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Gheibzadeh MS, Manyumwa CV, Tastan Bishop Ö, Shahbani Zahiri H, Parkkila S, Zolfaghari Emameh R. Genome Study of α-, β-, and γ-Carbonic Anhydrases from the Thermophilic Microbiome of Marine Hydrothermal Vent Ecosystems. BIOLOGY 2023; 12:770. [PMID: 37372055 DOI: 10.3390/biology12060770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/29/2023]
Abstract
Carbonic anhydrases (CAs) are metalloenzymes that can help organisms survive in hydrothermal vents by hydrating carbon dioxide (CO2). In this study, we focus on alpha (α), beta (β), and gamma (γ) CAs, which are present in the thermophilic microbiome of marine hydrothermal vents. The coding genes of these enzymes can be transferred between hydrothermal-vent organisms via horizontal gene transfer (HGT), which is an important tool in natural biodiversity. We performed big data mining and bioinformatics studies on α-, β-, and γ-CA coding genes from the thermophilic microbiome of marine hydrothermal vents. The results showed a reasonable association between thermostable α-, β-, and γ-CAs in the microbial population of the hydrothermal vents. This relationship could be due to HGT. We found evidence of HGT of α- and β-CAs between Cycloclasticus sp., a symbiont of Bathymodiolus heckerae, and an endosymbiont of Riftia pachyptila via Integrons. Conversely, HGT of β-CA genes from the endosymbiont Tevnia jerichonana to the endosymbiont Riftia pachyptila was detected. In addition, Hydrogenovibrio crunogenus SP-41 contains a β-CA gene on genomic islands (GIs). This gene can be transferred by HGT to Hydrogenovibrio sp. MA2-6, a methanotrophic endosymbiont of Bathymodiolus azoricus, and a methanotrophic endosymbiont of Bathymodiolus puteoserpentis. The endosymbiont of R. pachyptila has a γ-CA gene in the genome. If α- and β-CA coding genes have been derived from other microorganisms, such as endosymbionts of T. jerichonana and Cycloclasticus sp. as the endosymbiont of B. heckerae, through HGT, the theory of the necessity of thermostable CA enzymes for survival in the extreme ecosystem of hydrothermal vents is suggested and helps the conservation of microbiome natural diversity in hydrothermal vents. These harsh ecosystems, with their integral players, such as HGT and endosymbionts, significantly impact the enrichment of life on Earth and the carbon cycle in the ocean.
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Affiliation(s)
- Mohammad Sadegh Gheibzadeh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Colleen Varaidzo Manyumwa
- Research Unit in Bioinformatics (Rubi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (Rubi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Hossein Shahbani Zahiri
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
- Fimlab Ltd., Tampere University Hospital, 33520 Tampere, Finland
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
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2
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Grenier V, Gonzalez E, Brereton NJB, Pitre FE. Dynamics of bacterial and archaeal communities during horse bedding and green waste composting. PeerJ 2023; 11:e15239. [PMID: 37159830 PMCID: PMC10163874 DOI: 10.7717/peerj.15239] [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: 09/18/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.
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Affiliation(s)
- Vanessa Grenier
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de Recherche en Biologie Végétale, Montréal, Québec, Canada
| | - Emmanuel Gonzalez
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill Genome Centre, McGill University, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Nicholas JB Brereton
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Frederic E. Pitre
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de Recherche en Biologie Végétale, Montréal, Québec, Canada
- Montreal Botanical Garden, Montréal, Québec, Canada
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3
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Bergsten P, Vannier P, Mougeolle A, Rigaud L, Marteinsson VT. Rhodothermus bifroesti sp. nov., a thermophilic bacterium isolated from the basaltic subsurface of the volcanic island Surtsey. Int J Syst Evol Microbiol 2022; 72. [PMID: 35072600 DOI: 10.1099/ijsem.0.005214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Novel thermophilic heterotrophic bacteria were isolated from the subsurface of the volcanic island Surtsey off the south coast of Iceland. The strains were isolated from tephra core and borehole fluid samples collected below 70 m depth. The Gram-negative bacteria were rod-shaped (0.3-0.4 µm wide, 1.5-7 µm long), aerobic, non-sporulating and non-motile. Optimal growth was observed at 70 °C, at pH 7-7.5 and with 1% NaCl. Phylogenetic analysis identified the strains as members of the genus Rhodothermus. The type strain, ISCAR-7401T, was genetically distinct from its closest relatives Rhodothermus marinus DSM 4252T and Rhodothermus profundi PRI 2902T based on 16S rRNA gene sequence similarity (95.81 and 96.01%, respectively), genomic average nucleotide identity (73.73 and 72.61%, respectively) and digital DNA-DNA hybridization (17.6 and 16.9%, respectively). The major fatty acids of ISCAR-7401T were iso-C17:0, anteiso-C15:0, anteiso-C17:0 and iso-C15:0 (>10 %). The major isoprenoid quinone was MK-7 while phosphatidylethanolamine, diphosphatidylglycerol, an unidentified aminophospholipid and a phospholipid were the predominant polar lipid components. Based on comparative chemotaxonomic, genomic and phylogenetic analyses, we propose that the isolated strain represents a novel species of the genus Rhodothermus with the name Rhodothermus bifroesti sp. nov. The type strain is ISCAR-7401T (=DSM 112103T=CIP 111906T).
