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Octaviana S, Lorenczyk S, Ackert F, Fenske L, Wink J. Four new members of the family Cytophagaceae: Chryseosolibacter histidini gen. nov., sp. nov., Chryseosolibacter indicus gen. nov., sp. nov., Dawidia cretensis, gen. nov., sp. nov., and Dawidia soli, gen. nov., sp. nov. isolated from diverse habitat. Antonie Van Leeuwenhoek 2022; 115:1059-1072. [PMID: 35732971 PMCID: PMC9296434 DOI: 10.1007/s10482-022-01756-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/28/2022] [Indexed: 11/29/2022]
Abstract
Four novel strains were isolated: PWU4T and PWU20T were both from soil in Germany, PWU5T was isolated from soil in India and PWU37T was obtained from sheep faeces collected on the Island of Crete. Cells of each were observed to be Gram-negative, strictly aerobic, rod shaped, and to grow optimally between 28 and 34 °C, between pH 7.0 and 8.0 and without the addition of NaCl. The strains were found to be catalase and oxidase-negative and able to grow on most mono- and disaccharides, a few polysaccharides and organic acids. Their predominant menaquinone was identified as MK-7. Their major fatty acids were identified as C16:1ω7c (PWU4T and PWU20T) and C16:1ω5c (PWU5T and PWU37T). The DNA G + C contents of strains PWU4T, PWU20T, PWU5T and PWU37T were determined to be 50.2 mol%, 51.6 mol %, 39.8 mol% and 53.8 mol%, respectively. The 16S rRNA gene sequence analysis revealed that the close relatives Ohtaekwangia koreensis 3B-2T and Ohtaekwangia kribbensis 10AOT share less than 93.8% sequence similarity. The strains were classified in two groups, where PWU4T and PWU20T share 93.0% sequence similarity, and PWU5T and PWU37T share 97.5% sequence similarity. However, the members of each group were concluded to represent different species based on the low average nucleotide identity (ANI) of their genomes, 69.7% and 83.8%, respectively. We propose that the four strains represent four novel species of two new genera in the family Cytophagaceae. The type species of the novel genus Chryseosolibacter is Chryseosolibacter histidini gen. nov., sp. nov. with the type strain PWU4T (= DSM 111594T = NCCB 100798T), whilst strain PWU20T (= DSM 111597T = NCCB 100800T) is the type strain of a second species, Chryseosolibacter indicus sp. nov. The type species of the novel genus Dawidia is Dawidia cretensis gen. nov., sp. nov. with the type strain PWU5T (= DSM 111596T = NCCB 100799T), whilst strain PWU37T (= DSM 111595T = NCCB 100801T) is the type stain of a second species, Dawidia soli sp. nov.
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Affiliation(s)
- Senlie Octaviana
- Microbial Strain Collection, Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany.,Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Stefan Lorenczyk
- Faculty of Mechanical Engineering, Technical University of Braunschweig, Schleinitzstraße 20, 38106, Brunswick, Germany
| | - Frederike Ackert
- Microbial Strain Collection, Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany
| | - Linda Fenske
- Bioinformatic and Systems Biology, Justus Liebig University Gießen, Heinrich-Buff-Ring 58, 35390, Gießen, Germany
| | - Joachim Wink
- Microbial Strain Collection, Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany.
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Bziuk N, Maccario L, Sørensen SJ, Schikora A, Smalla K. Barley Rhizosphere Microbiome Transplantation – A Strategy to Decrease Susceptibility of Barley Grown in Soils With Low Microbial Diversity to Powdery Mildew. Front Microbiol 2022; 13:830905. [PMID: 35685930 PMCID: PMC9173696 DOI: 10.3389/fmicb.2022.830905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/26/2022] [Indexed: 11/23/2022] Open
Abstract
Beneficial bacteria in the rhizosphere are known to trigger faster and stronger plant immune responses to biotic and abiotic stressors. In the present study, we aimed to test the hypothesis that a rhizosphere microbiome transplant (RMT) may improve the immune response and reduce the disease rates of barley (Hordeum vulgare). This hypothesis was tested in a greenhouse system with the powdery mildew-causing fungus Blumeria graminis f. sp. hordei (Bgh). Detached rhizosphere microbiome from barley grown in a field soil was transplanted to barley seedlings grown in potting soil with reduced microbial diversity. Saline-treated plants served as control. At the three-leaf stage, barley was infected with Bgh. Decreased susceptibility to Bgh was observed for barley treated with the RMT as displayed by lower Bgh pustule counts in a detached leaf assay. A trend toward enhanced relative transcript abundances of the defense-related genes PR1b and PR17b was observed in leaves, 24 h after the Bgh challenge, when compared to the control. Moreover, 10 days after the Bgh challenge, the barley rhizosphere microbiome was harvested and analyzed by sequencing of 16S rRNA gene amplicons. The microbial community composition was significantly influenced by the RMT and displayed higher microbial diversity compared to the control. Furthermore, microbial beta-diversity and predicted functional profiles revealed a treatment-dependent clustering. Bacterial isolates from the RMT showed in vitro plant beneficial traits related to induced resistance. Our results showed that transplantation of a rhizosphere microbiome could be a sustainable strategy to improve the health of plants grown in potting soil with low microbial diversity under greenhouse conditions.
