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Kim MC, Ju YH, Hwang UA, Liu P, Pak SH, Peng F. Pengzhenrongella sicca gen. nov., sp. nov., a new member of suborder Micrococcineae isolated from High Arctic tundra soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 34559624 DOI: 10.1099/ijsem.0.004988] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yellow bacterial strain, designated LRZ-2T, was isolated from High Arctic tundra near the settlement Ny-Ålesund in the Svalbard Archipelago, Norway. The cells were Gram-stain-positive, aerobic and non-sporulating. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain LRZ-2T represented a novel member of the suborder Micrococcineae. Its nearest phylogenetic neighbours were the members of the genus Luteimicrobium, with 16S rRNA gene sequence similarity of 95.3-96.9 %. The average nucleotide identity and digital DNA-DNA hybridization values between the genomes of strain LRZ-2T and its closely related strains were 77.4-74.3 % and 21.4-19.6 %, respectively. The DNA G+C content was 72.4 mol%. The peptidoglycan type of the isolate was A4β with an interpeptide bridge comprising l-ornithine and d-glutamic acid. The predominant menaquinone was MK-9 (H4) and the major fatty acids were anteiso-C15 : 0, C16 : 0, anteiso-C15 : 1 A, anteiso-C17 : 0 and iso-C15 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylinositol dimannoside, unidentified phosphoglycolipid, four unidentified phospholipids and two unidentified polar lipids. Strain LRZ-2T showed a 16S rRNA gene signature pattern consisting of nucleotides at positions 120 (A), 131-231 (C-G), 196 (C), 342-347 (C-G), 444-490 (A-U), 580-761 (C-G), 602-636 (C-G), 670-736 (A-U), 822-878 (G-C), 823-877 (G-C), 826-874 (C-G), 827 (U), 843 (C), 950-1231 (U-A), 1047-1210 (G-C), 1109 (C), 1145 (G), 1309-1328 (G-C), 1361 (G) and 1383 (C), which clearly distinguished it from all genera previously reported in the suborder Micrococcineae. On the basis of the phylogenetic, phenotypic and chemotaxonomic data, strain LRZ-2T is considered to represent a novel species of a new genus, for which the name Pengzhenrongella sicca gen. nov., sp. nov. is proposed. The type strain of Pengzhenrongella sicca is LRZ-2T (=CCTCC AB 2012163T=DSM 100332T).
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Affiliation(s)
- Myong Chol Kim
- Faculty of Forest Science, Kim Il Sung University, Pyongyang, Democratic People's Republic of Korea.,China Center for Type Culture Collection (CCTCC), College of Life Science, Wuhan University, Wuhan 430072, PR China
| | - Yun Hui Ju
- Faculty of Chemistry, Kim Il Sung University, Pyongyang, Democratic People's Republic of Korea
| | - Un A Hwang
- Faculty of Forest Science, Kim Il Sung University, Pyongyang, Democratic People's Republic of Korea
| | - Ping Liu
- China Center for Type Culture Collection (CCTCC), College of Life Science, Wuhan University, Wuhan 430072, PR China
| | - Sung Ho Pak
- Faculty of Forest Science, Kim Il Sung University, Pyongyang, Democratic People's Republic of Korea
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Science, Wuhan University, Wuhan 430072, PR China
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Rasool A, Nasim W, Xiao T, Ali W, Shafeeque M, Sultana SR, Fahad S, Munis MFH, Chaudhary HJ. Microbial diversity response in thallium polluted riverbank soils of the Lanmuchang. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 187:109854. [PMID: 31678700 DOI: 10.1016/j.ecoenv.2019.109854] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/19/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
Thallium (Tl) is a toxic element, but little is known about microbial communities' response to TI mobilization and sequestration. Here, we characterize the microbial communities and their feedbacks to Tl-pollution in riverbank soils to understand the distribution of microbial metal tolerance. These soils have been affected by pollution sourced from a Tl-rich mineralized area in Lanmuchang, Guizhou, China. In all studied soil samples, Proteobacteria, Acidobacteria, and Actinobacteria were revealed relatively in higher abundance at the phylum level. The results indicated that a number of microbial communities including Gemmatimonadetes, and Actinobacteria were correlated with total Tl, suggesting potential roles of these microbes to Tl tolerance. The patterns of phylogenetic beta-diversity in studied samples showed a high diversity of the microbial community in soils with high Tl concentrations. Sequence analysis of microbial community indicated that most of the environmental parameters in soils were associated with the major phylogenetic groups such as Gemmobacteria, Bryobacteria, Proteobacteria, Actinobacteria, Firmicutes, and Rhodobacteria. Some species of microbes, Nocardioides (genus), Actinomycetales (Order), Ralstonia (phyla) and Sphingomonas (genus) might are tolerant of Tl. These results provide direction to the microbial communities in the presence of elevated Tl concentration in Lanmuchang and shed light on bioremediation of Tl polluted locations.
