidation-reduction reactions involving minerals or substrates generated through interaction of water with minerals. Terrestrial hydrothermal environments host abundant and diverse non-photosynthetic communities and a variety of minerals that can sustain microbial metabolism. Minerals and substrates generated through interaction of minerals with water are differentially distributed in hot spring environments which, in turn, shapes the distribution of microbial life and the metabolic processes that support it. Emerging evidence suggests that terrestrial hydrothermal environments may have played a role in supporting the metabolism of the earliest forms of microbial life. It follows that these environments and their microbial inhabitants are increasingly being studied as analogs of early Earth ecosystems. Here we review current understanding of the processes that lead to variation in the availability of minerals or mineral-sourced substrates in terrestrial hydrothermal environments. In addition, we summarize proposed mechanisms of mineral substrate acquisition and metabolism in microbial cells inhabiting terrestrial hydrothermal environments, highlighting the importance of the dynamic interplay between biotic and abiotic reactions in influencing mineral substrate bioavailability. An emphasis is placed on mechanisms involved in the solubilization, acquisition, and metabolism of sulfur- and iron-bearing minerals, since these elements were likely integrated into the metabolism of the earliest anaerobic cells.
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15
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Frolova AA, Slobodkina GB, Baslerov RV, Novikov AA, Bonch-Osmolovskaya EA, Slobodkin AI. Thermosulfurimonas marina sp. nov., an Autotrophic Sulfur-Disproportionating and Nitrate-Reducing Bacterium Isolated from a Shallow-Sea Hydrothermal Vent. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718040082] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Tepidibaculum saccharolyticum gen. nov., sp. nov. a moderately thermophilic, anaerobic, spore-forming bacterium isolated from a terrestrial hot spring. Extremophiles 2018; 22:761-768. [DOI: 10.1007/s00792-018-1036-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 06/12/2018] [Indexed: 10/14/2022]
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17
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López G, Díaz-Cárdenas C, David Alzate J, Gonzalez LN, Shapiro N, Woyke T, Kyrpides NC, Restrepo S, Baena S. Description of Alicyclobacillus montanus sp. nov., a mixotrophic bacterium isolated from acidic hot springs. Int J Syst Evol Microbiol 2018; 68:1608-1615. [PMID: 29557767 DOI: 10.1099/ijsem.0.002718] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three morphologically similar thermo-acidophilic strains, USBA-GBX-501, USBA-GBX-502 and USBA-GBX-503T, were isolated from acidic thermal springs at the National Natural Park Los Nevados (Colombia). All isolates were spore-forming, Gram-stain-positive and motile, growing aerobically at 25-55 °C (optimum ~45 °C) and at pH 1.5-4.5 (optimum pH ~3.0). Phylogenetic analysis of the 16S rRNA gene sequences of these isolates showed an almost identical sequence (99.0 % similarity) and they formed a robust cluster with the closest relative Alicyclobacillus tolerans DSM 16297T with a sequence similarity of 99.0 %. Average similarity to other species of the genus Alicyclobacillus was 93.0 % and average similarity to species of the genus Effusibacillus was 90 %. In addition, the level of DNA-DNA hybridization between strain USBA-GBX-503T and Alicyclobacillus tolerans DSM 16297T was 31.7 %. The genomic DNA G+C content of strain USBA-GBX-503T was 44.6 mol%. The only menaquinone was MK-7 (100.0 %). No ω-alicyclic fatty acids were detected in strain USBA-GBX-503T, and the major cellular fatty acids were C18 : 1ω7c, anteiso-C17 : 0 and iso-C17 : 0. Based on phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA-DNA relatedness values, along with low levels of identity at the whole genome level (ANIb and ANIm values of <67.0 and <91.0 %, respectively), it can be concluded that strain USBA-GBX-503T represents a novel species of the genus Alicyclobacillus, for which the name Alicyclobacillus montanus sp. nov. is proposed. The type strain is USBA-GBX-503T (=CMPUJ UGB U503T=CBMAI1927T).
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Affiliation(s)
- G López
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá DC, Colombia.,Colombian Center for Genomics and Bioinformatics of Extreme Environments - GeBiX, Bogotá, DC, Colombia
| | - C Díaz-Cárdenas
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá DC, Colombia
| | - J David Alzate
- Biological Sciences Department, Universidad de los Andes, Cra 1 No. 18A-12, Bogotá DC, Colombia
| | - L N Gonzalez
- Biological Sciences Department, Universidad de los Andes, Cra 1 No. 18A-12, Bogotá DC, Colombia
| | - N Shapiro
- Genome Biology Program, Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - T Woyke
- Genome Biology Program, Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - N C Kyrpides
- Genome Biology Program, Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - S Restrepo
- Biological Sciences Department, Universidad de los Andes, Cra 1 No. 18A-12, Bogotá DC, Colombia
| | - S Baena
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá DC, Colombia.,Colombian Center for Genomics and Bioinformatics of Extreme Environments - GeBiX, Bogotá, DC, Colombia
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Ranawat P, Rawat S. Metal-tolerant thermophiles: metals as electron donors and acceptors, toxicity, tolerance and industrial applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:4105-4133. [PMID: 29238927 DOI: 10.1007/s11356-017-0869-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
Metal-tolerant thermophiles are inhabitants of a wide range of extreme habitats like solfatara fields, hot springs, mud holes, hydrothermal vents oozing out from metal-rich ores, hypersaline pools and soil crusts enriched with metals and other elements. The ability to withstand adverse environmental conditions, like high temperature, high metal concentration and sometimes high pH in their niche, makes them an interesting subject for understanding mechanisms behind their ability to deal with multiple duress simultaneously. Metals are essential for biological systems, as they participate in biochemistries that cannot be achieved only by organic molecules. However, the excess concentration of metals can disrupt natural biogeochemical processes and can impose toxicity. Thermophiles counteract metal toxicity via their unique cell wall, metabolic factors and enzymes that carry out metal-based redox transformations, metal sequestration by metallothioneins and metallochaperones as well as metal efflux. Thermophilic metal resistance is heterogeneous at both genetic and physiology levels and may be chromosomally, plasmid or transposon encoded with one or more genes being involved. These effective response mechanisms either individually or synergistically make proliferation of thermophiles in metal-rich habitats possibly. This article presents the state of the art and future perspectives of responses of thermophiles to metals at genetic as well as physiological levels.
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Affiliation(s)
- Preeti Ranawat
- Department of Botany and Microbiology, Hemvati Nandan Bahuguna Garhwal University, Srinagar (Garhwal), Uttarakhand, India
| | - Seema Rawat
- School of Life Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India.