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Affiliation(s)
- Nina Bziuk
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Lorrie Maccario
- Section of Microbiology, Copenhagen University, Copenhagen, Denmark
| | | | - Adam Schikora
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- *Correspondence: Kornelia Smalla,
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Kraut-Cohen J, Zolti A, Shaltiel-Harpaz L, Argaman E, Rabinovich R, Green SJ, Minz D. Effects of tillage practices on soil microbiome and agricultural parameters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135791. [PMID: 31810706 DOI: 10.1016/j.scitotenv.2019.135791] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/18/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
No-tillage (NT) is a common soil-conservation management practice with known agricultural advantages and drawbacks. However, its short- and long-term effects on the soil microbiome have not been well established. Here, we compared conventional (CT), minimal (MT) and NT practices in two agricultural fields in the north of Israel over a period of 3 years. Edaphic properties, plant-associated pests, weed species abundance and soil microbial community structure were assessed to examine the effects of tillage. Tillage significantly altered physical and chemical soil properties, and a significant increase in hydrolytic and redox microbial activities was observed in NT soils from both sites. Consistent with this, the microbial community structure of NT samples diverged significantly over time from those of CT samples. Repetitive tillage and even a single tillage event caused significant changes in the relative abundance of microorganisms at taxonomic levels ranging from phylum to OTU. However, no significant difference between treatments was found in microbial community alpha-diversity or crop yield. Conversely, higher levels of weed diversity and some pests number were found in NT samples. Overall, we demonstrate that tillage plays a major role in shaping microbial community structure, and in influencing additional environmental, ecological and agricultural soil parameters.
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Affiliation(s)
- Judith Kraut-Cohen
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel.
| | - Avihai Zolti
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel; Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Liora Shaltiel-Harpaz
- Migal Galilee Research Institute, P.O. Box 831, Kiryat Shmona, 11016, Israel; Department of Environmental Sciences, Tel Hai College, Upper Galilee, 12210, Israel
| | - Eli Argaman
- Soil Erosion Research Station, Soil Conservation & Drainage Division, Ministry of Agriculture & Rural Development, Israel
| | | | - Stefan J Green
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
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Kim H, Kang H, Joh K. Allopseudarcicella aquatilis gen. nov., sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2019; 69:3574-3580. [DOI: 10.1099/ijsem.0.003664] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Haneul Kim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Heeyoung Kang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Kiseong Joh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
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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: 190] [Impact Index Per Article: 38.0] [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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Chen WM, Cai CY, Sheu SY. Sandaracinomonas limnophila gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from a freshwater mesocosm. Int J Syst Evol Microbiol 2019; 70:2178-2185. [PMID: 31199228 DOI: 10.1099/ijsem.0.003532] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated FSY-15T was isolated from a freshwater mesocosm in Taiwan and characterised using a polyphasic taxonomic approach. Cells of strain FSY-15T were Gram-negative, aerobic, non-spore forming, non-motile rods and formed orange coloured colonies. Growth occurred at 20-30 °C (optimum, 25 °C), at pH 6-7.5 (optimum, pH 7) and with 0-0.5 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-15T formed a phylogenetic lineage in the the family Cytophagaceae. Strain FSY-15T was most closely related to the genera Pseudarcicella and Arcicella, and the levels of 16S rRNA gene sequence identity with respect to members of related genera are less than 94.1 %. Strain FSY-15T showed less than 68.8 % average nucleotide identity and less than 24.7 % digital DNA-DNA hybridisation identity compared to the type strains of related genera within the family Cytophagaceae. The predominant fatty acids were iso-C15 : 0, C16 : 1ω5c and the major hydroxyl fatty acid was iso-C15 : 0 3-OH. The major isoprenoid quinone was MK-7 and the DNA G+C content was 35.8 mol%. The major polar lipids were phosphatidylethanolamine and several uncharacterised aminophospholipid, aminolipid, phospholipid and lipid. The major polyamine was spermidine. On the basis of the genotypic and phenotypic data, strain FSY-15T represents a novel species of a new genus in the family Cytophagaceae, for which the name Sandaracinomonas limnophila gen. nov., sp. nov. is proposed. The type strain is FSY-15T (=BCRC 81011T =LMG 29732T =KCTC 52445T).
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Affiliation(s)
- Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung city, Taiwan ROC
| | - Cheng-Ye Cai
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan ROC
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan ROC
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Szuróczki S, Khayer B, Spröer C, Toumi M, Szabó A, Felföldi T, Schumann P, Tóth E. Arundinibacter roseus gen. nov., sp. nov., a new member of the family Cytophagaceae. Int J Syst Evol Microbiol 2019; 69:2076-2081. [PMID: 31099731 DOI: 10.1099/ijsem.0.003436] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-stain-negative, aerobic, non-motile, oxidase- and catalase positive, rod-shaped, pink-coloured bacterial strains, DMA-K-7aT, DMA-K-1 and DMG-N-1, were isolated from water sampled at Lake Fertő/Neusiedler See (Hungary). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strains form a distinct linage within the family Cytophagaceae of the phylum Bacteroidetes, and their closest relatives are Rhabdobacter roseus R49T (95.66 %) and Dyadobacter sediminis Z12T (95.38 %). The assembled genome of strain DMA-K-7aT had a total length of 5.8 Mb and a DNA G+C content of 45.7 mol%. The major isoprenoid quinone was menaquinone-7 (MK-7). The major cellular fatty acids were C16 : 1 ω7c, iso-C15 : 0, C16 : 1 ω5c, C16 : 0 and iso-C17 : 0 3-OH. The polar lipid profile contained phosphatidylethanolamine, phosphatidylserine, an unknown aminolipid, an unknown glycolipid and five unknown lipids. Flexirubin-type pigments were absent. Strain DMA-K-7aT (=DSM 106737T=NCAIM B.02641T) is proposed as the type strain of a new genus and species in the family Cytophagaceae, for which the name Arundinibacter roseus gen. nov., sp. nov. is proposed.