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Affiliation(s)
- Atta Rasool
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Department of Environmental Sciences, COMSATS University, Islamabad (CUI), Vehari, 61100, Pakistan
| | - Wajid Nasim
- Department of Environmental Sciences, COMSATS University, Islamabad (CUI), Vehari, 61100, Pakistan; CIHEAM-Institut Agronomique Méditerranéen de Montpellier (IAMM), 3191Route de Mende, Montpellier, France; CSIRO Sustainable Ecosystems, National Research Flagship, Towoomba, QLD, 4350, Australia; Department of Agronomy, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur (IUB), Bahawalpur, Pakistan
| | - Tangfu Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Waqar Ali
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Muhammad Shafeeque
- University of Chinese Academy of Sciences, Beijing, 100049, China; Key Lab of Ecosystem Network Observation and Modelling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101, Beijing, China
| | - Syeda Refat Sultana
- Department of Environmental Sciences, COMSATS University, Islamabad (CUI), Vehari, 61100, Pakistan
| | - Shah Fahad
- Department of Agriculture, University of Swabi, Khyber Pakhtunkhwa (KPK), Pakistan
| | | | - Hassan Javed Chaudhary
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
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Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 421] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - 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
| | - 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
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Xiao E, Krumins V, Tang S, Xiao T, Ning Z, Lan X, Sun W. Correlating microbial community profiles with geochemical conditions in a watershed heavily contaminated by an antimony tailing pond. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 215:141-153. [PMID: 27182975 DOI: 10.1016/j.envpol.2016.04.087] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/22/2016] [Accepted: 04/25/2016] [Indexed: 06/05/2023]
Abstract
Mining activities have introduced various pollutants to surrounding aquatic and terrestrial environments, causing adverse impacts to the environment. Indigenous microbial communities are responsible for the biogeochemical cycling of pollutants in diverse environments, indicating the potential for bioremediation of such pollutants. Antimony (Sb) has been extensively mined in China and Sb contamination in mining areas has been frequently encountered. To date, however, the microbial composition and structure in response to Sb contamination has remained overlooked. Sb and As frequently co-occur in sulfide-rich ores, and co-contamination of Sb and As is observed in some mining areas. We characterized, for the first time, the microbial community profiles and their responses to Sb and As pollution from a watershed heavily contaminated by Sb tailing pond in Southwest China. The indigenous microbial communities were profiled by high-throughput sequencing from 16 sediment samples (535,390 valid reads). The comprehensive geochemical data (specifically, physical-chemical properties and different Sb and As extraction fractions) were obtained from river water and sediments at different depths as well. Canonical correspondence analysis (CCA) demonstrated that a suite of in situ geochemical and physical factors significantly structured the overall microbial community compositions. Further, we found significant correlations between individual phylotypes (bacterial genera) and the geochemical fractions of Sb and As by Spearman rank correlation. A number of taxonomic groups were positively correlated with the Sb and As extractable fractions and various Sb and As species in sediment, suggesting potential roles of these phylotypes in Sb biogeochemical cycling.