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Affiliation(s)
- Pauline Bergsten
- Matís, Exploration & Utilization of Genetic Resources, Reykjavík, Iceland
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Pauline Vannier
- Matís, Exploration & Utilization of Genetic Resources, Reykjavík, Iceland
| | - Alan Mougeolle
- Matís, Exploration & Utilization of Genetic Resources, Reykjavík, Iceland
| | - Louise Rigaud
- Matís, Exploration & Utilization of Genetic Resources, Reykjavík, Iceland
| | - Viggó Thór Marteinsson
- Matís, Exploration & Utilization of Genetic Resources, Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Reykjavík, Iceland
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4
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Björnsdóttir SH, Pétursdóttir SK, Gudmundsdóttir EE, Olgudóttir E, Stefansson SK, Róbertsdóttir T, Sigurpálsson ÁH, Ólafsdóttir SK, Fridjónsson ÓH, Hreggvidsson GÓ. Rhodocaloribacter litoris gen. nov., sp. nov., isolated from an intertidal hot spring. Int J Syst Evol Microbiol 2021; 71. [PMID: 34672921 DOI: 10.1099/ijsem.0.005073] [Citation(s) in RCA: 7] [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
Red-pigmented strains of non-sporeforming, aerobic, chemoorganotrophic bacteria were isolated from intertidal hot springs in Laugarvík, NW-Iceland. Cells stained Gram-negative and formed pleomorphic rods that often had swollen ends and occurred singly or in filaments. Growth was observed at 40-65 °C (optimum at 60 °C), pH 6-9 (optimum at 6.5-8) and 0.5-5% (optimum at 1-2%) (w/v) NaCl. Strain ISCAR-4553T contained MK-7 as the main respiratory quinone and saturated iso and anteiso branched chains of 17 and 15 carbons as the main cellular fatty acids (83.4%). The G+C content of the DNA is 67.3 mol%. The highest 16S rRNA gene sequence similarity was with the genus Roseithermus (92.0%) and followed by Rhodothermus, Rubrivirga and Rubricoccus (88-90%). Genome and phenotype comparisons supported the affiliation of the novel isolates and the genus Roseithermus to the family Rhodothermaceae of the phylum Rhodothermaeota. The described isolates are proposed to be classified as representatives of a novel species belonging to a novel genus, with the name Rhodocaloribacter litoris gen. nov., sp. nov. The type strain is ISCAR-4553T (=DSM 110790T = ATCC TSD-179T).
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Affiliation(s)
- Snædís H Björnsdóttir
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland
| | | | | | | | - Sigmar K Stefansson
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland
| | - Tara Róbertsdóttir
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland
| | - Ásbjörn H Sigurpálsson
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland
| | | | | | - Gudmundur Ó Hreggvidsson
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland.,Matis, Vínlandsleið 12, IS-113 Reykjavík, Iceland
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5
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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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6
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Complete Genome Sequences of Rhodothermus marinus Strains AA2-13 and AA3-38, Isolated from Arima Onsen Hot Spring in Japan. Microbiol Resour Announc 2020; 9:9/2/e01475-19. [PMID: 31919149 PMCID: PMC6952675 DOI: 10.1128/mra.01475-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We isolated Rhodothermus marinus strains AA2-13 and AA3-38 from Arima Onsen, a hot spring in Japan, and sequenced their genomes. The average nucleotide identity between their genomes was 99.2%, and that with the genome of R. marinus strain DSM 4252T (isolated from Iceland) was ∼95.2%, suggesting close relationships among these strains. We isolated Rhodothermus marinus strains AA2-13 and AA3-38 from Arima Onsen, a hot spring in Japan, and sequenced their genomes. The average nucleotide identity between their genomes was 99.2%, and that with the genome of R. marinus strain DSM 4252T (isolated from Iceland) was ∼95.2%, suggesting close relationships among these strains.