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19
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Thermostilla marina gen. nov., sp. nov., a thermophilic, facultatively anaerobic planctomycete isolated from a shallow submarine hydrothermal vent. Int J Syst Evol Microbiol 2016; 66:633-638. [DOI: 10.1099/ijsem.0.000767] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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20
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Slobodkin AI, Slobodkina GB, Panteleeva AN, Chernyh NA, Novikov AA, Bonch-Osmolovskaya EA. Dissulfurimicrobium hydrothermale gen. nov., sp. nov., a thermophilic, autotrophic, sulfur-disproportionating deltaproteobacterium isolated from a hydrothermal pond. Int J Syst Evol Microbiol 2016; 66:1022-1026. [DOI: 10.1099/ijsem.0.000828] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- A. I. Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect 33 bld. 2, 119071 Moscow, Russia
| | - G. B. Slobodkina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect 33 bld. 2, 119071 Moscow, Russia
| | - A. N. Panteleeva
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect 33 bld. 2, 119071 Moscow, Russia
| | - N. A. Chernyh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect 33 bld. 2, 119071 Moscow, Russia
| | - A. A. Novikov
- Gubkin Russian State University of Oil and Gas, Leninskiy Prospect 65, 117485 Moscow, Russia
| | - E. A. Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect 33 bld. 2, 119071 Moscow, Russia
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21
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Pérez-Rodríguez I, Rawls M, Coykendall DK, Foustoukos DI. Deferrisoma palaeochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea. Int J Syst Evol Microbiol 2015; 66:830-836. [PMID: 26610851 DOI: 10.1099/ijsem.0.000798] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic, anaerobic, mixotrophic bacterium, designated strain MAG-PB1T, was isolated from a shallow-water hydrothermal vent system in Palaeochori Bay off the coast of the island of Milos, Greece. The cells were Gram-negative, rugose, short rods, approximately 1.0 μm long and 0.5 μm wide. Strain MAG-PB1T grew at 30-70 °C (optimum 60 °C), 0-50 g NaCl l- 1 (optimum 15-20 g l- 1) and pH 5.5-8.0 (optimum pH 6.0). Generation time under optimal conditions was 2.5 h. Optimal growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Fe(III), Mn(IV), arsenate and selenate were used as electron acceptors. Peptone, tryptone, Casamino acids, sucrose, yeast extract, d-fructose, α-d-glucose and ( - )-d-arabinose also served as electron donors. No growth occurred in the presence of lactate or formate. The G+C content of the genomic DNA was 66.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Deferrisoma camini, the first species of a recently described genus in the Deltaproteobacteria. Based on the 16S rRNA gene phylogenetic analysis and on physiological, biochemical and structural characteristics, the strain was found to represent a novel species, for which the name Deferrisoma palaeochoriense sp. nov. is proposed. The type strain is MAG-PB1T ( = JCM 30394T = DSM 29363T).
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Affiliation(s)
| | - Matthew Rawls
- Geophysical Laboratory, Carnegie Institution of Washington, Washington DC, 20015, USA.,Department of Oceanic, Atmospheric and Earth Sciences, George Mason University, Fairfax, VA 22030, USA
| | - D Katharine Coykendall
- US Geological Survey, National Fish Health Research Laboratory, Leetown Science Center, Kearneysville, WV 25430, USA
| | - Dionysis I Foustoukos
- Geophysical Laboratory, Carnegie Institution of Washington, Washington DC, 20015, USA
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22
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Slobodkina GB, Baslerov RV, Novikov AA, Viryasov MB, Bonch-Osmolovskaya EA, Slobodkin AI. Inmirania thermothiophila gen. nov., sp. nov., a thermophilic, facultatively autotrophic, sulfur-oxidizing gammaproteobacterium isolated from a shallow-sea hydrothermal vent. Int J Syst Evol Microbiol 2015; 66:701-706. [PMID: 26582356 DOI: 10.1099/ijsem.0.000773] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic, facultatively autotrophic bacterium, strain S2479T, was isolated from a thermal spring located in a tidal zone of a geothermally heated beach (Kuril Islands, Russia). Cells of strain S2479T were rod-shaped and motile with a Gram-negative cell-wall type. The temperature range for growth was 35-68 °C (optimum 65 °C), and the pH range for growth was pH 5.5-8.8 (optimum pH 6.5). Growth of strain S2479T was observed in the presence of NaCl concentrations ranging from 0.5 to 3.5 % (w/v) (optimum 1.5-2.0 %). The strain oxidized sulfur and thiosulfate as sole energy sources for autotrophic growth under anaerobic conditions with nitrate as electron acceptor. Strain S2479T was also capable of heterotrophic growth by reduction of nitrate with oxidation of low-chain fatty acids and a limited number of other carboxylic acids or with complex proteinaceous compounds. Nitrate was reduced to N2. Sulfur compounds were oxidized to sulfate. Strain S2479T did not grow aerobically during incubation at atmospheric concentration of oxygen but was able to grow microaerobically (1 % of oxygen in gas phase). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was a member of the family Ectothiorhodospiraceae, order Chromatiales, class Gammaproteobacteria. On the basis of phylogenetic and phenotypic properties, strain S2479T represents a novel species of a new genus, for which the name Inmirania thermothiophila gen. nov., sp. nov. is proposed. The type strain of the type species is S2479T ( = DSM 100275T = VKM B-2962T).
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Affiliation(s)
- Galina B Slobodkina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071 Moscow, Russia
| | - Roman V Baslerov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect 33, bld. 2, 119071 Moscow, Russia
| | - Andrei A Novikov
- Gubkin Russian State University of Oil and Gas, Leninskiy Prospect 65, 117485 Moscow, Russia
| | - Mikhail B Viryasov
- Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1, 119899 Moscow, Russia
| | - Elizaveta A Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071 Moscow, Russia
| | - Alexander I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071 Moscow, Russia
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23
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Bhattacharya P, Barnebey A, Zemla M, Goodwin L, Auer M, Yannone SM. Complete genome sequence of the chromate-reducing bacterium Thermoanaerobacter thermohydrosulfuricus strain BSB-33. Stand Genomic Sci 2015; 10:74. [PMID: 26445627 PMCID: PMC4595116 DOI: 10.1186/s40793-015-0028-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 05/29/2015] [Indexed: 11/10/2022] Open
Abstract
Thermoanaerobacter thermohydrosulfuricus BSB-33 is a thermophilic gram positive obligate anaerobe isolated from a hot spring in West Bengal, India. Unlike other T. thermohydrosulfuricus strains, BSB-33 is able to anaerobically reduce Fe(III) and Cr(VI) optimally at 60 °C. BSB-33 is the first Cr(VI) reducing T. thermohydrosulfuricus genome sequenced and of particular interest for bioremediation of environmental chromium contaminations. Here we discuss features of T. thermohydrosulfuricus BSB-33 and the unique genetic elements that may account for the peculiar metal reducing properties of this organism. The T. thermohydrosulfuricus BSB-33 genome comprises 2597606 bp encoding 2581 protein genes, 12 rRNA, 193 pseudogenes and has a G + C content of 34.20 %. Putative chromate reductases were identified by comparative analyses with other Thermoanaerobacter and chromate-reducing bacteria.