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Affiliation(s)
- S Szuróczki
- 1Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny., 1/C, H-1117 Budapest, Hungary
| | - B Khayer
- 2Department of Water Hygiene, National Public Health Center, Albert Flórián út 2-6. H-1097 Budapest, Hungary
| | - C Spröer
- 3Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - M Toumi
- 1Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny., 1/C, H-1117 Budapest, Hungary
| | - A Szabó
- 1Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny., 1/C, H-1117 Budapest, Hungary
| | - T Felföldi
- 1Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny., 1/C, H-1117 Budapest, Hungary
| | - P Schumann
- 3Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - E Tóth
- 1Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny., 1/C, H-1117 Budapest, Hungary
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8
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Li Y, Guo XH, Dang YR, Sun LL, Zhang XY, Chen XL, Qin QL, Wang P. Complete genome sequence of Arcticibacterium luteifluviistationis SM1504 T, a cytophagaceae bacterium isolated from Arctic surface seawater. Stand Genomic Sci 2018; 13:33. [PMID: 30505389 PMCID: PMC6258284 DOI: 10.1186/s40793-018-0335-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/10/2018] [Indexed: 11/10/2022] Open
Abstract
Arcticibacterium luteifluviistationis SM1504T was isolated from Arctic surface seawater and classified as a novel genus of the phylum Bacteroides. To date, no Arcticibacterium genomes have been reported, their genomic compositions and metabolic features are still unknown. Here, we reported the complete genome sequence of A. luteifluviistationis SM1504T, which comprises 5,379,839 bp with an average GC content of 37.20%. Genes related to various stress (such as radiation, osmosis and antibiotics) resistance and gene clusters coding for carotenoid and flexirubin biosynthesis were detected in the genome. Moreover, the genome contained a 245-kb genomic island and a 15-kb incomplete prophage region. A great percentage of proteins belonging to carbohydrate metabolism especially in regard to polysaccharides utilization were found. These related genes and metabolic characteristics revealed genetic basis for adapting to the diverse extreme Arctic environments. The genome sequence of A. luteifluviistationis SM1504T also implied that the genus Arcticibacterium may act as a vital organic carbon matter decomposer in the Arctic seawater ecosystem.
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Affiliation(s)
- Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
| | - Xiao-Han Guo
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
| | - Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
| | - Lin-Lin Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No.1, Wenhai Rd, Qingdao, 266237 China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No.1, Wenhai Rd, Qingdao, 266237 China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No.1, Wenhai Rd, Qingdao, 266237 China
| | - Peng Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
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Ambika Manirajan B, Suarez C, Ratering S, Rusch V, Geissler-Plaum R, Cardinale M, Schnell S. Spirosoma pollinicola sp. nov., isolated from pollen of common hazel (Corylus avellana L.). Int J Syst Evol Microbiol 2018; 68:3248-3254. [DOI: 10.1099/ijsem.0.002973] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Binoy Ambika Manirajan
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Christian Suarez
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Stefan Ratering
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Volker Rusch
- 2Institute for Integrative Biology, Old Herborn University Foundation, Herborn, Germany
| | - Rita Geissler-Plaum
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Massimiliano Cardinale
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
| | - Sylvia Schnell
- 1Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, 35392, Germany
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10
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Ohn JE, Ten LN, Kim BO, Cho YJ, Jung HY. Hymenobacter rufus sp. nov., a bacterium isolated from soil. Int J Syst Evol Microbiol 2018; 68:2983-2989. [PMID: 30028287 DOI: 10.1099/ijsem.0.002934] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, S1-2-2-6T, was isolated from a soil sample collected in Jeollabuk-do province, Republic of Korea. Cells of this strain were observed to be Gram-stain-negative, short and rod-shaped, and colonies were red to pink in colour. Analysis of 16S rRNA gene sequences identified this strain as representing a member of the genus Hymenobacter in the family Cytophagaceae, with the highest levels of sequence similarity being observed in relation to Hymenobacter terrae DG7AT (98.2 %), Hymenobacter rubidus DG7BT (97.9 %), Hymenobacter soli PB17T (97.7 %), and Hymenobacter daeguensis 16F3Y-2T (97.3 %). Growth of S1-2-2-6T was observed at 4-30 °C, pH 6-8 and in the presence of 0-0.5 % NaCl. The predominant respiratory quinone of this strain was menaquinone-7, the major fatty acids were C15 : 0 iso, C15 : 0 anteiso, and Summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), and the major polar lipid was phosphatidylethanolamine. The genomic DNA G+C content of S1-2-2-6T was 60.7 mol%. DNA-DNA hybridization experiments with H. terrae, H. rubidus, H. soli and H. daeguensisresulted in relatedness values of 35.9 and 38.4 %, 34.2 and 30.4 %, 28.3 and 33.1 %, and 23.5 and 27.9 %, respectively. These DNA-DNA hybridization results, in addition to some differentiating phenotypic properties, clearly indicate that S1-2-2-6T is a representative of a novel species of the genus Hymenobacter, for which the name Hymenobacter rufus sp. nov. is proposed. The type strain is S1-2-2-6T (=KCTC 52736T=JCM 32196T).
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Affiliation(s)
- Jeong-Eun Ohn
- 1School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Leonid N Ten
- 2School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Byung-Oh Kim
- 1School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Young-Je Cho
- 3School of Food Science and Biotechnology/Food and Bio-Industry Research Institute, Kyungpook National University, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hee-Young Jung
- 4Institute of Plant Medicine, Kyungpook National University, Daegu 41566, Republic of Korea.,2School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
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Chhetri G, Yang D, Choi J, Kim H, Seo T. Edaphorhabdus rosea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from soil in South Korea. Antonie van Leeuwenhoek 2018; 111:2385-2392. [PMID: 30027519 DOI: 10.1007/s10482-018-1127-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/09/2018] [Indexed: 11/30/2022]
Abstract
A Gram-stain negative, aerobic, oxidase and catalase positive, non-flagellated, pink coloured bacterium with gliding motility, designated as strain UDD1T was isolated from soil. The bacterium lacked flexirubin-type pigments. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain UDD1T formed a lineage within the family Cytophagaceae of the phylum Bacteroidetes, and forms a distinct clade with type strains of the closely related genus Pontibacter with similarities of 91.36-93.62%. Strain UDD1T contained MK-7 as the predominant menaquinone and summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B) and iso-C15:0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine and an unidentified glycolipid. The DNA G+C content of strain UDD1T was 49 mol%. On the basis of phenotypic, genotypic and phylogenetic analyses, the strain UDD1T represents a novel species of a new genus in the family Cytophagaceae, for which the name Edaphorhabdus rosea gen. nov., sp. nov., is proposed. The type strain of Edaphorhabdus rosea is UDD1T (= KCTC 62117T = JCM 32366T). The Digital Protologue Database Taxon number for strain UDD1T is GA00058.
