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Marinigracilibium pacificum gen. nov., sp. nov., a starch-degrading bacterium isolated from tropical western Pacific. Antonie Van Leeuwenhoek 2023; 116:185-192. [PMID: 36374402 DOI: 10.1007/s10482-022-01792-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022]
Abstract
The Gram-stain-negative, golden-yellow-colored, non-spore-forming, strictly aerobic, slender rod-shaped bacterial strain, designated KN852T, was isolated from a seamount in the tropical western Pacific. The predominant respiratory quinone was MK-7 and the polar lipid profiles contained phosphatidylethanolamine, one unidentified phospholipid and six unidentified polar lipids. The predominant cellular fatty acids were iso-C15:0, summed feature 3(C16:1ω7c and/or iso-C15:0 2OH), iso-C17:0 3OH and iso-C15:1 G. Phylogenetic analyses of 16S rRNA gene sequence revealed that strain KN852T was affiliated with the family Flammeovirgaceae of the phylum Bacteroidota and formed a distinct lineage. The genomic DNA G + C content of strain KN852T was 34.8%. Collectively, based on phenotypic, chemotaxonomic, phylogenetic and genomic evidence presented, strain KN852T represents a novel species of a novel genus of the family Flammeovirgaceae, for which the name Marinigracilibium pacificum gen. nov., sp. nov. is proposed. The type strain is KN852T (= CGMCC 1.17119T = KCTC 72433T).
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2
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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: 174] [Impact Index Per Article: 34.8] [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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3
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Xu X, Zarecki R, Medina S, Ofaim S, Liu X, Chen C, Hu S, Brom D, Gat D, Porob S, Eizenberg H, Ronen Z, Jiang J, Freilich S. Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions. ISME JOURNAL 2018; 13:494-508. [PMID: 30291327 DOI: 10.1038/s41396-018-0288-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 09/10/2018] [Accepted: 09/14/2018] [Indexed: 12/26/2022]
Abstract
Microbial communities play a vital role in biogeochemical cycles, allowing the biodegradation of a wide range of pollutants. The composition of the community and the interactions between its members affect degradation rate and determine the identity of the final products. Here, we demonstrate the application of sequencing technologies and metabolic modeling approaches towards enhancing biodegradation of atrazine-a herbicide causing environmental pollution. Treatment of agriculture soil with atrazine is shown to induce significant changes in community structure and functional performances. Genome-scale metabolic models were constructed for Arthrobacter, the atrazine degrader, and four other non-atrazine degrading species whose relative abundance in soil was changed following exposure to the herbicide. By modeling community function we show that consortia including the direct degrader and non-degrader differentially abundant species perform better than Arthrobacter alone. Simulations predict that growth/degradation enhancement is derived by metabolic exchanges between community members. Based on simulations we designed endogenous consortia optimized for enhanced degradation whose performances were validated in vitro and biostimulation strategies that were tested in pot experiments. Overall, our analysis demonstrates that understanding community function in its wider context, beyond the single direct degrader perspective, promotes the design of biostimulation strategies.
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Affiliation(s)
- Xihui Xu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.,Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Raphy Zarecki
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Shlomit Medina
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Shany Ofaim
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel.,Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Xiaowei Liu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chen Chen
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shunli Hu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dan Brom
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Daniella Gat
- Department of Environmental Hydrology and Microbiology, The Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Sede-Boqer, 8499000, Israel
| | - Seema Porob
- Department of Environmental Hydrology and Microbiology, The Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Sede-Boqer, 8499000, Israel
| | - Hanan Eizenberg
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Zeev Ronen
- Department of Environmental Hydrology and Microbiology, The Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Sede-Boqer, 8499000, Israel
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel.
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Mehta A, Sidhu C, Pinnaka AK, Roy Choudhury A. Extracellular polysaccharide production by a novel osmotolerant marine strain of Alteromonas macleodii and its application towards biomineralization of silver. PLoS One 2014; 9:e98798. [PMID: 24932690 PMCID: PMC4059621 DOI: 10.1371/journal.pone.0098798] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 05/06/2014] [Indexed: 01/14/2023] Open
Abstract
The present study demonstrates exopolysaccharide production by an osmotolerant marine isolate and also describes further application of the purified polysaccharide for production of colloidal suspension of silver nanoparticles with narrow size distribution. Phylogenetic analysis based on 16S r RNA gene sequencing revealed close affinity of the isolate to Alteromonas macleodii. Unlike earlier reports, where glucose was used as the carbon source, lactose was found to be the most suitable substrate for polysaccharide production. The strain was capable of producing 23.4 gl(-1) exopolysaccharide with a productivity of 7.8 gl(-1) day(-1) when 15% (w/v) lactose was used as carbon source. Furthermore, the purified polysaccharide was able to produce spherical shaped silver nanoparticles of around 70 nm size as characterized by Uv-vis spectroscopy, Dynamic light scattering and Transmission electron microscopy. These observations suggested possible commercial potential of the isolated strain for production of a polysaccharide which has the capability of synthesizing biocompatible metal nanoparticle.