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García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 2019; 10:2083. [PMID: 31608019 PMCID: PMC6767994 DOI: 10.3389/fmicb.2019.02083] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/23/2019] [Indexed: 11/25/2022] Open
Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Park MJ, Oh JH, Yang SH, Kwon KK. Roseithermus sacchariphilus gen. nov., sp. nov. and proposal of Salisaetaceae fam. nov., representing new family in the order Rhodothermales. Int J Syst Evol Microbiol 2019; 69:1213-1219. [PMID: 30777820 DOI: 10.1099/ijsem.0.003293] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium with cells that were pinkish-cream-coloured, aerobic, rod-shaped, 0.62-1.00 µm wide and 2.3-3.3 µm long, designated as strain MEBiC09517T, was isolated from Buksung-Po, a small port in Incheon, Republic of Korea. Strain MEBiC09517T had low 16S rRNA gene sequence similarity to validly reported strains; among them, Rubrivirgaprofundi SAORIC-476T displayed highest sequence similarity (89.9 %). Nevertheless, the novel strain shared a phylogenetic line with members of the genus Rhodothermus, not the genus Rubrivirga. Optimum growth conditions of strain MEBiC09517T were at 50-55 °C, pH 7 and in 2.0-4.0 % salt concentration. Strain MEBiC09517T was found to be an obligate marine bacterium that requires KCl, MgCl2 and CaCl2 as well as NaCl for growth. A phosphatidylethanolamine, a diphosphatidylglycerol, three glycolipids and four unidentified lipids were the strain's predominant polar lipid components. The fatty acid of the cell wall mainly consisted of carbons with 16 or 18 chain lengths such as C16 : 0, C18 : 0, C18 : 1 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The predominant menaquinone was MK-7. The DNA G+C content is 68.65 mol%. Strain MEBiC09517T differs from genera of the order Rhodothermales in terms of fatty acid composition, growth conditions, and range of carbon source utilization. Based on phylogenetic analysis using the strain's 16S rRNA gene sequence and results of physiological tests, strain MEBiC09517T (KCCM=43267T, JCM=32374T) is proposed as Roseithermus sacchariphilus gen. nov., sp. nov. Additionally, the novel family Salisaetaceae fam. nov. based on phylogenetic analysis and physiological characteristics is suggested.
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Affiliation(s)
- Mi-Jeong Park
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea.,Major of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Ji Hye Oh
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Sung-Hyun Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Kae Kyoung Kwon
- Major of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea.,Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
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Fortney NW, He S, Converse BJ, Boyd ES, Roden EE. Investigating the Composition and Metabolic Potential of Microbial Communities in Chocolate Pots Hot Springs. Front Microbiol 2018; 9:2075. [PMID: 30245673 PMCID: PMC6137239 DOI: 10.3389/fmicb.2018.02075] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/14/2018] [Indexed: 01/14/2023] Open
Abstract
Iron (Fe) redox-based metabolisms likely supported life on early Earth and may support life on other Fe-rich rocky planets such as Mars. Modern systems that support active Fe redox cycling such as Chocolate Pots (CP) hot springs provide insight into how life could have functioned in such environments. Previous research demonstrated that Fe- and Si-rich and slightly acidic to circumneutral-pH springs at CP host active dissimilatory Fe(III) reducing microorganisms. However, the abundance and distribution of Fe(III)-reducing communities at CP is not well-understood, especially as they exist in situ. In addition, the potential for direct Fe(II) oxidation by lithotrophs in CP springs is understudied, in particular when compared to indirect oxidation promoted by oxygen producing Cyanobacteria. Here, a culture-independent approach, including 16S rRNA gene amplicon and shotgun metagenomic sequencing, was used to determine the distribution of putative Fe cycling microorganisms in vent fluids and sediment cores collected along the outflow channel of CP. Metagenome-assembled genomes (MAGs) of organisms native to sediment and planktonic microbial communities were screened for extracellular electron transfer (EET) systems putatively involved in Fe redox cycling and for CO2 fixation pathways. Abundant MAGs containing putative EET systems were identified as part of the sediment community at locations where Fe(III) reduction activity has previously been documented. MAGs encoding both putative EET systems and CO2 fixation pathways, inferred to be FeOB, were also present, but were less abundant components of the communities. These results suggest that the majority of the Fe(III) oxides that support in situ Fe(III) reduction are derived from abiotic oxidation. This study provides new insights into the interplay between Fe redox cycling and CO2 fixation in sustaining chemotrophic communities in CP with attendant implications for other neutral-pH hot springs.