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Dahye Yang
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Jiwon Choi
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Hyungdong Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea.
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Hymenobacter aquatilis sp. nov., isolated from a mesotrophic artificial lake. Int J Syst Evol Microbiol 2018; 68:2036-2041. [DOI: 10.1099/ijsem.0.002792] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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13
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Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov., two novel members of the family Cytophagaceae isolated from forest soil. Arch Microbiol 2018; 200:1067-1074. [PMID: 29737366 DOI: 10.1007/s00203-018-1521-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/06/2018] [Accepted: 04/26/2018] [Indexed: 10/17/2022]
Abstract
Two strains of bacteria designated strains S-53T and A27T were isolated from forest soil and subjected to polyphasic characterization. Cells were aerobic, Gram-staining-negative, catalase- and oxidase- positive, non-motile, non-spore-forming, rod-shaped, and yellow-pigmented. Flexirubin-type pigments were present. Both strains were positive for PNPG, hydrolysed casein, and tyrosine. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strains S-53T and A27T formed a lineage within the family Cytophagaceae that were distinct from various members of the genus Dyadobacter (98.9-93.2% sequence similarity). Closest member for strain S-53T was Dyadobacter jejuensis AM1R11T (95.7%) and for A27T Dyadobacter endophyticus 65T (98.9%). The predominant respiratory quinone was MK-7 for both strains. The major polar lipid for both strains was phosphatidylethanolamine. The major cellular fatty acids for both strains were summed feature 3 (C16:1ω7c and/or C16:1ω6c), iso-C15:0, C16:1ω5c, and C16:0. The DNA G+C content of strains ranges from 46.5 to 48.7 mol%. On the basis of phenotypic, genotypic, chemotaxonomic, and phylogenetic analysis, both strains S-53T and A27T represent a novel member in the genus Dyadobacter, for which the name Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov. are proposed, respectively. The type strain of D. flavus is S-53T (= KEMB 9005-541T = KACC 19149T = NBRC 112681T) and type strain of D. terricola is A27T (= KEMB 9005-524T = KACC 19147T = NBRC 112680T).
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Kang JW, Choi S, Choe HN, Seong CN. Hymenobacter defluvii sp. nov., isolated from wastewater of an acidic water neutralization facility. Int J Syst Evol Microbiol 2017; 68:277-282. [PMID: 29148363 DOI: 10.1099/ijsem.0.002497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A non-motile, pink-coloured and rod-shaped bacterium, designated strain POA9T, was isolated from a wastewater treatment facility, Republic of Korea. Cells were Gram-reaction-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were C16 : 1ω5c, iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and anteiso-C15 : 0. The strain contained MK-7 as the only isoprenoid quinone, phosphatidylethanolamine as the major polar lipid and sym-homospermidine as the major polyamine. The DNA G+C content was 57 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain POA9T forms a distinct evolutionary lineage within the radiation enclosing the members of the genus Hymenobacter, sharing the highest similarity with Hymenobacter actinosclerus CCUG 39621T (95.5 % sequence similarity) followed by Hymenobacterseoulensis 16F7GT (95.5 %), Hymenobactertibetensis XTM003T (95.4 %), Hymenobacterrutilus K2-33028T (95.4 %) and Hymenobacter psychrotolerans Tibet-IIU11T (94.9 %). A number of phenotypic characteristics distinguished strain POA9T from the related members of the genus Hymenobacter. On the basis of the evidence presented in this study, a novel species, Hymenobacter defluvii sp. nov., is proposed for strain POA9T (=KCTC 52270T=JCM 31658T).
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Affiliation(s)
- Joo Won Kang
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Seon Choi
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Han Na Choe
- Biological Resource Center, KRIBB, Jeongeup 56212, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
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15
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Chaudhary DK, Dahal RH, Altankhuu K, Kim J. Ravibacter arvi gen. nov., sp. nov., isolated from farmland soil during development of new culture techniques. Int J Syst Evol Microbiol 2017; 67:5252-5260. [PMID: 29087270 DOI: 10.1099/ijsem.0.002456] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel strains, J77-1T and J76-1, were isolated from farmland soil and were taxonomically characterized by a polyphasic approach. Both strains were yellow, Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacteria. These strains were non-sporulating, catalase-positive and oxidase-negative. J77-1T and J76-1 were able to grow at 15-40 °C, pH 5.0-10.0, and 0-1.0 % (w/v) NaCl concentration. Phylogenetic analyses revealed that both strains formed a distinct separate lineage within the family Cytophagaceae of the phylum Bacteroidetes. J77-1T and J76-1 showed low 16S rRNA gene sequence similarity to the most closely related type strain Dyadobacter koreensis WPCB159T (85.09 %) and exhibited less than 85.0 % sequence similarity with other members of the family Cytophagaceae. The pairwise sequence similarity between strains J77-1T and J76-1 was observed to be 99.86 %. In both strains, the only respiratory quinone was menaquinone-7 (MK-7); the major polar lipid was phosphatidylethanolamine; and the major fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, iso-C15 : 0, iso-C17 : 0 3-OH C16 : 1ω5c, and C16 : 0 3-OH. The genomic DNA G+C content values of J77-1T and J76-1 were 50.1 and 50.9 mol%, respectively. On the basis of the results of phenotypic, genotypic and phylogenetic analysis, J77-1T represents a novel species of a novel genus, for which the name Ravibacter arvi gen. nov., sp. nov. is proposed, within the family Cytophagaceae. The type strain of Ravibacter arvi is J77-1T (=KEMB 9005-548T=KACC 19172T=JCM 31920T), and J76-1 is an additional strain.