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Affiliation(s)
- Enzong Xiao
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Song Tang
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon S7N5B3, Canada
| | - Tangfu Xiao
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; Innovation Center and Key Laboratory of Waters Safety & Protection in the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Xiaolong Lan
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weimin Sun
- Guangdong Institute of Eco-environment and Soil Sciences, Guangzhou 510650, China; Department of Microbiology and Biochemistry, Rutgers University, New Brunswick, NJ 08901, USA.
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5
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Park S, Jung YT, Won SM, Yoon JH. Demequina litorisediminis sp. nov., isolated from a tidal flat, and emended description of the genus Demequina. Int J Syst Evol Microbiol 2016; 66:4197-4203. [PMID: 27469507 DOI: 10.1099/ijsem.0.001335] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, facultatively anaerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, GHD-1T, was isolated from a tidal flat sediment on the Yellow Sea, South Korea. It grew optimally at 30 °C, at pH 6.5-8.0 and in the presence of 1.0-2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain GHD-1T fell within the cluster comprising the type strains of species of the genus Demequina. Strain GHD-1T exhibited 16S rRNA gene sequence similarity values of 97.0-98.8 % to the type strains of Demequinaglobuliformis, D. salsinemoris, D. flava, D. sediminicola and D. activiva, and of 95.5-96.9 % to the type strains of the other species of the genus Demequina. The peptidoglycan type of strain GHD-1T is A4β based on l-Orn-l-Ser-l-Asp. It contained DMK-9(H4) and DMK-8(H4) as the major menaquinones and anteiso-C15 : 0, C16 : 0, iso-C16 : 0 and anteiso-C17 : 0 as the major fatty acids. The major polar lipids were phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified glycolipid. The DNA G+C content of strain GHD-1T was 68.7 mol%, and its DNA-DNA relatedness values with the type strains of five phylogenetically related species of the genus Demequina were 13-29 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain GHD-1T is separated from other recognized species of the genus Demequina. On the basis of the data presented, strain GHD-1T is considered to represent a novel species of the genus Demequina, for which the name Demequina litorisediminis sp. nov. is proposed. The type strain is GHD-1T (=KCTC 52260T=NBRC 112299T).
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Yong-Taek Jung
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea.,University of Science and Technology (UST), 113 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Sung-Min Won
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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6
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Yang J, Li X, Huang L, Jiang H. Actinobacterial Diversity in the Sediments of Five Cold Springs on the Qinghai-Tibet Plateau. Front Microbiol 2015; 6:1345. [PMID: 26648925 PMCID: PMC4663260 DOI: 10.3389/fmicb.2015.01345] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/16/2015] [Indexed: 11/13/2022] Open
Abstract
The actinobacterial diversity was investigated in the sediments of five cold springs in Wuli region on the Qinghai-Tibet Plateau using 16S rRNA gene phylogenetic analysis. The actinobacterial communities of the studied cold springs were diverse and the obtained actinobacterial operational taxonomic units were classified into 12 actinobacterial orders (e.g., Acidimicrobiales, Corynebacteriales, Gaiellales, Geodermatophilales, Jiangellales, Kineosporiales, Micromonosporales, Micrococcales, Nakamurellales, Propionibacteriales, Pseudonocardiales, Streptomycetales) and unclassified Actinobacteria. The actinobacterial composition varied among the investigated cold springs and were significantly correlated (r = 0.748, P = 0.021) to environmental variables. The actinobacterial communities in the cold springs were more diverse than other cold habitats on the Tibetan Plateau, and their compositions showed unique geographical distribution characteristics. Statistical analyses showed that biogeographical isolation and unique environmental conditions might be major factors influencing actinobacterial distribution among the investigated cold springs.
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Affiliation(s)
- Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Xiaoyan Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Liuqin Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
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7
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Draft genome sequences of eight type strains of the genus demequina. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00281-15. [PMID: 25883289 PMCID: PMC4400432 DOI: 10.1128/genomea.00281-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here, we report the draft genome sequences of the type strains of Demequina aestuarii, Demequina aurantiaca, Demequina flava, Demequina globuliformis, Demequina lutea, Demequina oxidasica, Demequina salsinemoris, and Demequina sediminicola. The genome sequences presented here will facilitate taxonomical, ecological, and functional studies of members of the genus Demequina.