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Affiliation(s)
- Pamela Bhattacharya
- Life Sciences Division, Lawrence Berkeley National Laboratory, Building 84, Mail Stop 84-171, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Adam Barnebey
- Life Sciences Division, Lawrence Berkeley National Laboratory, Building 84, Mail Stop 84-171, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Marcin Zemla
- Life Sciences Division, Lawrence Berkeley National Laboratory, Building 84, Mail Stop 84-171, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Lynne Goodwin
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Manfred Auer
- Life Sciences Division, Lawrence Berkeley National Laboratory, Building 84, Mail Stop 84-171, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Steven M Yannone
- Life Sciences Division, Lawrence Berkeley National Laboratory, Building 84, Mail Stop 84-171, 1 Cyclotron Road, Berkeley, CA 94720 USA
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Slobodkin A, Gavrilov S, Ionov V, Iliyin V. Spore-Forming Thermophilic Bacterium within Artificial Meteorite Survives Entry into the Earth's Atmosphere on FOTON-M4 Satellite Landing Module. PLoS One 2015; 10:e0132611. [PMID: 26151136 PMCID: PMC4494708 DOI: 10.1371/journal.pone.0132611] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/16/2015] [Indexed: 11/18/2022] Open
Abstract
One of the key conditions of the lithopanspermia hypothesis is that microorganisms situated within meteorites could survive hypervelocity entry from space through the Earth's atmosphere. So far, all experimental proof of this possibility has been based on tests with sounding rockets which do not reach the transit velocities of natural meteorites. We explored the survival of the spore-forming thermophilic anaerobic bacterium, Thermoanaerobacter siderophilus, placed within 1.4-cm thick basalt discs fixed on the exterior of a space capsule (the METEORITE experiment on the FOTON-M4 satellite). After 45 days of orbital flight, the landing module of the space vehicle returned to Earth. The temperature during the atmospheric transit was high enough to melt the surface of basalt. T. siderophilus survived the entry; viable cells were recovered from 4 of 24 wells loaded with this microorganism. The identity of the strain was confirmed by 16S rRNA gene sequence and physiological tests. This is the first report on the survival of a lifeform within an artificial meteorite after entry from space orbit through Earth's atmosphere at a velocity that closely approached the velocities of natural meteorites. The characteristics of the artificial meteorite and the living object applied in this study can serve as positive controls in further experiments on testing of different organisms and conditions of interplanetary transport.
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Affiliation(s)
- Alexander Slobodkin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - Sergey Gavrilov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - Victor Ionov
- Russian Federation State Research Center Institute of Biomedical Problems, Russian Academy of Sciences, Khoroshevskoe Shosse 76 A, 123007 Moscow, Russia
| | - Vyacheslav Iliyin
- Russian Federation State Research Center Institute of Biomedical Problems, Russian Academy of Sciences, Khoroshevskoe Shosse 76 A, 123007 Moscow, Russia
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Pyrobaculum ferrireducens sp. nov., a hyperthermophilic Fe(III)-, selenate- and arsenate-reducing crenarchaeon isolated from a hot spring. Int J Syst Evol Microbiol 2015; 65:851-856. [DOI: 10.1099/ijs.0.000027] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel hyperthermophilic, anaerobic, archaeon was isolated from a terrestrial hot spring at Uzon Caldera, Kronotsky Nature Reserve, Kamchatka, Russia. The isolate, strain 1860T, grew optimally at 90–95 °C and pH 6.0–7.0. The cells were non-motile straight rods, 1.5–5.0 µm in length, covered with surface-layer lattice. Strain 1860T utilized complex proteinaceous compounds as electron donors and ferrihydrite, Fe(III) citrate, nitrate, thiosulfate, selenite, selenate and arsenate as electron acceptors for growth. The sequence of the 16S rRNA gene of strain 1860T had 97.9–98.7 % similarity with those of members of the genus
Pyrobaculum
. On the basis of its physiological properties and phylogenetic analyses including in silico genome to genome hybridization, the isolate is considered to represent a novel species, for which the name Pyrobaculum ferrireducens sp. nov. is proposed. The type strain is 1860T ( = DSM 28942T = VKM B-2856T).
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26
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Recent Advances in Second Generation Ethanol Production by Thermophilic Bacteria. ENERGIES 2014. [DOI: 10.3390/en8010001] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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27
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Siddique T, Kuznetsov P, Kuznetsova A, Li C, Young R, Arocena JM, Foght JM. Microbially-accelerated consolidation of oil sands tailings. Pathway II: solid phase biogeochemistry. Front Microbiol 2014; 5:107. [PMID: 24711806 PMCID: PMC3968759 DOI: 10.3389/fmicb.2014.00107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 03/02/2014] [Indexed: 11/15/2022] Open
Abstract
Consolidation of clay particles in aqueous tailings suspensions is a major obstacle to effective management of oil sands tailings ponds in northern Alberta, Canada. We have observed that microorganisms indigenous to the tailings ponds accelerate consolidation of mature fine tailings (MFT) during active metabolism by using two biogeochemical pathways. In Pathway I, microbes alter porewater chemistry to indirectly increase consolidation of MFT. Here, we describe Pathway II comprising significant, direct and complementary biogeochemical reactions with MFT mineral surfaces. An anaerobic microbial community comprising Bacteria (predominantly Clostridiales, Synergistaceae, and Desulfobulbaceae) and Archaea (Methanolinea/Methanoregula and Methanosaeta) transformed FeIII minerals in MFT to amorphous FeII minerals during methanogenic metabolism of an added organic substrate. Synchrotron analyses suggested that ferrihydrite (5Fe2O3. 9H2O) and goethite (α-FeOOH) were the dominant FeIII minerals in MFT. The formation of amorphous iron sulfide (FeS) and possibly green rust entrapped and masked electronegative clay surfaces in amended MFT. Both Pathways I and II reduced the surface charge potential (repulsive forces) of the clay particles in MFT, which aided aggregation of clays and formation of networks of pores, as visualized using cryo-scanning electron microscopy (SEM). These reactions facilitated the egress of porewater from MFT and increased consolidation of tailings solids. These results have large-scale implications for management and reclamation of oil sands tailings ponds, a burgeoning environmental issue for the public and government regulators.