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Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Life Science, College of Natural Sciences and Engineering, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Ram Hari Dahal
- Department of Life Science, College of Natural Sciences and Engineering, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Khulan Altankhuu
- Department of Life Science, College of Natural Sciences and Engineering, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences and Engineering, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
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Huang K, Xu Y, Zhang J, Chen C, Gao F, Zhao FJ. Arsenicibacter rosenii gen. nov., sp. nov., an efficient arsenic methylating and volatilizing bacterium isolated from an arsenic-contaminated paddy soil. Int J Syst Evol Microbiol 2017; 67:3186-3191. [PMID: 28829026 DOI: 10.1099/ijsem.0.002068] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A novel bacterium with strong arsenic (As) methylation and volatilization abilities, designated strain SM-1T, was isolated from an As-contaminated paddy soil. SM-1T is strictly aerobic, rod-shaped, non-motile, Gram-negative and orange-coloured. Phylogenetic analysis revealed that strain SM-1T showed low 16S rRNA gene sequence similarities (≤88 %) to members of established genera in the family Cytophagaceae. Growth of this strain was observed at 15-45 °C (optimum, 37 °C), pH 6.0-8.0 (optimum, 7.0) and 0-0.5 % (w/v) NaCl. The major cellular fatty acids were C16 : 1ω5c and iso-C15 : 0. The respiratory quinone was MK-7, and the predominant polar lipids were phosphatidylethanolamine, an unidentified lipid (L), and an unidentified aminolipid (AL2). The DNA G+C content was 51.5 mol%. On the basis of phenotypic, phylogenetic and chemotaxonomic properties, strain SM-1T represents a novel species in a new genus within the family Cytophagaceae, for which the name Arsenicibacter rosenii gen. nov., sp. nov. is proposed. The type strain of Arsenicibacter rosenii is SM-1T (=CCTCC AB 2017086T=KCTC 52624T).
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Affiliation(s)
- Ke Huang
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yan Xu
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jun Zhang
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Chuan Chen
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Fan Gao
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Fang-Jie Zhao
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.,Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
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17
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Kang H, Kim H, Song J, Cho JC, Joh K, Joung Y. Lacihabitans lacunae sp. nov., isolated from a lagoon. Int J Syst Evol Microbiol 2017; 67:2509-2513. [PMID: 28809153 DOI: 10.1099/ijsem.0.001899] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A non-motile, orange-pigmented bacterium, designated strain HME7103T, was isolated from lagoon water in the Republic of Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME7103T formed a lineage within the genus Lacihabitans and family Cytophagaceae. Strain HME7103T was closely related to Lacihabitans soyangensis HME6675T (95.7 % 16S rRNA gene sequence similarity). The major fatty acids of strain HME7103T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and iso-C15 : 0. The major respiratory quinone was MK-7. The major polyamine was spermidine. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, one unidentified aminophospholipid and three unidentified polar lipids. The DNA G+C content of strain HME7103T was 40.6 mol%. On the basis of the evidence presented in this study, strain HME7103T represents a novel species within the genus Lacihabitans, for which the name Lacihabitans lacunae sp. nov. is proposed. The type strain is HME7103T (=KCTC 23619T=CECT 7956T).
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Affiliation(s)
- Heeyoung Kang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Haneul Kim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Jaeho Song
- Department of Biological Science, Inha University, Incheon 22212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Science, Inha University, Incheon 22212, Republic of Korea
| | - Kiseong Joh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Yochan Joung
- Department of Biological Science, Inha University, Incheon 22212, Republic of Korea
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18
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Kang JW, Lee JH, Choe HN, Seong CN. Hymenobacter tenuis sp. nov., isolated from wastewater of an acidic water neutralization facility. Int J Syst Evol Microbiol 2017; 67:2171-2177. [PMID: 28691666 DOI: 10.1099/ijsem.0.001918] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A non-motile, red-pink-coloured, rod-shaped bacterium, designated strain POB6T, was isolated from a wastewater treatment facility, Republic of Korea. Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, C16 : 1ω5c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The strain contained menaquinone MK-7 as the only isoprenoid quinone, phosphatidylethanolamine as the major polar lipid and sym-homospermidine as the major polyamine. The DNA G+C content was 61 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain POB6T forms a distinct evolutionary lineage within the radiation enclosing the members of the genus Hymenobacter, sharing the highest similarity with Hymenobacterrigui WPCP131T (97.5 %) followed by Hymenobacter xinjiangensis X2-1gT (97.2 %), Hymenobacter perfusus A1-12T (97.2 %) and Hymenobacter gelipurpurascens Txg-1T (97.1 %). A number of phenotypic characteristics distinguished strain POB6T from related members of the genus Hymenobacter. On the basis of the evidence presented in this study, a novel species, Hymenobacter tenuis sp. nov., is proposed, with POB6T (=KCTC 52271T=JCM 31659T) as the type strain.
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Affiliation(s)
- Joo Won Kang
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Han Na Choe
- Biological Resource Center, KRIBB, Jeongeup 56212, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
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Li DD, Peng M, Wang N, Wang XJ, Zhang XY, Chen XL, Su HN, Zhang YZ, Shi M. Arcticibacterium luteifluviistationis gen. nov., sp. nov., isolated from Arctic seawater. Int J Syst Evol Microbiol 2017; 67:664-669. [PMID: 27902275 DOI: 10.1099/ijsem.0.001690] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, aerobic, non-motile and yellow-pigmented bacterium, designated strain SM1504T, was isolated from Arctic seawater. It hydrolysed aesculin and gelatin but did not reduce nitrate to nitrite. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain SM1504T constituted a distinct phylogenetic line within the family Cytophagaceae and was closely related to species of the genera Lacihabitans, Emticicia, Fluviimonas and Leadbetterella, with respect to which low sequence similarities between 88.9 and 91.6 % were observed. The major fatty acids of strain SM1504T were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH) and iso-C15 : 0. The predominant polar lipids of strain SM1504T were phosphatidylethanolamine and one unidentified lipid. The only respiratory quinone detected in strain SM1504T was MK7. The DNA G+C content of strain SM1504T was 40.8 mol%. On the basis of the phylogenetic, chemotaxonomic and phenotypic characterization in this study, strain SM1504T is considered to represent a novel species in a new genus of the family Cytophagaceae, for which the name Arcticibacterium luteifluviistationis gen. nov., sp. nov. is proposed. The type strain is SM1504T (=KCTC 42716T=CCTCC AB 2015348T).