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Affiliation(s)
- Ananya Mehta
- CSIR - Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Chandni Sidhu
- CSIR - Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Anil Kumar Pinnaka
- CSIR - Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Anirban Roy Choudhury
- CSIR - Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
- * E-mail:
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5
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Kim JJ, Kim JH, Kwon YK, Kwon KK, Yang SH, Jang J, Heo SJ, Park HS, Jung WK, Lee Y, Kang DH, Oh C. Algivirga pacifica gen. nov., sp. nov., a Novel Agar-Degrading Marine Bacterium of the Family Flammeovirgaceae Isolated from Micronesia. Curr Microbiol 2013; 67:742-7. [DOI: 10.1007/s00284-013-0429-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 06/27/2013] [Indexed: 11/29/2022]
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Bhumika V, Srinivas TNR, Ravinder K, Anil Kumar P. Mariniradius saccharolyticus gen. nov., sp. nov., a member of the family
Cyclobacteriaceae
isolated from marine aquaculture pond water, and emended descriptions of the genus
Aquiflexum
and
Aquiflexum balticum. Int J Syst Evol Microbiol 2013; 63:2088-2094. [DOI: 10.1099/ijs.0.043919-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel marine, Gram-stain-negative, oxidase- and catalase- positive, rod-shaped bacterium, designated strain AK6T, was isolated from marine aquaculture pond water collected in Andhra Pradesh, India. The fatty acids were dominated by iso-C15 : 0, iso-C17 : 1ω9c, iso-C15 : 1 G, iso-C17 : 0 3-OH and anteiso-C15 : 0. Strain AK6T contained MK-7 as the sole respiratory quinone and phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid and seven unidentified lipids as polar lipids. The DNA G+C content of strain AK6T was 45.6 mol%. Phylogenetic analysis showed that strain AK6T formed a distinct branch within the family
Cyclobacteriaceae
and clustered with
Aquiflexum balticum
DSM 16537T and other members of the family
Cyclobacteriaceae
. 16S rRNA gene sequence analysis confirmed that
Aquiflexum balticum
DSM 16537T was the nearest neighbour, with pairwise sequence similarity of 90.1 %, while sequence similarity with the other members of the family was <88.5 %. Based on differentiating phenotypic characteristics and phylogenetic inference, strain AK6T is proposed as a representative of a new genus and species of the family
Cyclobacteriaceae
, as Mariniradius saccharolyticus gen. nov., sp. nov. The type strain of Mariniradius saccharolyticus is AK6T ( = MTCC 11279T = JCM 17389T). Emended descriptions of the genus
Aquiflexum
and
Aquiflexum balticum
are also proposed.
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Affiliation(s)
- V. Bhumika
- CSIR – Institute of Microbial Technology, Microbial Type Culture Collection and Gene bank, Sector 39A, Chandigarh – 160 036, India
| | - T. N. R. Srinivas
- CSIR – National Institute of Oceanography, Regional centre, PB No. 1913, Dr. Salim Ali Road, Kochi – 682018 (Kerala), India
| | - K. Ravinder
- CSIR – Institute of Microbial Technology, Microbial Type Culture Collection and Gene bank, Sector 39A, Chandigarh – 160 036, India
| | - P. Anil Kumar
- CSIR – Institute of Microbial Technology, Microbial Type Culture Collection and Gene bank, Sector 39A, Chandigarh – 160 036, India
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Draft Genome Sequence of Cesiribacter andamanensis Strain AMV16T, Isolated from a Soil Sample from a Mud Volcano in the Andaman Islands, India. GENOME ANNOUNCEMENTS 2013; 1:1/3/e00240-13. [PMID: 23682146 PMCID: PMC3656208 DOI: 10.1128/genomea.00240-13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here we report the 4.75-Mb genome of Cesiribacter andamanensis strain AMV16T, isolated from a soil sample from a mud volcano in the Andaman Islands, India.