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Affiliation(s)
- Tariq Siddique
- Department of Renewable Resources, University of Alberta Edmonton, AB, Canada
| | - Petr Kuznetsov
- Department of Renewable Resources, University of Alberta Edmonton, AB, Canada
| | - Alsu Kuznetsova
- Department of Renewable Resources, University of Alberta Edmonton, AB, Canada
| | - Carmen Li
- Department of Biological Sciences, University of Alberta Edmonton, AB, Canada
| | - Rozlyn Young
- Department of Biological Sciences, University of Alberta Edmonton, AB, Canada
| | - Joselito M Arocena
- Environmental Science and Engineering, University of Northern British Columbia Prince George, BC, Canada
| | - Julia M Foght
- Department of Biological Sciences, University of Alberta Edmonton, AB, Canada
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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: 60] [Impact Index Per Article: 5.5] [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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29
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Slobodkina GB, Panteleeva AN, Kostrikina NA, Kopitsyn DS, Bonch-Osmolovskaya EA, Slobodkin AI. Tepidibacillus fermentans gen. nov., sp. nov.: a moderately thermophilic anaerobic and microaerophilic bacterium from an underground gas storage. Extremophiles 2013; 17:833-9. [PMID: 23881258 DOI: 10.1007/s00792-013-0564-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 07/09/2013] [Indexed: 10/26/2022]
Abstract
A novel moderately thermophilic bacterium, strain STGH(T), was isolated from Severo-Stavropolskoye underground gas storage (Russia). Cells of strain STGH(T) were spore-forming motile straight rods 0.3 μm in diameter and 2.0-4.0 μm in length having a Gram-positive cell wall structure. The temperature range for growth was 36-65 °C, with an optimum at 50-52 °C. The pH range for growth was 5.5-8.0, with an optimum at pH 7.0-7.5. Growth of strain STGH(T) was observed at NaCl concentrations ranging from 0 to 4.0 % (w/v) with an optimum at 1.0 % (w/v). Strain STGH(T) grew anaerobically by reduction of nitrate, thiosulfate, S(0) and AQDS using a number of complex proteinaceous compounds, organic acids and carbohydrates as electron donors. Nitrate was reduced to nitrite; thiosulfate and sulfur were reduced to sulfide. It also was able to ferment pyruvate, glucose, fructose, and maltose. The strain STGH(T) did not grow under aerobic conditions during incubation with atmospheric concentration of oxygen but was able to microaerobic growth (up to 10 % of oxygen in gas phase). The G+C content of DNA of strain STGH(T) was 34.8 mol%. 16S rRNA gene sequence analysis revealed that the isolated organism belongs to the class Bacilli. We propose to assign strain STGH(T) to a new species of a novel genus Tepidibacillus fermentans gen. nov., sp.nov. The type strain is STGH(T) (=DSM 23802(T), =VKM B-2671(T)).
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Affiliation(s)
- G B Slobodkina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312, Moscow, Russia.
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30
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Huang Y, Sun Y, Ma S, Chen L, Zhang H, Deng Y. Isolation and characterization ofKeratinibaculum paraultunensegen. nov., sp. nov., a novel thermophilic, anaerobic bacterium with keratinolytic activity. FEMS Microbiol Lett 2013; 345:56-63. [DOI: 10.1111/1574-6968.12184] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 05/22/2013] [Accepted: 05/22/2013] [Indexed: 11/27/2022] Open
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Wagner ID, Varghese LB, Hemme CL, Wiegel J. Multilocus sequence analysis of Thermoanaerobacter isolates reveals recombining, but differentiated, populations from geothermal springs of the Uzon Caldera, Kamchatka, Russia. Front Microbiol 2013; 4:169. [PMID: 23801987 PMCID: PMC3689144 DOI: 10.3389/fmicb.2013.00169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 06/04/2013] [Indexed: 01/15/2023] Open
Abstract
Thermal environments have island-like characteristics and provide a unique opportunity to study population structure and diversity patterns of microbial taxa inhabiting these sites. Strains having ≥98% 16S rRNA gene sequence similarity to the obligately anaerobic Firmicutes Thermoanaerobacter uzonensis were isolated from seven geothermal springs, separated by up to 1600 m, within the Uzon Caldera (Kamchatka, Russian Far East). The intraspecies variation and spatial patterns of diversity for this taxon were assessed by multilocus sequence analysis (MLSA) of 106 strains. Analysis of eight protein-coding loci (gyrB, lepA, leuS, pyrG, recA, recG, rplB, and rpoB) revealed that all loci were polymorphic and that nucleotide substitutions were mostly synonymous. There were 148 variable nucleotide sites across 8003 bp concatenates of the protein-coding loci. While pairwise FST values indicated a small but significant level of genetic differentiation between most subpopulations, there was a negligible relationship between genetic divergence and spatial separation. Strains with the same allelic profile were only isolated from the same hot spring, occasionally from consecutive years, and single locus variant (SLV) sequence types were usually derived from the same spring. While recombination occurred, there was an “epidemic” population structure in which a particular T. uzonensis sequence type rose in frequency relative to the rest of the population. These results demonstrate spatial diversity patterns for an anaerobic bacterial species in a relative small geographic location and reinforce the view that terrestrial geothermal springs are excellent places to look for biogeographic diversity patterns regardless of the involved distances.
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Affiliation(s)
- Isaac D Wagner
- Department of Microbiology, University of Georgia Athens, GA, USA
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32
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Slobodkin AI, Reysenbach AL, Slobodkina GB, Kolganova TV, Kostrikina NA, Bonch-Osmolovskaya EA. Dissulfuribacter thermophilus gen. nov., sp. nov., a thermophilic, autotrophic, sulfur-disproportionating, deeply branching deltaproteobacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2013; 63:1967-1971. [DOI: 10.1099/ijs.0.046938-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic, anaerobic, chemolithoautotrophic bacterium (strain S69T) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Center and Valu Fa Ridge, Pacific Ocean, at a depth of 1910 m using anoxic medium with elemental sulfur as the only energy source. Cells of strain S69T were Gram-negative short rods, 0.4–0.6 µm in diameter and 1.0–2.5 µm in length, motile with a single polar flagellum. The temperature range for growth was 28–70 °C, with an optimum at 61 °C. The pH range for growth was 5.6–7.9, with optimum growth at pH 6.8. Growth of strain S69T was observed at NaCl concentrations ranging from 0.9 to 5.0 %, with an optimum at 1.8–2.7 (w/v). Strain S69T grew anaerobically with elemental sulfur as an energy source and bicarbonate/CO2 as a carbon source. Elemental sulfur was disproportionated to sulfide and sulfate. Growth was enhanced in the presence of poorly crystalline Fe(III) oxide (ferrihydrite) as a sulfide-scavenging agent. Strain S69T was also able to grow by disproportionation of thiosulfate and sulfite. Sulfate was not used as an electron acceptor either with H2 or with organic electron donors. Analysis of the 16S rRNA gene sequence revealed that the isolate formed a distinct phylogenetic branch within the
Deltaproteobacteria
. On the basis of its physiological properties and results of phylogenetic analyses, strain S69T is considered to represent a novel species of a new genus, for which the name Dissulfuribacter thermophilus gen. nov., sp. nov. is proposed. The type strain of Dissulfuribacter thermophilus is S69T ( = DSM 25762T = VKM B-2760T).