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Affiliation(s)
- Dan-Dan Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Ming Peng
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Ning Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Xiu-Juan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Mei Shi
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China.,State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
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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: 147] [Impact Index Per Article: 18.4] [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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Kim H, Kang H, Joung Y, Joh K. Runella palustris sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 2016; 67:676-680. [PMID: 27902287 DOI: 10.1099/ijsem.0.001692] [Citation(s) in RCA: 6] [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 novel, Gram-stain-negative, aerobic, non-motile and filamentous bacterial strain, designated HMF3829T, was isolated from wetland freshwater in Gyeong-an wetland, Republic of Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMF3829T formed a lineage within the genus Runella. Strain HMF3829T was closely related to Runella slithyformis DSM 19594T (95.2 % 16S rRNA gene sequence similarity), Runellalimosa DSM 17973T (94.9 %), Runellazeae NS12T (94.2 %) and Runella defluvii EMB13T (94.0 %). The major fatty acids of strain HMF3829T were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω5c and iso-C17 : 0 3-OH. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The polar lipids of strain HMF3829T consisted of phosphatidylethanolamine, three unidentified aminolipids, one unidentified phospholipid, three unidentified aminophospholipids and 12 unidentified lipids. The DNA G+C content of strain HMF3829T was 46.2 mol%. On the basis of the evidence presented in this study, strain HMF3829T represents a novel species of the genus Runella, for which the name Runella palustris sp. nov. is proposed. The type strain is HMF3829T (=KCTC 42850T=CECT 8978T).
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Affiliation(s)
- Haneul Kim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Heeyoung Kang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Yochan Joung
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Kiseong Joh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
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Kang JW, Baik KS, Im WT, Seong CN. Hymenobacter coalescens sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 2016; 66:3546-3551. [DOI: 10.1099/ijsem.0.001226] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Joo Won Kang
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Keun Sik Baik
- Department of Food Science and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyoung National University, Anseong 17579, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
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Telluribacter humicola gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from soil in South Korea. Antonie van Leeuwenhoek 2016; 109:1525-1533. [DOI: 10.1007/s10482-016-0754-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/08/2016] [Indexed: 10/21/2022]
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Periplasmic Cytophaga hutchinsonii Endoglucanases Are Required for Use of Crystalline Cellulose as the Sole Source of Carbon and Energy. Appl Environ Microbiol 2016; 82:4835-4845. [PMID: 27260354 DOI: 10.1128/aem.01298-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/25/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The soil bacterium Cytophaga hutchinsonii actively digests crystalline cellulose by a poorly understood mechanism. Genome analyses identified nine genes predicted to encode endoglucanases with roles in this process. No predicted cellobiohydrolases, which are usually involved in the utilization of crystalline cellulose, were identified. Chromosomal deletions were performed in eight of the endoglucanase-encoding genes: cel5A, cel5B, cel5C, cel9A, cel9B, cel9C, cel9E, and cel9F Each mutant retained the ability to digest crystalline cellulose, although the deletion of cel9C caused a modest decrease in cellulose utilization. Strains with multiple deletions were constructed to identify the critical cellulases. Cells of a mutant lacking both cel5B and cel9C were completely deficient in growth on cellulose. Cell fractionation and biochemical analyses indicate that Cel5B and Cel9C are periplasmic nonprocessive endoglucanases. The requirement of periplasmic endoglucanases for cellulose utilization suggests that cellodextrins are transported across the outer membrane during this process. Bioinformatic analyses predict that Cel5A, Cel9A, Cel9B, Cel9D, and Cel9E are secreted across the outer membrane by the type IX secretion system, which has been linked to cellulose utilization. These secreted endoglucanases may perform the initial digestion within amorphous regions on the cellulose fibers, releasing oligomers that are transported into the periplasm for further digestion by Cel5B and Cel9C. The results suggest that both cell surface and periplasmic endoglucanases are required for the growth of C. hutchinsonii on cellulose and that novel cell surface proteins may solubilize and transport cellodextrins across the outer membrane. IMPORTANCE The bacterium Cytophaga hutchinsonii digests crystalline cellulose by an unknown mechanism. It lacks processive cellobiohydrolases that are often involved in cellulose digestion. Critical cellulolytic enzymes were identified by genetic analyses. Intracellular (periplasmic) nonprocessive endoglucanases performed an important role in cellulose utilization. The results suggest a model involving partial digestion at the cell surface, solubilization and uptake of cellodextrins across the outer membrane by an unknown mechanism, and further digestion within the periplasm. The ability to sequester cellodextrins and digest them intracellularly may limit losses of soluble cellobiose to other organisms. C. hutchinsonii uses an unusual approach to digest cellulose and is a potential source of novel proteins to increase the efficiency of conversion of cellulose into soluble sugars and biofuels.
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Liu Y, Du J, Lai Q, Dong C, Xie Y, Shao Z. Jiulongibacter sediminis gen. nov., sp. nov., a new member of the family Cytophagaceae, isolated from the surface sediment of the Jiulong River in China. Int J Syst Evol Microbiol 2016; 66:2347-2353. [DOI: 10.1099/ijsem.0.001038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Juan Du
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Chunming Dong
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Yanrong Xie
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
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Dahal RH, Kim J. Rhabdobacter roseus gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 2016; 66:308-314. [DOI: 10.1099/ijsem.0.000714] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 443-760, South Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 443-760, South Korea
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Srinivasan S, Joo ES, Lee JJ, Kim MK. Hymenobacter humi sp. nov., a bacterium isolated from soil. Antonie van Leeuwenhoek 2015; 107:1411-9. [PMID: 25822157 DOI: 10.1007/s10482-015-0436-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 03/24/2015] [Indexed: 11/26/2022]
Abstract
A red-pink coloured, Gram-negative, rod-shaped bacterium designated as strain DG31A(T) was isolated from soil collected in Seoul, South Korea. The isolate was found to grow optimally at 25 °C on R2A agar. The highest degrees of 16S rRNA gene sequence similarities of the strain were found with Hymenobacter arizonensis JCM 13504(T) (98.0 %), Hymenobacter glaciei VUG-A130(T) (96.1 %), Hymenobacter soli PB17(T) (95.2 %), Hymenobacter antarcticus VUG-A42aa(T) (94.7 %) and Hymenobacter chitinivorans Txc1(T) (92.8 %). The DNA G+C content of the novel strain, DG31A(T), was determined to be 60.8 mol%. Chemotaxonomic data revealed that the major fatty acids were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c; 26.7 %), C16:1 ω5c (18.9 %) and anteiso-C15:0 (12.9 %); the major polar lipid was identified as phosphatidylethanolamine; the polyamine pattern was found to contain sym-homospermidine; and the major quinone was identified as MK-7. The DNA-DNA relatedness of strain DG31A(T) with respect to H. arizonensis JCM 13504(T) was 19.5 ± 2.9 % (reciprocal, 19.3 ± 0.6 %). Based on these data, strain DG31A(T) should be classified within the genus Hymenobacter as a novel species for which the name Hymenobacter humi sp. nov. is proposed, with the type strain DG31A(T) (=KCTC 32523(T) = JCM 19635(T)).