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Affiliation(s)
- Nathaniel W. Fortney
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Shaomei He
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, United States
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Brandon J. Converse
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Eric S. Boyd
- Department of Microbiology and Immunology, NASA Astrobiology Institute, Montana State University, Bozeman, MT, United States
| | - Eric E. Roden
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, United States
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10
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Liew KJ, Teo SC, Shamsir MS, Sani RK, Chong CS, Chan KG, Goh KM. Complete genome sequence of Rhodothermaceae bacterium RA with cellulolytic and xylanolytic activities. 3 Biotech 2018; 8:376. [PMID: 30105201 PMCID: PMC6087703 DOI: 10.1007/s13205-018-1391-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/06/2018] [Indexed: 11/26/2022] Open
Abstract
Rhodothermaceae bacterium RA is a halo-thermophile isolated from a saline hot spring. Previously, the genome of this bacterium was sequenced using a HiSeq 2500 platform culminating in 91 contigs. In this report, we report on the resequencing of its complete genome using a PacBio RSII platform. The genome has a GC content of 68.3%, is 4,653,222 bp in size, and encodes 3711 genes. We are interested in understanding the carbohydrate metabolic pathway, in particular the lignocellulosic biomass degradation pathway. Strain RA harbors 57 glycosyl hydrolase (GH) genes that are affiliated with 30 families. The bacterium consists of cellulose-acting (GH 3, 5, 9, and 44) and hemicellulose-acting enzymes (GH 3, 10, and 43). A crude cell-free extract of the bacterium exhibited endoglucanase, xylanase, β-glucosidase, and β-xylosidase activities. The complete genome information coupled with biochemical assays confirms that strain RA is able to degrade cellulose and xylan. Therefore, strain RA is another excellent member of family Rhodothermaceae as a repository of novel and thermostable cellulolytic and hemicellulolytic enzymes.
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Affiliation(s)
- Kok Jun Liew
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Seng Chong Teo
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, USA
| | - Chun Shiong Chong
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Kok-Gan Chan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang, 212013 People’s Republic of China
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
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Albuquerque L, Polónia ARM, Barroso C, Froufe HJC, Lage O, Lobo-da-Cunha A, Egas C, da Costa MS. Raineya orbicola gen. nov., sp. nov. a slightly thermophilic bacterium of the phylum Bacteroidetes and the description of Raineyaceae fam. nov. Int J Syst Evol Microbiol 2018; 68:982-989. [PMID: 29458463 PMCID: PMC5982127 DOI: 10.1099/ijsem.0.002556] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 12/22/2017] [Indexed: 11/18/2022] Open
Abstract
An isolate, designated SPSPC-11T, with an optimum growth temperature of about 50 °C and an optimum pH for growth between 7.5 and 8.0, was recovered from a hot spring in central Portugal. Based on phylogenetic analysis of its 16S rRNA sequence, the new organism is most closely related to the species of the genus Thermonema but with a pairwise sequence similarity of <85 %. The isolate was orange-pigmented, formed non-motile long filaments and rod-shaped cells that stain Gram-negative. The organism was strictly aerobic, oxidase-positive and catalase-positive. The major fatty acids were iso-C15:0, iso-C15 : 0 2-OH and iso-C17 : 0 3-OH. The major polar lipids were one aminophospholipid, two aminolipids and three unidentified lipids. Menaquinone 7 was the major respiratory quinone. The DNA G+C content of strain SPSPC-11T was 37.6 mol% (draft genome sequence). The high quality draft genome sequence corroborated many of the phenotypic characteristics of strain SPSPC-11T. Based on genotypic, phylogenetic, physiological and biochemical characterization we describe a new species of a novel genus represented by strain SPSPC-11T (=CECT 9012T=LMG 29233T) for which we propose the name Raineya orbicola gen. nov., sp. nov. We also describe the family Raineyaceae to accommodate this new genus and species.
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Affiliation(s)
- Luciana Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Ana Rita M. Polónia
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Cristina Barroso
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal
| | - Hugo J. C. Froufe
- Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal
| | - Olga Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n° 4169-007 Porto, Portugal
- CIMAR/CIIMAR – Centro Interdisciplinar de Investigação Marinha e Ambiental – Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Alexandre Lobo-da-Cunha
- CIMAR/CIIMAR – Centro Interdisciplinar de Investigação Marinha e Ambiental – Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
- Laboratório de Biologia Celular, Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Conceição Egas
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal
| | - Milton S. da Costa
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
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Hahnke RL, Meier-Kolthoff JP, García-López M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Göker M. Genome-Based Taxonomic Classification of Bacteroidetes. Front Microbiol 2016; 7:2003. [PMID: 28066339 PMCID: PMC5167729 DOI: 10.3389/fmicb.2016.02003] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/30/2016] [Indexed: 01/15/2023] Open
Abstract
The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.