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8
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Park S, Jung YT, Won SM, Lee JS, Yoon JH. Demequina activiva sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2015; 65:2042-2047. [PMID: 25825247 DOI: 10.1099/ijs.0.000217] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, facultatively anaerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, designated BS-12M(T), was isolated from a tidal flat sediment on the South Sea, South Korea. Strain BS-12M(T) grew optimally at 35 °C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain BS-12M(T) fell within the cluster comprising the type strains of species of the genus Demequina, joining the type strain of Demequina aestuarii with which it shared the highest sequence similarity (98.6%). It exhibited 16S rRNA gene sequence similarity of 96.1-97.9% to the type strains of other species of the genus Demequina. The peptidoglycan type of strain BS-12M(T) was A4β based on L-Orn -L-Ser -D-Glu. Strain BS-12M(T) contained demethylmenaquinone-9(H4) as the major menaquinone and anteiso-C15:0 and C16:0 as the major fatty acids. The major polar lipids of strain BS-12M(T) were phosphatidylinositol and phosphatidylinositolmannoside. The DNA G+C content of strain BS-12M(T) was 70.7 mol% and its DNA-DNA relatedness values with the type strains of five phylogenetically related species of the genus Demequina were 15-34%. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain BS-12M(T) is separate from other species of the genus Demequina. On the basis of the data presented, strain BS-12M(T) is considered to represent a novel species of the genus Demequina, for which the name Demequina activiva sp. nov. is proposed. The type strain is BS-12M(T) ( =KCTC 29674(T) = NBRC 110675T).
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Yong-Taek Jung
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
- University of Science and Technology (UST), 113 Gwahak-ro, Yuseong-gu, Daejeon, South Korea
| | - Sung-Min Won
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Jung-Sook Lee
- Microbiological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejeon, South Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
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Abstract
Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost features and between sites. Some microorganisms are even active at subzero temperatures in permafrost. An emerging concern is the impact of climate change and the possibility of subsequent permafrost thaw promoting microbial activity in permafrost, resulting in increased potential for greenhouse-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles.
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Affiliation(s)
- Janet K Jansson
- 1] Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS 70A-3317 Berkeley, California 94720, USA. [2] Joint Genome Institute (JGI), 2800 Mitchell Drive, Walnut Creek, California 94598, USA. [3] Joint BioEnergy Institute (JBEI), 5885 Hollis Street, Emeryville, California 94608, USA. [4] Danish Center for Permafrost (CENPERM), University of Copenhagen, Oester Voldgade 10, DK-1350 Copenhagen, Denmark. [5] Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, California 94720-3102, USA
| | - Neslihan Taş
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS 70A-3317 Berkeley, California 94720, USA
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Hamada M, Tamura T, Yamamura H, Suzuki KI, Hayakawa M. Demequina
flava sp. nov. and
Demequina
sediminicola sp. nov., isolated from sea sediment. Int J Syst Evol Microbiol 2013; 63:249-253. [DOI: 10.1099/ijs.0.039297-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel Gram-stain-positive bacteria, designated HR08-7T and HR08-43T, were isolated from a sea sediment sample from Rishiri Island, Hokkaido, Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strains HR08-7T and HR08-43T and the members of the genus
Demequina
formed a monophyletic cluster with similarity range of 95.5–99.0 %. The peptidoglycan type of strains HR08-7T and HR08-43T was A4β. The predominant menaquinone of both strains was demethylmenaquinone DMK-9(H4) and the major fatty acid was anteiso-C15 : 0. The DNA G+C contents of strains HR08-7T and HR08-43T were 64.5 and 62.4 mol%, respectively. The results of phylogenetic analysis and DNA–DNA hybridization, along with differences of strains HR08-7T and HR08-43T from the recognized
Demequina
species in phenotypic characteristics, indicate that the two strains merit classification as representatives of two novel species of the genus
Demequina
, for which the names
Demequina
flava sp. nov. and
Demequina
sediminicola sp. nov. are proposed; the type strains are HR08-7T ( = NBRC 105854T = DSM 24865T) and HR08-43T ( = NBRC 105855T = DSM 24867T), respectively.