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MESH Headings
- Bacterial Typing Techniques
- Base Composition
- Cluster Analysis
- Culture Media/chemistry
- Cytophagaceae/classification
- Cytophagaceae/genetics
- Cytophagaceae/isolation & purification
- Cytophagaceae/physiology
- Cytosol/chemistry
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phospholipids/analysis
- Phylogeny
- Pigments, Biological/metabolism
- Quinones/analysis
- RNA, Ribosomal, 16S/genetics
- Republic of Korea
- Sequence Analysis, DNA
- Soil Microbiology
- Temperature
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Affiliation(s)
- Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 139-774, Korea
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Mukherjee S, Lapidus A, Shapiro N, Cheng JF, Han J, Reddy TBK, Huntemann M, Ivanova N, Mikhailova N, Chen A, Palaniappan K, Spring S, Göker M, Markowitz V, Woyke T, Tindall BJ, Klenk HP, Kyrpides NC, Pati A. High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India. Stand Genomic Sci 2015; 10:8. [PMID: 26203325 PMCID: PMC4511580 DOI: 10.1186/1944-3277-10-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/24/2014] [Indexed: 12/21/2022] Open
Abstract
Pontibacter roseus is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here we describe the features of Pontibacter roseus strain SRC-1(T) along with its complete genome sequence and annotation from a culture of DSM 17521(T). The 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50 RNA genes and is a part of Genomic Encyclopedia of Type Strains: KMG-I project.
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Affiliation(s)
| | - Alla Lapidus
- T. Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia
- Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - TBK Reddy
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | | | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Stefan Spring
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Brian J Tindall
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
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Zhou H, Wang X, Yang T, Zhang W, Chen G, Liu W. Identification and characterization of a novel locus in Cytophaga hutchinsonii involved in colony spreading and cellulose digestion. Appl Microbiol Biotechnol 2015; 99:4321-31. [DOI: 10.1007/s00253-015-6412-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/07/2015] [Accepted: 01/12/2015] [Indexed: 12/01/2022]
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Fluviimonas pallidilutea gen. nov., sp. nov., a new member of the family
Cytophagaceae
isolated from a freshwater river. Int J Syst Evol Microbiol 2013; 63:3861-3867. [DOI: 10.1099/ijs.0.052423-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated TQQ6T was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain TQQ6T were strictly aerobic, Gram-staining-negative, poly-β-hydroxybutyrate-containing, non-motile, non-spore-forming, long rods surrounded by a thick capsule and forming pale orange colonies. Growth occurred at 20–40 °C (optimum, 25 °C), at pH 7.0–9.0 (optimum, pH 8.0) and with 0–0.5 % NaCl (optimum, 0 %). The predominant fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), iso-C17 : 0 3-OH, C16 : 1ω5c and C16 : 0. The major isoprenoid quinone was MK-7 and the DNA G+C content was 42.2 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, two uncharacterized aminophospholipids and three uncharacterized phospholipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TQQ6T represents a distinct phyletic line that reflects a novel generic status within the family
Cytophagaceae
with relatively low sequence similarities (less than 90 %) to members of other genera with validly published names. On the basis of the genotypic and phenotypic data, strain TQQ6T represents a new genus and novel species of the family
Cytophagaceae
, for which the name Fluviimonas pallidilutea gen. nov., sp. nov. is proposed. The type strain is TQQ6T ( = BCRC 80447T = LMG 27056T = KCTC 32035T).