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Affiliation(s)
- A. I. Slobodkin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - A.-L. Reysenbach
- Department of Biology and Center for Life in Extreme Environments, Portland State University, PO Box 751, Portland, OR 97207-0751, USA
| | - G. B. Slobodkina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - T. V. Kolganova
- Bioengineering Center, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/1, 117312 Moscow, Russia
| | - N. A. Kostrikina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - E. A. Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
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Verbeke TJ, Zhang X, Henrissat B, Spicer V, Rydzak T, Krokhin OV, Fristensky B, Levin DB, Sparling R. Genomic evaluation of Thermoanaerobacter spp. for the construction of designer co-cultures to improve lignocellulosic biofuel production. PLoS One 2013; 8:e59362. [PMID: 23555660 PMCID: PMC3608648 DOI: 10.1371/journal.pone.0059362] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 02/13/2013] [Indexed: 02/07/2023] Open
Abstract
The microbial production of ethanol from lignocellulosic biomass is a multi-component process that involves biomass hydrolysis, carbohydrate transport and utilization, and finally, the production of ethanol. Strains of the genus Thermoanaerobacter have been studied for decades due to their innate abilities to produce comparatively high ethanol yields from hemicellulose constituent sugars. However, their inability to hydrolyze cellulose, limits their usefulness in lignocellulosic biofuel production. As such, co-culturing Thermoanaerobacter spp. with cellulolytic organisms is a plausible approach to improving lignocellulose conversion efficiencies and yields of biofuels. To evaluate native lignocellulosic ethanol production capacities relative to competing fermentative end-products, comparative genomic analysis of 11 sequenced Thermoanaerobacter strains, including a de novo genome, Thermoanaerobacter thermohydrosulfuricus WC1, was conducted. Analysis was specifically focused on the genomic potential for each strain to address all aspects of ethanol production mentioned through a consolidated bioprocessing approach. Whole genome functional annotation analysis identified three distinct clades within the genus. The genomes of Clade 1 strains encode the fewest extracellular carbohydrate active enzymes and also show the least diversity in terms of lignocellulose relevant carbohydrate utilization pathways. However, these same strains reportedly are capable of directing a higher proportion of their total carbon flux towards ethanol, rather than non-biofuel end-products, than other Thermoanaerobacter strains. Strains in Clade 2 show the greatest diversity in terms of lignocellulose hydrolysis and utilization, but proportionately produce more non-ethanol end-products than Clade 1 strains. Strains in Clade 3, in which T. thermohydrosulfuricus WC1 is included, show mid-range potential for lignocellulose hydrolysis and utilization, but also exhibit extensive divergence from both Clade 1 and Clade 2 strains in terms of cellular energetics. The potential implications regarding strain selection and suitability for industrial ethanol production through a consolidated bioprocessing co-culturing approach are examined throughout the manuscript.
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Affiliation(s)
- Tobin J. Verbeke
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Xiangli Zhang
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Bernard Henrissat
- Centre national de la recherche scientifique, Aix-Marseille Université, Marseille, France
| | - Vic Spicer
- Department of Physics & Astronomy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Thomas Rydzak
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Oleg V. Krokhin
- Department of Internal Medicine & Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Brian Fristensky
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - David B. Levin
- Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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Wery N, Cambon-Bonavita MA, Lesongeur F, Barbier G. Diversity of anaerobic heterotrophic thermophiles isolated from deep-sea hydrothermal vents of the Mid-Atlantic Ridge. FEMS Microbiol Ecol 2012; 41:105-14. [PMID: 19709244 DOI: 10.1111/j.1574-6941.2002.tb00971.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Abstract During the 'MARVEL' oceanographical cruise performed in September 1997, samples were collected from the deep-sea vents of hydrothermal sites on the Mid-Atlantic Ridge. Eighty-four thermophilic and hyperthermophilic heterotrophic microorganisms were isolated using different culture media containing cellobiose, xylan, starch, lipidic or proteic substrates. These isolates were obtained in anaerobic conditions, at 65 degrees C, 85 degrees C and 95 degrees C. Fifty of them were classified using amplified ribosomal DNA restriction analysis, random amplified polymorphic DNA and 16S rDNA sequencing. The strains classified have been assigned to the archaeal order Thermococcales and to the bacterial orders Thermotogales and Clostridiales. Variations in growth temperature and carbon sources were efficient enough to generate taxonomic diversity within enrichment cultures. Presumptive new genera and new species were isolated. Two isolates were confirmed as type strains of new species of new genera recently described: Marinitoga camini and Caloranaerobacter azorensis.
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Affiliation(s)
- Nathalie Wery
- Laboratoire de Microbiologie et de Biotechnologie des Extrêmophiles, DRV-VP, IFREMER Centre de Brest, BP70, 29280 Plouzané, France
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Rittmann S, Herwig C. A comprehensive and quantitative review of dark fermentative biohydrogen production. Microb Cell Fact 2012; 11:115. [PMID: 22925149 PMCID: PMC3443015 DOI: 10.1186/1475-2859-11-115] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 08/03/2012] [Indexed: 01/25/2023] Open
Abstract
Biohydrogen production (BHP) can be achieved by direct or indirect biophotolysis, photo-fermentation and dark fermentation, whereof only the latter does not require the input of light energy. Our motivation to compile this review was to quantify and comprehensively report strains and process performance of dark fermentative BHP. This review summarizes the work done on pure and defined co-culture dark fermentative BHP since the year 1901. Qualitative growth characteristics and quantitative normalized results of H2 production for more than 2000 conditions are presented in a normalized and therefore comparable format to the scientific community.Statistically based evidence shows that thermophilic strains comprise high substrate conversion efficiency, but mesophilic strains achieve high volumetric productivity. Moreover, microbes of Thermoanaerobacterales (Family III) have to be preferred when aiming to achieve high substrate conversion efficiency in comparison to the families Clostridiaceae and Enterobacteriaceae. The limited number of results available on dark fermentative BHP from fed-batch cultivations indicates the yet underestimated potential of this bioprocessing application. A Design of Experiments strategy should be preferred for efficient bioprocess development and optimization of BHP aiming at improving medium, cultivation conditions and revealing inhibitory effects. This will enable comparing and optimizing strains and processes independent of initial conditions and scale.