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Affiliation(s)
- Moriyuki Hamada
- Division of Applied Biological Sciences, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Takeda-4, Kofu, Yamanashi 400-8511, Japan
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomohiko Tamura
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hideki Yamamura
- Division of Applied Biological Sciences, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Takeda-4, Kofu, Yamanashi 400-8511, Japan
| | - Ken-ichiro Suzuki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Masayuki Hayakawa
- Division of Applied Biological Sciences, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Takeda-4, Kofu, Yamanashi 400-8511, Japan
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11
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Hamada M, Tamura T, Yamamura H, Suzuki KI, Hayakawa M. Lysinimicrobium mangrovi gen. nov., sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove. Int J Syst Evol Microbiol 2012; 62:1731-1735. [DOI: 10.1099/ijs.0.035493-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain of Gram-staining-positive bacterium, designated HI08-69T, was isolated from the rhizosphere of a mangrove on Iriomote Island, Japan, and its taxonomic position was investigated by a polyphasic approach. The strain had peptidoglycan of the A4α type, with lysine as the diagnostic diamino acid. The predominant menaquinone was demethylmenaquinone DMK-9(H4) and the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified polar lipid but minor amounts of other polar lipids were also detected. The genomic DNA G+C content of strain HI08-69T was 71.7 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, the novel strain and members of the genus
Demequina
formed a monophyletic cluster, with pairwise sequence similarities of 95.6–96.8 %. However, strain HI08-69T was clearly distinguishable from all established members of the genus
Demequina
in terms of several chemotaxonomic characteristics. On the basis of the phenotypic and genotypic characteristics, strain HI08-69T represents a novel species in a new genus for which the name Lysinimicrobium mangrovi gen. nov., sp. nov. is proposed. The type strain of the type species is HI08-69T ( = NBRC 105856T = DSM 24868T).
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Affiliation(s)
- Moriyuki Hamada
- Division of Applied Biological Sciences, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Takeda-4, Kofu, Yamanashi 400-8511, Japan
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomohiko Tamura
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hideki Yamamura
- Division of Applied Biological Sciences, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Takeda-4, Kofu, Yamanashi 400-8511, Japan
| | - Ken-ichiro Suzuki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Masayuki Hayakawa
- Division of Applied Biological Sciences, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Takeda-4, Kofu, Yamanashi 400-8511, Japan
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Demequina globuliformis sp. nov., Demequina oxidasica sp. nov. and Demequina aurantiaca sp. nov., actinobacteria isolated from marine environments, and proposal of Demequinaceae fam. nov. Int J Syst Evol Microbiol 2011; 61:1322-1329. [DOI: 10.1099/ijs.0.024299-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-stain-positive actinobacterial strains, designated YM24-125T, YM05-1041T and YM12-102T, were isolated from marine environments. Phylogenetic analysis based on 16S rRNA gene sequences indicated that they belonged to the suborder Micrococcineae and were most closely related to members of the genus Demequina with 95.0–98.4 % sequence similarities. Cells of strains YM05-1041T and YM12-102T were rod-shaped, similar to members of the genus Demequina, while cells of strain YM24-125T were cocci to short ovoid rods. All strains grew in the absence of NaCl, but tolerated up to 15 % NaCl. The major menaquinone was demethylmenaquinone DMK-9 (H4) and the major polar lipids were phosphatidylinositol, diphosphatidylglycerol and phosphatidyglycerol. All strains contained straight-chain, iso-branched and anteiso-branched saturated fatty acids. The DNA G+C contents were 65.3–67.3 mol%. The peptidoglycans of strains YM05-1041T and YM12-102T were the A4β type with ornithine while that of strain YM24-125T contained ornithine and lysine as diamino acids. Phylogenetic analyses and differences in physiological and biochemical characteristics indicated that these three isolates represent novel species within the genus Demequina, for which the names Demequina globuliformis sp. nov. (with YM24-125T = NBRC 106266T = KCTC 19747T = MBIC 08349T as the type strain), Demequina oxidasica sp. nov. (with YM05-1041T = NBRC 106264T = KCTC 19746T = MBIC 08346T as the type strain) and Demequina aurantiaca sp. nov. (with YM12-102T = NBRC 106265T = KCTC 19745T = MBIC 08347T as the type strain) are proposed. Based on differences in the quinone system, the presence of demethylmenaquinone DMK-9(H4) and the pattern of 16S rRNA signatures, the three novel strains and current members of the genus Demequina represent a unique family within the suborder Micrococcineae. Therefore, the family Demequinaceae fam. nov. is also proposed.