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Affiliation(s)
- Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Supratim Mukherjee
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Natalia N. Ivanova
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Nikos C. Kyrpides
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
- Department of Biological Sciences, Faculty of Science, King Abdulaziz UniversityJeddah, Saudi Arabia
| | | | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
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13
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Xia J, Dunlap CA, Flor-Weiler L, Rooney AP, Chen GJ, Du ZJ. Longibacter salinarum gen. nov., sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2016; 66:3287-3292. [DOI: 10.1099/ijsem.0.001190] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jun Xia
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Christopher A. Dunlap
- US Department of Agriculture, Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, Peoria, IL 61604, USA
| | - Lina Flor-Weiler
- US Department of Agriculture, Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, Peoria, IL 61604, USA
| | - Alejandro P. Rooney
- US Department of Agriculture, Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, Peoria, IL 61604, USA
| | - Guan-Jun Chen
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
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14
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Goh KM, Chan KG, Lim SW, Liew KJ, Chan CS, Shamsir MS, Ee R, Adrian TGS. Genome Analysis of a New Rhodothermaceae Strain Isolated from a Hot Spring. Front Microbiol 2016; 7:1109. [PMID: 27471502 PMCID: PMC4943939 DOI: 10.3389/fmicb.2016.01109] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/04/2016] [Indexed: 11/21/2022] Open
Abstract
A bacterial strain, designated RA, was isolated from water sample of a hot spring on Langkawi Island of Malaysia using marine agar. Strain RA is an aerophilic and thermophilic microorganism that grows optimally at 50–60°C and is capable of growing in marine broth containing 1–10% (w/v) NaCl. 16S rRNA gene sequence analysis demonstrated that this strain is most closely related (<90% sequence identity) to Rhodothermaceae, which currently comprises of six genera: Rhodothermus (two species), Salinibacter (three species), Salisaeta (one species), Rubricoccus (one species), Rubrivirga (one species), and Longimonas (one species). Notably, analysis of average nucleotide identity (ANI) values indicated that strain RA may represent the first member of a novel genus of Rhodothermaceae. The draft genome of strain RA is 4,616,094 bp with 3630 protein-coding gene sequences. Its GC content is 68.3%, which is higher than that of most other genomes of Rhodothermaceae. Strain RA has genes for sulfate permease and arylsulfatase to withstand the high sulfur and sulfate contents of the hot spring. Putative genes encoding proteins involved in adaptation to osmotic stress were identified which encode proteins namely Na+/H+ antiporters, a sodium/solute symporter, a sodium/glutamate symporter, trehalose synthase, malto-oligosyltrehalose synthase, choline-sulfatase, potassium uptake proteins (TrkA and TrkH), osmotically inducible protein C, and the K+ channel histidine kinase KdpD. Furthermore, genome description of strain RA and comparative genome studies in relation to other related genera provide an overview of the uniqueness of this bacterium.