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Affiliation(s)
- Simon Rittmann
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Gumpendorferstraße 1a, Vienna University of Technology, Vienna, 1060, Austria
| | - Christoph Herwig
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Gumpendorferstraße 1a, Vienna University of Technology, Vienna, 1060, Austria
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Slobodkina GB, Panteleeva AN, Sokolova TG, Bonch-Osmolovskaya EA, Slobodkin AI. Carboxydocella manganica sp. nov., a thermophilic, dissimilatory Mn(IV)- and Fe(III)-reducing bacterium from a Kamchatka hot spring. Int J Syst Evol Microbiol 2012; 62:890-894. [DOI: 10.1099/ijs.0.027623-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic, anaerobic, dissimilatory Mn(IV)- and Fe(III)-reducing bacterium (strain SLM 61T) was isolated from a terrestrial hot spring on the Kamchatka peninsula. The cells were straight rods, 0.5–0.6 µm in diameter and 1.0–6.0 µm long, and exhibited tumbling motility by means of peritrichous flagellation. The strain grew at 26–70 °C, with an optimum at 58–60 °C, and at pH 5.5–8.0, with an optimum at pH 6.5. Growth of SLM 61T was observed at 0–2.0 % (w/v) NaCl, with an optimum at 0.5 % (w/v). The generation time under optimal growth conditions was 40 min. Strain SLM 61T grew and reduced Mn(IV), Fe(III) or nitrate with a number of organic acids and complex proteinaceous compounds as electron donors. It was capable of chemolithoautotrophic growth using molecular hydrogen as an electron donor, Fe(III) but not Mn(IV) or nitrate as an electron acceptor and CO2 as a carbon source. It also was able to ferment pyruvate, yeast extract, glucose, fructose, sucrose and maltose. The G+C content of DNA of strain SLM 61T was 50.9 mol%. 16S rRNA gene sequence analysis revealed that the closest relative of the isolated organism was
Carboxydocella thermautotrophica
41T (96.9 % similarity). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Carboxydocella manganica sp. nov. is proposed. The type strain is SLM 61T ( = DSM 23132T = VKM B-2609T). C. manganica is the first described representative of the genus
Carboxydocella
that possesses the ability to reduce metals and does not utilize CO.
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Affiliation(s)
- G. B. Slobodkina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - A. N. Panteleeva
- Bioengineering Center, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/1, 117312 Moscow, Russia
| | - T. G. Sokolova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - E. A. Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - A. I. Slobodkin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
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Nepomnyashchaya YN, Slobodkina GB, Baslerov RV, Chernyh NA, Bonch-Osmolovskaya EA, Netrusov AI, Slobodkin AI. Moorella humiferrea sp. nov., a thermophilic, anaerobic bacterium capable of growth via electron shuttling between humic acid and Fe(III). Int J Syst Evol Microbiol 2012; 62:613-617. [DOI: 10.1099/ijs.0.029009-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An anaerobic, thermophilic, spore-forming bacterium (strain 64-FGQT) was isolated from a terrestrial hydrothermal spring from the Kamchatka peninsula, Russia. This strain utilized lactate as an electron donor, insoluble poorly crystalline Fe(III) oxide incorporated into alginate beads as a potential electron acceptor and 9,10-anthraquinone-2,6-disulfonate (AQDS) as an electron-shuttling compound. Vegetative cells of strain 64-FGQT were Gram-stain-positive, peritrichously flagellated, motile, straight rods, 0.3–0.5 µm in diameter and 2.0–5.0 µm long, growing singly or forming short chains. Cells formed round refractive endospores in terminal swollen sporangia. The temperature range for growth was 46–70 °C, with an optimum at 65 °C. The pH range for growth was 5.5–8.5, with an optimum at pH 7.0. The substrates utilized by strain 64-FGQT in the presence of AQDS as an electron acceptor included lactate, malate, succinate, glycerol and yeast extract. The strain fermented galactose, fructose, maltose, sucrose, pyruvate and peptone. Strain 64-FGQT used AQDS, humic acid, thiosulfate, nitrate and perchlorate as electron acceptors for growth. Fe(III) was not directly reduced, but strain 64-FGQT was able to grow and reduce Fe(III) oxide in the presence of small amounts of AQDS or humic acid as electron-shuttling compounds. The G+C content of the DNA of strain 64-FGQT was 51 mol%. 16S rRNA gene sequence analysis placed the isolate in the genus Moorella, with the type strain of Moorella glycerini as its closest relative (97.2 % similarity). Based on phylogenetic analysis and physiological characteristics, strain 64-FGQT is considered to represent a novel species of the genus Moorella, for which the name Moorella humiferrea sp. nov. is proposed; the type strain is 64-FGQT ( = DSM 23265T = VKM B-2603T).
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Affiliation(s)
| | - G. B. Slobodkina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - R. V. Baslerov
- Bioengineering Center, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/1, 117312 Moscow, Russia
| | - N. A. Chernyh
- Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - E. A. Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - A. I. Netrusov
- Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - A. I. Slobodkin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
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Slobodkin AI, Reysenbach AL, Slobodkina GB, Baslerov RV, Kostrikina NA, Wagner ID, Bonch-Osmolovskaya EA. Thermosulfurimonas dismutans gen. nov., sp. nov., an extremely thermophilic sulfur-disproportionating bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2011; 62:2565-2571. [PMID: 22199218 DOI: 10.1099/ijs.0.034397-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extremely thermophilic, anaerobic, chemolithoautotrophic bacterium (strain S95(T)) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Center, Pacific Ocean, at a depth of 1910 m. Cells of strain S95(T) were oval to short Gram-negative rods, 0.5-0.6 µm in diameter and 1.0-1.5 µm in length, growing singly or in pairs. Cells were motile with a single polar flagellum. The temperature range for growth was 50-92 °C, with an optimum at 74 °C. The pH range for growth was 5.5-8.0, with an optimum at pH 7.0. Growth of strain S95(T) was observed at NaCl concentrations ranging from 1.5 to 3.5% (w/v). Strain S95(T) grew anaerobically with elemental sulfur as an energy source and bicarbonate/CO(2) as a carbon source. Elemental sulfur was disproportionated to sulfide and sulfate. Growth was enhanced in the presence of poorly crystalline iron(III) oxide (ferrihydrite) as a sulfide-scavenging agent. Strain S95(T) was also able to grow by disproportionation of thiosulfate and sulfite. Sulfate was not used as an electron acceptor. Analysis of the 16S rRNA gene sequence revealed that the isolate belongs to the phylum Thermodesulfobacteria. On the basis of its physiological properties and results of phylogenetic analyses, it is proposed that the isolate represents the sole species of a new genus, Thermosulfurimonas dismutans gen. nov., sp. nov.; S95(T) (=DSM 24515(T)=VKM B-2683(T)) is the type strain of the type species. This is the first description of a thermophilic micro-organism that disproportionates elemental sulfur.