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Matsumoto A, Nakai K, Morisaki K, Ōmura S, Takahashi Y. Demequina salsinemoris sp. nov., isolated on agar media supplemented with ascorbic acid or rutin. Int J Syst Evol Microbiol 2010; 60:1206-1209. [DOI: 10.1099/ijs.0.012617-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains, KV-810T, KV-811 and KV-816, were isolated from mangrove soil from a southern island in Japan on media supplemented with ascorbic acid or rutin. These strains contained l-ornithine as the diagnostic diamino acid in the cell-wall peptidoglycan and DMK-9(H4) as the predominant menaquinone. The G+C content of the DNA was 70–72 mol%. These characteristics in combination with 16S rRNA gene sequence analysis revealed that the novel strains belonged to the genus Demequina. The DNA–DNA hybridization values showed that the three new strains belonged to the same species, a novel species of the genus Demequina. Therefore strains KV-810T, KV-811 and KV-816 are proposed as representing a novel species, Demequina salsinemoris sp. nov. The type strain is KV-810T (=DSM 22060T=NBRC 105323T).
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Affiliation(s)
- Atsuko Matsumoto
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Kengo Nakai
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Kurimi Morisaki
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yōko Takahashi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
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Description of Tessaracoccus profundi sp.nov., a deep-subsurface actinobacterium isolated from a Chesapeake impact crater drill core (940 m depth). Antonie van Leeuwenhoek 2009; 96:515-26. [PMID: 19669589 DOI: 10.1007/s10482-009-9367-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 07/13/2009] [Indexed: 10/20/2022]
Abstract
A novel actinobacterium, designated CB31(T), was isolated from a 940 m depth sample of a drilling core obtained from the Chesapeake meteor impact crater. The strain was isolated aerobically on R2A medium agar plates supplemented with NaCl (20 g l(-1)) and MgCl2 x 6 H2O (3 g l(-1)). The colonies were circular, convex, smooth and orange. Cells were slightly curved, rod-shaped in young cultures and often appeared in pairs. In older cultures cells were coccoid. Cells stained Gram-positive, were non-motile and did not form endospores. The diagnostic diamino acid of the peptidoglycan was LL: -diaminopimelic acid. The polar lipids included phosphatidylglycerol, diphosphatidglycerol, four different glycolipids, two further phospholipids and one unidentified lipid. The dominant menaquinone was MK-9(H(4)) (70%). The major cellular fatty acid was anteiso C15:0 (83%). The DNA G + C content was 68 mol%. The strain grew anaerobically by reducing nitrate to nitrite or by fermenting glucose. It was catalase positive and oxidase negative. It grew between 10 and 45 degrees C, with an optimum between 35 and 40 degrees C. The pH range for growth was 5.7-9.3, with an optimum at pH 7.5. The closest phylogenetic neighbors based on 16S rRNA gene sequence identity were members of the genus Tessaracoccus (95-96% identity). On the basis of phenotypic and phylogenetic distinctiveness, strain CB31(T) is considered to represent a novel species of the genus Tessaracoccus, for which we propose the name Tessaracoccus profundi sp. nov.. It is the first member of this genus that has been isolated from a deep subsurface environment. The type strain is CB31(T) (=NCIMB 14440(T) = DSM 21240(T)).
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