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Affiliation(s)
- Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Soon Wee Lim
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Kok Jun Liew
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Tan-Guan-Sheng Adrian
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
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Raulf FF, Fabricius K, Uthicke S, de Beer D, Abed RMM, Ramette A. Changes in microbial communities in coastal sediments along natural CO2gradients at a volcanic vent in Papua New Guinea. Environ Microbiol 2015; 17:3678-91. [DOI: 10.1111/1462-2920.12729] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 11/12/2014] [Accepted: 11/23/2014] [Indexed: 01/05/2023]
Affiliation(s)
- Felix F. Raulf
- HGF-MPG Joint Research Group on Deep Sea Ecology and Technology; Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Katharina Fabricius
- Water Quality and Ecosystem Health; Australian Institute of Marine Science; Townsville Australia
| | - Sven Uthicke
- Water Quality and Ecosystem Health; Australian Institute of Marine Science; Townsville Australia
| | - Dirk de Beer
- Microsensor Group; Max Planck Institute for Marine Microbiology; Bremen Germany
| | | | - Alban Ramette
- HGF-MPG Joint Research Group on Deep Sea Ecology and Technology; Max Planck Institute for Marine Microbiology; Bremen Germany
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Anders H, Dunfield PF, Lagutin K, Houghton KM, Power JF, MacKenzie AD, Vyssotski M, Ryan JLJ, Hanssen EG, Moreau JW, Stott MB. Thermoflavifilum aggregans gen. nov., sp. nov., a thermophilic and slightly halophilic filamentous bacterium from the phylum Bacteroidetes. Int J Syst Evol Microbiol 2014; 64:1264-1270. [PMID: 24425740 DOI: 10.1099/ijs.0.057463-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly aerobic, thermophilic, moderately acidophilic, non-spore-forming bacterium, strain P373(T), was isolated from geothermally heated soil at Waikite, New Zealand. Cells were filamentous rods, 0.2-0.4 µm in diameter and grew in chains up to 80 µm in length. On the basis of 16S rRNA gene sequence similarity, strain P373(T) was shown to belong to the family Chitinophagaceae (class Sphingobacteriia) of the phylum Bacteroidetes, with the most closely related cultivated strain, Chitinophaga pinensis UQM 2034(T), having 87.6 % sequence similarity. Cells stained Gram-negative, and were catalase- and oxidase-positive. The major fatty acids were i-15 : 0 (10.8 %), i-17 : 0 (24.5 %) and i-17 : 0 3-OH (35.2 %). Primary lipids were phosphatidylethanolamine, two unidentified aminolipids and three other unidentified polar lipids. The presence of sulfonolipids (N-acyl-capnines) was observed in the total lipid extract by mass spectrometry. The G+C content of the genomic DNA was 47.3 mol% and the primary respiratory quinone was MK-7. Strain P373(T) grew at 35-63 °C with an optimum temperature of 60 °C, and at pH 5.5-8.7 with an optimum growth pH of 7.3-7.4. NaCl tolerance was up to 5 % (w/v) with an optimum of 0.1-0.25 % (w/v). Cell colonies were non-translucent and pigmented vivid yellow-orange. Cells displayed an oxidative chemoheterotrophic metabolism. The distinct phylogenetic position and the phenotypic characteristics separate strain P373(T) from all other members of the phylum Bacteroidetes and indicate that it represents a novel species in a new genus, for which the name Thermoflavifilum aggregans gen. nov., sp. nov. is proposed. The type strain of the type species is P373(T) ( = ICMP 20041(T) = DSM 27268(T)).
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Affiliation(s)
- Heike Anders
- Lehrstuhl für Tierhygiene, Technische Universität München, Weihenstephaner Berg 3 0D-85354, Freising, Germany
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary T2N 1N4, Canada
| | - Kirill Lagutin
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - Karen M Houghton
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | - Jean F Power
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | | | | | - Jason L J Ryan
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - Eric G Hanssen
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - John W Moreau
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - Matthew B Stott
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
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Hjorleifsdottir S, Aevarsson A, Hreggvidsson GO, Fridjonsson OH, Kristjansson JK. Isolation, growth and genome of the Rhodothermus RM378 thermophilic bacteriophage. Extremophiles 2013; 18:261-70. [PMID: 24318108 DOI: 10.1007/s00792-013-0613-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 11/21/2013] [Indexed: 01/04/2023]
Abstract
Several bacteriophages that infect different strains of the thermophilic bacterium Rhodothermus marinus were isolated and their infection pattern was studied. One phage, named RM378 was cultivated and characterized. The RM378 genome was also sequenced and analyzed. The phage was grouped as a member of the Myoviridae family with A2 morphology. It had a moderately elongated head, with dimensions of 85 and 95 nm between opposite apices and a 150 nm long tail, attached with a connector to the head. RM378 showed a virulent behavior that followed a lytic cycle of infection. It routinely gave lysates with 10(11) pfu/ml, and sometimes reached titers as high as 10(13) pfu/ml. The titer remained stable up to 65 °C but the phage lost viability when incubated at higher temperatures. Heating for 30 min at 96 °C lowered the titer by 10(4). The RM378 genome consisted of ds DNA of 129.908 bp with a GC ratio of 42.0% and contained about 120 ORFs. A few structural proteins, such as the major head protein corresponding to the gp23 in T4, could be identified. Only 29 gene products as probable homologs to other proteins of known function could be predicted, with most showing only low similarity to known proteins in other bacteriophages. These and other studies based on sequence analysis of a large number of phage genomes showed RM378 to be distantly related to all other known T4-like phages.