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Affiliation(s)
- A I Slobodkin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - A-L Reysenbach
- Department of Biology and Center for Life in Extreme Environments, Portland State University, PO Box 751, Portland, OR 97207-0751, USA
| | - G B Slobodkina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - R V Baslerov
- Bioengineering Center, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/1, 117312 Moscow, Russia
| | - N A Kostrikina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - I D Wagner
- Department of Biology and Center for Life in Extreme Environments, Portland State University, PO Box 751, Portland, OR 97207-0751, USA
| | - E A Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
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Slobodkina GB, Reysenbach AL, Panteleeva AN, Kostrikina NA, Wagner ID, Bonch-Osmolovskaya EA, Slobodkin AI. Deferrisoma camini gen. nov., sp. nov., a moderately thermophilic, dissimilatory iron(III)-reducing bacterium from a deep-sea hydrothermal vent that forms a distinct phylogenetic branch in the Deltaproteobacteria. Int J Syst Evol Microbiol 2011; 62:2463-2468. [PMID: 22140176 DOI: 10.1099/ijs.0.038372-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately thermophilic, anaerobic, dissimilatory iron(III)-reducing bacterium (strain S3R1(T)) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Centre in the Pacific Ocean at a depth of about 2150 m. Cells of strain S3R1(T) were ovals to short rods with a single polar flagellum, Gram-stain-negative, 0.5-0.6 µm in diameter and 0.8-1.3 µm long, growing singly or in pairs. The temperature range for growth was 36-62 °C, with an optimum at 50 °C. The pH range for growth was 5.5-7.5, with an optimum at pH 6.5. Growth of strain S3R1(T) was observed at NaCl concentrations ranging from 1.0 to 5.0 % (w/v), with an optimum at 2.0-2.5 % (w/v). The isolate used acetate, fumarate, malate, maleinate, succinate, propanol, palmitate, stearate, peptone and yeast extract as electron donors for growth and iron(III) reduction. All electron donors were oxidized completely to CO(2) and H(2)O. Iron(III) (in the form of ferrihydrite, ferric citrate or ferric nitrilotriacetate) and elemental sulfur (S(0)) were the electron acceptors that supported growth. The DNA G+C content was 64.4 mol%. Results of 16S rRNA gene sequence analysis showed that the novel bacterium was related to representatives of the orders Desulfuromonadales and Syntrophobacterales with 84-86 % sequence similarity and formed a distinct phylogenetic branch in the Deltaproteobacteria. On the basis of its physiological properties and results of phylogenetic analyses, it is proposed that the new isolate represents the sole species of a novel genus, Deferrisoma camini gen. nov., sp. nov. The type strain of Deferrisoma camini is S3R1(T) ( = DSM 24185(T) = VKM B-2672(T)).
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Affiliation(s)
- G B Slobodkina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya, Oktyabrya 7/2, 117312 Moscow, Russia
| | - A-L Reysenbach
- Department of Biology and Center for Life in Extreme Environments, Portland State University, PO Box 751, Portland, OR 97207-0751, USA
| | - A N Panteleeva
- Bioengineering Center, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/1, 117312 Moscow, Russia
| | - N A Kostrikina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya, Oktyabrya 7/2, 117312 Moscow, Russia
| | - I D Wagner
- Department of Biology and Center for Life in Extreme Environments, Portland State University, PO Box 751, Portland, OR 97207-0751, USA
| | - E A Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya, Oktyabrya 7/2, 117312 Moscow, Russia
| | - A I Slobodkin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya, Oktyabrya 7/2, 117312 Moscow, Russia
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Slobodkina GB, Kolganova TV, Kostrikina NA, Bonch-Osmolovskaya EA, Slobodkin AI. Caloribacterium cisternae gen. nov., sp. nov., an anaerobic thermophilic bacterium from an underground gas storage reservoir. Int J Syst Evol Microbiol 2011; 62:1543-1547. [PMID: 21856985 DOI: 10.1099/ijs.0.033076-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic, moderately thermophilic bacterium (strain SGL43(T)) was isolated from Severo-Stavropolskoye underground gas storage reservoir (Russia). Cells of strain SGL43(T) were motile straight rods, 0.4 µm in diameter and 2.0-3.0 µm in length. The temperature range for growth was 28-65 °C, with optimum growth at 50 °C. The pH range for growth was 5.5-8.0, with optimum growth at pH 7.0-7.5. Growth of strain SGL43(T) was observed at NaCl concentrations of 0-4.0% (w/v) with optimum growth at 1.0% (w/v) NaCl. Substrates utilized by strain SGL43(T) included peptone, yeast extract, glucose, fructose, maltose, galactose, pyruvate and citrate. Products of glucose or citrate fermentation were acetate, hydrogen and CO(2). Thiosulfate was reduced to sulfide. The DNA G+C content of strain SGL43(T) was 43.1 mol%. 16S rRNA gene sequence analysis revealed that strain SGL43(T) belongs to the order Thermoanaerobacterales (phylum 'Firmicutes'). The closest relative of strain SGL43(T) was Thermoanaerobacterium saccharolyticum (86.2% 16S rRNA gene sequence similarity with the type strain). Based on the data presented here, strain SGL43(T) is considered to represent a novel species of a new genus, for which the name Caloribacterium cisternae gen. nov., sp. nov. is proposed. The type strain of Caloribacterium cisternae, the type species of the genus, is SGL43(T) (=DSM 23830(T)=VKM B-2670(T)).