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31
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Copeland A, Zhang X, Misra M, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Pan C, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Djao ODN, Göker M, Sikorski J, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Stand Genomic Sci 2012; 6:145-54. [PMID: 22768358 PMCID: PMC3387789 DOI: 10.4056/sigs.2475579] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Runella slithyformis Larkin and Williams 1978 is the type species of the genus Runella, which belongs to the Cytophagaceae, a family that was only recently classified to the order Cytophagales in the class Cytophagia. The species is of interest because it is able to grow at temperatures as low as 4°C. This is the first completed genome sequence of a member of the genus Runella and the sixth sequence from the family Cytophagaceae. The 6,919,729 bp long genome consists of a 6.6 Mbp circular genome and five circular plasmids of 38.8 to 107.0 kbp length, harboring a total of 5,974 protein-coding and 51 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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32
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Abt B, Teshima H, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Tindall BJ, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Leadbetterella byssophila type strain (4M15). Stand Genomic Sci 2011; 4:2-12. [PMID: 21475582 PMCID: PMC3072089 DOI: 10.4056/sigs.1413518] [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: 01/19/2023] Open
Abstract
Leadbetterella byssophila Weon et al. 2005 is the type species of the genus Leadbetterella of the family Cytophagaceae in the phylum Bacteroidetes. Members of the phylum Bacteroidetes are widely distributed in nature, especially in aquatic environments. They are of special interest for their ability to degrade complex biopolymers. L. byssophila occupies a rather isolated position in the tree of life and is characterized by its ability to hydrolyze starch and gelatine, but not agar, cellulose or chitin. Here we describe the features of this organism, together with the complete genome sequence, and annotation. L. byssophila is already the 16th member of the family Cytophagaceae whose genome has been sequenced. The 4,059,653 bp long single replicon genome with its 3,613 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Lail K, Sikorski J, Saunders E, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Brettin T, Detter JC, Schütze A, Rohde M, Tindall BJ, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Chen F. Complete genome sequence of Spirosoma linguale type strain (1). Stand Genomic Sci 2010; 2:176-85. [PMID: 21304700 PMCID: PMC3035282 DOI: 10.4056/sigs.741334] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spirosoma linguale Migula 1894 is the type species of the genus. S. linguale is a free-living and non-pathogenic organism, known for its peculiar ringlike and horseshoe-shaped cell morphology. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is only the third completed genome sequence of a member of the family Cytophagaceae. The 8,491,258 bp long genome with its eight plasmids, 7,069 protein-coding and 60 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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34
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The Flexibacteriales and their systematic position. Antonie van Leeuwenhoek 2010; 12:215-22. [PMID: 20255089 DOI: 10.1007/bf02272668] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Affiliation(s)
- W H Fuller
- Iowa Agricultural Experiment Station, Ames, Iowa
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36
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Hungate RE. Studies on Cellulose Fermentation: III. The Culture and Isolation for Cellulose-decomposing Bacteria from the Rumen of Cattle. J Bacteriol 2006; 53:631-45. [PMID: 16561317 PMCID: PMC518363 DOI: 10.1128/jb.53.5.631-645.1947] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- R E Hungate
- Department of Bacteriology and Public Health, Washington State College, Pullman, Washington
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37
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Affiliation(s)
- R Y Stanier
- Hopkins Marine Station, Pacific Grove, California
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38
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Affiliation(s)
- R Y Stanier
- Department of Bacteriology, University of California at Los Angeles, California, and Hopkins Marine Station, Pacific Grove, California
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39
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Stanier RY. THE CYTOPHAGA GROUP: A CONTRIBUTION TO THE BIOLOGY OF MYXOBACTERIA. BACTERIOLOGICAL REVIEWS 2006; 6:143-96. [PMID: 16350082 PMCID: PMC440862 DOI: 10.1128/br.6.3.143-196.1942] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- R Y Stanier
- Hopkins Marine Station of Stanford University, Pacific Grove, California
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40
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WEEKS OB. Flavobacterium aquatile (Frankland and Frankland) Bergey et al., type species of the genus Flavobacterium. J Bacteriol 2003; 69:649-58. [PMID: 14392121 PMCID: PMC357604 DOI: 10.1128/jb.69.6.649-658.1955] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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SORIANO S, LEWIN RA. GLIDING MICROBES: SOME TAXONOMIC RECONSIDERATIONS. Antonie van Leeuwenhoek 1996; 31:66-79. [PMID: 14293404 DOI: 10.1007/bf02045876] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Poirier TP, Tonelli SJ, Holt SC. Ultrastructure of gliding bacteria: scanning electron microscopy of Capnocytophaga sputigena, Capnocytophaga gingivalis, and Capnocytophaga ochracea. Infect Immun 1979; 26:1146-58. [PMID: 528052 PMCID: PMC414740 DOI: 10.1128/iai.26.3.1146-1158.1979] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
When examined by both light and scanning electron microscopy, Capnocytophaga gingivalis, C. sputigena, and C. ochracea displayed three distinct growth zones: the original streak, an intermediate zone, and the advancing edge, or halo zone. On Trypticase (BBL Microbiology Systems)-soy-blood agar, the cells translocated by gliding. C. gingivalis and C. sputigena formed large, irregular isolated colonies, while C. ochracea formed a more confluent cell mass. The cells within the streak zone and in most of the intermediate zone were heaped into mounds, with the individual cells displaying a definite flow pattern, the latter characteristic of C. sputigena and C. gingivalis. The halo zone consisted of tracks of cells which appeared to have translocated back upon themselves, or were restricted in their outward movements by adjacent cells. Also present within the halo zone were small aggregates of cells, referred to as pioneer colonies. The cell surfaces of C. gingivalis and C. ochracea were smooth and free of any apparent extracellular material, whereas C. sputigena was covered with a thick amorphous material, as well as long, thick, cell surface-associated fibrils.
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Abstract
Nongliding mutants of Flexibacter FS-1 are unable to flex; revertants regain both forms of movement. A variety of conditions and treatments reversibly inhibit both gliding and flexing.
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45
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Holland ND, Nealson KH. The Fine Structure of the Echinoderm Cuticle and the Subcuticular Bacteria of Echinoderms. ACTA ZOOL-STOCKHOLM 1978. [DOI: 10.1111/j.1463-6395.1978.tb01032.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Henrichsen J. Bacterial surface translocation: a survey and a classification. BACTERIOLOGICAL REVIEWS 1972; 36:478-503. [PMID: 4631369 PMCID: PMC408329 DOI: 10.1128/br.36.4.478-503.1972] [Citation(s) in RCA: 294] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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47
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Stewart JR, Brown RM. Aligicidal nonfruiting myxobacteria with high G+C ratios. ARCHIV FUR MIKROBIOLOGIE 1971; 80:176-90. [PMID: 5129218 DOI: 10.1007/bf00411882] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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48
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Shewan JM. The importance of myxobacteria and flavobacteria for the applied microbiologist. THE JOURNAL OF APPLIED BACTERIOLOGY 1969; 32:1-4. [PMID: 5791931 DOI: 10.1111/j.1365-2672.1969.tb02180.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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49
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Mitchell TG, Hendrie MS, Shewan JM. The taxonomy, differentiation and identification of Cytophaga species. THE JOURNAL OF APPLIED BACTERIOLOGY 1969; 32:40-50. [PMID: 5791934 DOI: 10.1111/j.1365-2672.1969.tb02187.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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50
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