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18
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Albuquerque L, Rainey FA, Nobre MF, da Costa MS. Schleiferia thermophila gen. nov., sp. nov., a slightly thermophilic bacterium of the phylum ‘Bacteroidetes’ and the proposal of Schleiferiaceae fam. nov. Int J Syst Evol Microbiol 2011; 61:2450-2455. [DOI: 10.1099/ijs.0.028852-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial isolate, with an optimum growth temperature of about 50 °C and an optimum pH for growth between 7.5 and 8.5, was recovered from a hot spring in the Furnas area of the Island of São Miguel in the Azores. The novel isolate is orange-pigmented, forms non-motile, rod-shaped cells that stain Gram-negative, is strictly aerobic, oxidase-positive and catalase-negative. The major fatty acids of strain TU-20T are 16 : 1ω6c, 17 : 0 iso 3-OH and 15 : 0 iso. Menaquinone 6 is the major respiratory quinone. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics, we describe a novel species of a novel genus represented by strain TU-20T ( = DSM 21410T = LMG 24594T) for which we propose the name Schleiferia thermophila gen nov., sp. nov. We also propose the family Schleiferiaceae fam. nov. to accommodate this new genus.
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Affiliation(s)
- Luciana Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Fred A. Rainey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - M. Fernanda Nobre
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
| | - Milton S. da Costa
- BIOCANT, 3060-197 Cantanhede, Portugal
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
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Albuquerque L, Rainey FA, Nobre MF, da Costa MS. Hydrotalea sandarakina sp. nov., isolated from a hot spring runoff, and emended descriptions of the genus Hydrotalea and the species Hydrotalea flava. Int J Syst Evol Microbiol 2011; 62:1603-1608. [PMID: 21890728 DOI: 10.1099/ijs.0.034496-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial isolates, designated AF-51(T) and AF-50, with an optimum growth temperature of about 45 °C and an optimum pH for growth between 6.0 and 6.5, were recovered from a hot spring in the Furnas, Área da Fonte 1825, on the Island of São Miguel in the Azores. Based on 16S rRNA gene sequence analysis, these strains were related most closely to the type strain of Hydrotalea flava at a pairwise similarity of 95.7%. The two strains were orange-pigmented and formed non-motile, rod-shaped cells that stained Gram-negative and were aerobic and oxidase- and catalase-positive. The major fatty acids were iso-C(15:0), iso-C(17:0) 3-OH and iso-C(16:0). The major respiratory quinone was menaquinone 7. Based on phylogenetic, physiological and biochemical characteristics, these strains from the Azores are considered to represent a single novel species of the genus Hydrotalea, for which the name Hydrotalea sandarakina sp. nov. is proposed. The type strain is AF-51(T) (=DSM 23241(T)=LMG 25526(T)). We provide emended descriptions of the genus Hydrotalea and of H. flava to reflect new results obtained in this study.
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Affiliation(s)
- Luciana Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Fred A Rainey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - M Fernanda Nobre
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
| | - Milton S da Costa
- Microbiology Unit, BIOCANT Biotechnological Park, 3060-197 Cantanhede, Portugal.,Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
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Wang YX, Liu JH, Xiao W, Zhang XX, Li YQ, Lai YH, Ji KY, Wen ML, Cui XL. Fodinibius salinus gen. nov., sp. nov., a moderately halophilic bacterium isolated from a salt mine. Int J Syst Evol Microbiol 2011; 62:390-396. [PMID: 21441370 DOI: 10.1099/ijs.0.025502-0] [Citation(s) in RCA: 27] [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, moderately halophilic, rod-shaped bacterium, designated strain YIM D17(T), was isolated from a sample of sediment from a salt mine in Yunnan, south-western China. The taxonomy of strain YIM D17(T) was investigated using a polyphasic approach. Strain YIM D17(T) was Gram-stain-negative, strictly aerobic and non-motile and formed pink colonies on marine agar. Optimal growth occurred at 37 °C, pH 7.5-8.0 and in the presence of 10-15 % (w/v) NaCl. The major menaquinone was MK-7. The polar lipid profile was composed predominantly of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, one phospholipid, one glycolipid and one aminolipid. Minor amounts of other lipids were also detectable. The predominant cellular fatty acids were iso-C(17 : 1)ω9c/10-methyl-C(16 : 0) (24.0 %), iso-C(15 : 0) (23.6 %) and C(16 : 1)ω7c/C(16 : 1)ω6c (13.8 %). The DNA G+C content was 43.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct clade with the genera Gracilimonas and Balneola (both in the phylum Bacteroidetes) and was related to the species Gracilimonas tropica, Balneola vulgaris and Balneola alkaliphila, with sequence similarities of 85.6 %, 83.0 % and 82.8 % to the respective type strains. On the basis of its phenotypic, chemotaxonomic and phylogenetic features, strain YIM D17(T) represents a novel species of a new genus, for which the name Fodinibius salinus gen. nov., sp. nov. is proposed. The type strain is YIM D17(T) ( = ACCC 10716(T) = DSM 21935(T)).