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Affiliation(s)
- G B Slobodkina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - T V Kolganova
- Bioengineering Center, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/1, 117312 Moscow, Russia
| | - N A Kostrikina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - E A Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - A I Slobodkin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
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Nepomnyashaya YN, Slobodkina GB, Kolganova TV, Bonch-Osmolovskaya EA, Netrusov AI, Slobodkin AI. Phylogenetic composition of enrichment cultures of thermophilic prokaryotes reducing poorly crystalline Fe(III) oxide with and without direct contact between the cells and mineral. Microbiology (Reading) 2010. [DOI: 10.1134/s0026261710050115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production. J Bacteriol 2010; 192:6494-6. [PMID: 20889752 DOI: 10.1128/jb.01064-10] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Modern methods to develop microbe-based biomass conversion processes require a system-level understanding of the microbes involved. Clostridium species have long been recognized as ideal candidates for processes involving biomass conversion and production of various biofuels and other industrial products. To expand the knowledge base for clostridial species relevant to current biofuel production efforts, we have sequenced the genomes of 20 species spanning multiple genera. The majority of species sequenced fall within the class III cellulosome-encoding Clostridium and the class V saccharolytic Thermoanaerobacteraceae. Species were chosen based on representation in the experimental literature as model organisms, ability to degrade cellulosic biomass either by free enzymes or by cellulosomes, ability to rapidly ferment hexose and pentose sugars to ethanol, and ability to ferment synthesis gas to ethanol. The sequenced strains significantly increase the number of noncommensal/nonpathogenic clostridial species and provide a key foundation for future studies of biomass conversion, cellulosome composition, and clostridial systems biology.
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Isolation and characterization of a new CO-utilizing strain, Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans, isolated from a geothermal spring in Turkey. Extremophiles 2009; 13:885-94. [PMID: 19701714 PMCID: PMC2767516 DOI: 10.1007/s00792-009-0276-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2009] [Accepted: 08/03/2009] [Indexed: 11/26/2022]
Abstract
A novel anaerobic, thermophilic, Gram-positive, spore-forming, and sugar-fermenting bacterium (strain TLO) was isolated from a geothermal spring in Ayaş, Turkey. The cells were straight to curved rods, 0.4–0.6 μm in diameter and 3.5–10 μm in length. Spores were terminal and round. The temperature range for growth was 40–80°C, with an optimum at 70°C. The pH optimum was between 6.3 and 6.8. Strain TLO has the capability to ferment a wide variety of mono-, di-, and polysaccharides and proteinaceous substrates, producing mainly lactate, next to acetate, ethanol, alanine, H2, and CO2. Remarkably, the bacterium was able to grow in an atmosphere of up to 25% of CO as sole electron donor. CO oxidation was coupled to H2 and CO2 formation. The G + C content of the genomic DNA was 35.1 mol%. Based on 16S rRNA gene sequence analysis and the DNA–DNA hybridization data, this bacterium is most closely related to Thermoanaerobacter thermohydrosulfuricus and Thermoanaerobacter siderophilus (99% similarity for both). However, strain TLO differs from Thermoanaerobacter thermohydrosulfuricus in important aspects, such as CO-utilization and lipid composition. These differences led us to propose that strain TLO represents a subspecies of Thermoanaerobacter thermohydrosulfuricus, and we therefore name it Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans.
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Slobodkina GB, Kolganova TV, Querellou J, Bonch-Osmolovskaya EA, Slobodkin AI. Geoglobus acetivorans sp. nov., an iron(III)-reducing archaeon from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2009; 59:2880-3. [PMID: 19628601 DOI: 10.1099/ijs.0.011080-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A hyperthermophilic, anaerobic, dissimilatory Fe(III)-reducing, facultatively chemolithoautotrophic archaeon (strain SBH6(T)) was isolated from a hydrothermal sample collected from the deepest of the known World Ocean hydrothermal fields, Ashadze field (1 degrees 58' 21'' N 4 degrees 51' 47'' W) on the Mid-Atlantic Ridge, at a depth of 4100 m. The strain was enriched using acetate as the electron donor and Fe(III) oxide as the electron acceptor. Cells of strain SBH6(T) were irregular cocci, 0.3-0.5 mum in diameter. The temperature range for growth was 50-85 degrees C, with an optimum at 81 degrees C. The pH range for growth was 5.0-7.5, with an optimum at pH 6.8. Growth of SBH6(T) was observed at NaCl concentrations ranging from 1 to 6 % (w/v) with an optimum at 2.5 % (w/v). The isolate utilized acetate, formate, pyruvate, fumarate, malate, propionate, butyrate, succinate, glycerol, stearate, palmitate, peptone and yeast extract as electron donors for Fe(III) reduction. It was also capable of growth with H(2) as the sole electron donor, CO(2) as a carbon source and Fe(III) as an electron acceptor without the need for organic substances. Fe(III) [in the form of poorly crystalline Fe(III) oxide or Fe(III) citrate] was the only electron acceptor that supported growth. 16S rRNA gene sequence analysis revealed that the closest relative of the isolated organism was Geoglobus ahangari 234(T) (97.0 %). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Geoglobus acetivorans sp. nov. is proposed. The type strain is SBH6(T) (=DSM 21716(T) =VKM B-2522(T)).
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Affiliation(s)
- G B Slobodkina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, 117312 Moscow, Russia.
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Slobodkina GB, Kolganova TV, Chernyh NA, Querellou J, Bonch-Osmolovskaya EA, Slobodkin AI. Deferribacter autotrophicus sp. nov., an iron(III)-reducing bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2009; 59:1508-12. [DOI: 10.1099/ijs.0.006767-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Bhowmick D, Bal B, Chatterjee N, Ghosh A, Pal S. A low-GC Gram-positiveThermoanaerobacter-like bacterium isolated from an Indian hot spring contains Cr(VI) reduction activity both in the membrane and cytoplasm. J Appl Microbiol 2009; 106:2006-16. [DOI: 10.1111/j.1365-2672.2009.04159.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Miroshnichenko ML, Lebedinsky AV, Chernyh NA, Tourova TP, Kolganova TV, Spring S, Bonch-Osmolovskaya EA. Caldimicrobium rimae gen. nov., sp. nov., an extremely thermophilic, facultatively lithoautotrophic, anaerobic bacterium from the Uzon Caldera, Kamchatka. Int J Syst Evol Microbiol 2009; 59:1040-4. [DOI: 10.1099/ijs.0.006072-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Slepova TV, Sokolova TG, Kolganova TV, Tourova TP, Bonch-Osmolovskaya EA. Carboxydothermus siderophilus sp. nov., a thermophilic, hydrogenogenic, carboxydotrophic, dissimilatory Fe(III)-reducing bacterium from a Kamchatka hot spring. Int J Syst Evol Microbiol 2009; 59:213-7. [DOI: 10.1099/ijs.0.000620-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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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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