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8
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Shalley S, Pradip Kumar S, Srinivas TNR, Suresh K, Anil Kumar P. Marinilabilia nitratireducens sp. nov., a lipolytic bacterium of the family Marinilabiliaceae isolated from marine solar saltern. Antonie van Leeuwenhoek 2012; 103:519-25. [DOI: 10.1007/s10482-012-9834-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/15/2012] [Indexed: 11/25/2022]
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9
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Zhang L, Shen X, Liu Y, Li S. Nafulsella turpanensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from soil. Int J Syst Evol Microbiol 2012; 63:1639-1645. [PMID: 22904215 DOI: 10.1099/ijs.0.044651-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, rod-shaped, gliding and pale-pink-pigmented bacterium, designated strain ZLM-10(T), was isolated from a soil sample collected from an arid area in Xinjiang province, China, and characterized in a taxonomic study using a polyphasic approach. The novel strain grew optimally at 30-37 °C and in the presence of 2 % (w/v) sea salts. The only respiratory quinone detected was MK-7 and the major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and two unidentified aminophospholipids. The DNA G+C content was 45.4 mol%. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZLM-10(T) was a member of the phylum Bacteroidetes and appeared most closely related to Cesiribacter roseus 311(T) (90.2 % sequence similarity), Marivirga sericea LMG 13021(T) (89.2 %), Cesiribacter andamanensis AMV16(T) (89.1 %) and Marivirga tractuosa DSM 4126(T) (89.1 %). On the basis of phenotypic and genotypic data and phylogenetic inference, strain ZLM-10(T) should be classified as a novel species of a new genus in the family Flammeovirgaceae, for which the name Nafulsella turpanensis gen. nov., sp. nov. is proposed. The type strain of the type species is ZLM-10(T) ( = CCTCC AB 208222(T) = KCTC 23983(T)).
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Northwest A&F University, Yangling, Shaanxi 712100, PR China.,State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xihui Shen
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yingbao Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Shiqing Li
- College of Resource and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China.,State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Northwest A&F University, Yangling, Shaanxi 712100, PR China.,State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
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10
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Choi EJ, Beatty DS, Paul LA, Fenical W, Jensen PR. Mooreia alkaloidigena gen. nov., sp. nov. and Catalinimonas alkaloidigena gen. nov., sp. nov., alkaloid-producing marine bacteria in the proposed families Mooreiaceae fam. nov. and Catalimonadaceae fam. nov. in the phylum Bacteroidetes. Int J Syst Evol Microbiol 2012; 63:1219-1228. [PMID: 22753528 DOI: 10.1099/ijs.0.043752-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial strains CNX-216(T) and CNU-914(T) were isolated from marine sediment samples collected from Palmyra Atoll and off Catalina Island, respectively. Both strains were gram-negative and aerobic and produce deep-orange to pink colonies and alkaloid secondary metabolites. Cells of strain CNX-216(T) were short, non-motile rods, whereas cells of strain CNU-914(T) were short, curved rods with gliding motility. The DNA G+C contents of CNX-216(T) and CNU-914(T) were respectively 57.7 and 44.4 mol%. Strains CNX-216(T) and CNU-914(T) contained MK-7 as the predominant menaquinone and iso-C15 : 0 and C16 : 1ω5c as the major fatty acids. Phylogenetic analyses revealed that both strains belong to the order Cytophagales in the phylum Bacteroidetes. Strain CNX-216(T) exhibited low 16S rRNA gene sequence identity (87.1 %) to the nearest type strain, Cesiribacter roseus 311(T), and formed a well-supported lineage that is outside all currently described families in the order Cytophagales. Strain CNU-914(T) shared 97.6 % 16S rRNA gene sequence identity with 'Porifericola rhodea' N5EA6-3A2B and, together with 'Tunicatimonas pelagia' N5DB8-4 and four uncharacterized marine bacteria isolated as part of this study, formed a lineage that is clearly distinguished from other families in the order Cytophagales. Based on our polyphasic taxonomic characterization, we propose that strains CNX-216(T) and CNU-914(T) represent novel genera and species, for which we propose the names Mooreia alkaloidigena gen. nov., sp. nov. (type strain CNX-216(T) = DSM 25187(T) = KCCM 90102(T)) and Catalinimonas alkaloidigena gen. nov., sp. nov. (type strain CNU-914(T) = DSM 25186(T) = KCCM 90101(T)) within the new families Mooreiaceae fam. nov. and Catalimonadaceae fam. nov.