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Affiliation(s)
- Yong-Xia Wang
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Ji-Hui Liu
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Wei Xiao
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Xia Zhang
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100080, PR China
| | - Yi-Qing Li
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yong-Hong Lai
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Kai-Yan Ji
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Meng-Liang Wen
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xiao-Long Cui
- The Key Laboratory for Microbial Resources of the Ministry of Education, and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, PR China
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Empadinhas N, da Costa MS. Diversity, biological roles and biosynthetic pathways for sugar-glycerate containing compatible solutes in bacteria and archaea. Environ Microbiol 2010; 13:2056-77. [PMID: 21176052 DOI: 10.1111/j.1462-2920.2010.02390.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A decade ago the compatible solutes mannosylglycerate (MG) and glucosylglycerate (GG) were considered to be rare in nature. Apart from two species of thermophilic bacteria, Thermus thermophilus and Rhodothermus marinus, and a restricted group of hyperthermophilic archaea, the Thermococcales, MG had only been identified in a few red algae. Glucosylglycerate was considered to be even rarer and had only been detected as an insignificant solute in two halophilic microorganisms, a cyanobacterium, as a component of a polysaccharide and of a glycolipid in two actinobacteria. Unlike the hyper/thermophilic MG-accumulating microorganisms, branching close to the root of the Tree of Life, those harbouring GG shared a mesophilic lifestyle. Exceptionally, the thermophilic bacterium Persephonella marina was reported to accumulate GG. However, and especially owing to the identification of the key-genes for MG and GG synthesis and to the escalating numbers of genomes available, a plethora of new organisms with the resources to synthesize these solutes has been recognized. The accumulation of GG as an 'emergency' compatible solute under combined salt stress and nitrogen-deficient conditions now seems to be a disseminated survival strategy from enterobacteria to marine cyanobacteria. In contrast, the thermophilic and extremely radiation-resistant bacterium Rubrobacter xylanophilus is the only actinobacterium known to accumulate MG, and under all growth conditions tested. This review addresses the environmental factors underlying the accumulation of MG, GG and derivatives in bacteria and archaea and their roles during stress adaptation or as precursors for more elaborated macromolecules. The diversity of pathways for MG and GG synthesis as well as those for some of their derivatives is also discussed. The importance of glycerate-derived organic solutes in the microbial world is only now being recognized. Their stress-dependent accumulation and the molecular aspects of their interactions with biomolecules have already fuelled several emerging applications in biotechnology and biomedicine.
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Affiliation(s)
- Nuno Empadinhas
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal.
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Park S, Yoshizawa S, Kogure K, Yokota A. Rubricoccus marinus gen. nov., sp. nov., of the family 'Rhodothermaceae', isolated from seawater. Int J Syst Evol Microbiol 2010; 61:2069-2072. [PMID: 20851913 DOI: 10.1099/ijs.0.026294-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A coccoid- and amorphous-shaped, non-gliding, reddish bacterium, designated SG-29(T), was isolated from seawater in the western North Pacific Ocean near Japan. The strain was Gram-stain-negative, obligately aerobic, heterotrophic and catalase-positive. Nitrate was reduced to nitrogen and acid was produced from aesculin, turanose, 2-keto-gluconate and arabinose. Growth occurred with 1-5 % NaCl (optimum 2 % NaCl) and at 5-37 °C (optimum 20-30 °C). The G+C content of genomic DNA was 68.9 mol% (HPLC). The predominant isoprenoid quinone was MK-7 and the major cellular fatty acids (>10 %) were iso-C₁₇:₁ω9c, C₁₇:₁ω8c and iso-C₁₇:₀. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SG-29(T) belonged to the phylum Bacteroidetes. The most closely related strain was Rhodothermus obamensis JCM 9785(T), with which the isolate exhibited 86.1 % 16S rRNA gene sequence similarity. On the basis of phenotypic and phylogenetic features, strain SG-29(T) is classified in a novel genus and species within the family 'Rhodothermaceae', for which the name Rubricoccus marinus gen. nov., sp. nov. ( = NBRC 107124(T) = KCTC 23197(T)) is proposed.
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Affiliation(s)
- Sanghwa Park
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Kazuhiro Kogure
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Akira Yokota
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
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