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Affiliation(s)
- Eun Ju Choi
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0204, USA
| | - Deanna S Beatty
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0204, USA
| | - Lauren A Paul
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0204, USA
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0204, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0204, USA
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Liu M, Qi H, Luo X, Dai J, Peng F, Fang C. Cesiribacter roseus sp. nov., a pink-pigmented bacterium isolated from desert sand. Int J Syst Evol Microbiol 2012; 62:96-99. [DOI: 10.1099/ijs.0.028423-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A pink-pigmented, Gram-negative, rod-shaped, motile, strictly aerobic bacterium, designated strain 311T, was isolated from desert sand in Xinjiang, China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 311T was related closely to Cesiribacter
andamanensis AMV16T (94.6 % similarity). The DNA G+C content of strain 311T was 47.1 mol% and the major respiratory quinone was menaquinone 7 (MK-7). The main cellular fatty acids were C16 : 1ω5c (29.9 %), iso-C15 : 0 (21.9 %), iso-C17 : 0 3-OH (13.3 %) and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B; 13.0 %). Based on phenotypic and chemotaxonomic data and phylogenetic analysis, strain 311T is considered to represent a novel species of the genus Cesiribacter, for which the name Cesiribacter
roseus sp. nov. is proposed. The type strain is 311T ( = CCTCC AB 207142T = KACC 15456T).
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Affiliation(s)
- Ming Liu
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Huan Qi
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xuesong Luo
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China
| | - Jun Dai
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Fang Peng
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Chengxiang Fang
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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12
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Srinivas TNR, Nupur, Anil Kumar P. Aliidiomarina haloalkalitolerans sp. nov., a marine bacterium isolated from coastal surface seawater. Antonie van Leeuwenhoek 2011; 101:761-8. [PMID: 22200781 DOI: 10.1007/s10482-011-9690-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 12/13/2011] [Indexed: 11/30/2022]
Abstract
A novel Gram-negative, rod shaped, motile, non-sporing strictly aerobic bacterium, designated strain AK5(T), was isolated from a sea water sample collected near Visakhapatnam coast, Bay of Bengal, India. Colonies on marine agar were circular, 3-4 mm in diameter, creamish and rose with entire margin. Growth occurred at 10-40°C, 0.5-12% (w/v) NaCl and pH of 7-11. Strain AK5(T) was oxidase and catalase positive. The fatty acids were dominated by iso-branched saturated and unsaturated fatty acids with a high abundance of iso-C(15:0), iso-C(17:0) and summed feature 9 (as defined by MIDI). Q8 was found to be the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and four unidentified phospholipids as polar lipids. The DNA G+C content of strain AK5(T) was 54.7 ± 0.2 mol%. Phylogenetic analysis revealed that strain AK5(T) was a member of the genus Aliidiomarina and closely related to Aliidiomarina taiwanensis with a phylogenetic distance of 5.3% (94.7% 16S rRNA gene sequence similarity) and clustered with the same species. Results from the polyphasic taxonomy study support the conclusion that strain AK5(T) represents a novel Aliidiomarina species, for which the name Aliidiomarina haloalkalitolerans sp. nov. is proposed. The type strain of A. haloalkalitolerans is AK5(T) (= MTCC 11064(T) = JCM 17359(T)).
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Affiliation(s)
- T N R Srinivas
- Regional Centre, National Institute of Oceanography (CSIR), Kochi, Kerala, India.
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13
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Pagani I, Chertkov O, Lapidus A, Lucas S, Del Rio TG, Tice H, Copeland A, Cheng JF, Nolan M, Saunders E, Pitluck S, Held B, Goodwin L, Liolios K, Ovchinikova G, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Han C, Tapia R, Ngatchou-Djao OD, Rohde M, Göker M, Spring S, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Marivirga tractuosa type strain (H-43). Stand Genomic Sci 2011; 4:154-62. [PMID: 21677852 PMCID: PMC3111994 DOI: 10.4056/sigs.1623941] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Marivirga tractuosa (Lewin 1969) Nedashkovskaya et al. 2010 is the type species of the genus Marivirga, which belongs to the family Flammeovirgaceae. Members of this genus are of interest because of their gliding motility. The species is of interest because representative strains show resistance to several antibiotics, including gentamicin, kanamycin, neomycin, polymixin and streptomycin. This is the first complete genome sequence of a member of the family Flammeovirgaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,511,574 bp long chromosome and the 4,916 bp plasmid with their 3,808 protein-coding and 49 RNA genes are a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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