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Covas C, Figueiredo G, Gomes M, Santos T, Mendo S, Caetano TS. The Pangenome of Gram-Negative Environmental Bacteria Hides a Promising Biotechnological Potential. Microorganisms 2023; 11:2445. [PMID: 37894103 PMCID: PMC10609062 DOI: 10.3390/microorganisms11102445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Secondary metabolites (SMs) from environmental bacteria offer viable solutions for various health and environmental challenges. Researchers are employing advanced bioinformatic tools to investigate less-explored microorganisms and unearth novel bioactive compounds. In this research area, our understanding of SMs from environmental Gram-negative bacteria lags behind that of its Gram-positive counterparts. In this regard, Pedobacter spp. have recently gained attention, not only for their role as plant growth promoters but also for their potential in producing antimicrobials. This study focuses on the genomic analysis of Pedobacter spp. to unveil the diversity of the SMs encoded in their genomes. Among the 41 genomes analyzed, a total of 233 biosynthetic gene clusters (BGCs) were identified, revealing the potential for the production of diverse SMs, including RiPPs (27%), terpenes (22%), hybrid SMs (17%), PKs (12%), NRPs (9%) and siderophores (6%). Overall, BGC distribution did not correlate with phylogenetic lineage and most of the BGCs showed no significant hits in the MIBiG database, emphasizing the uniqueness of the compounds that Pedobacter spp. can produce. Of all the species examined, P. cryoconitis and P. lusitanus stood out for having the highest number and diversity of BGCs. Focusing on their applicability and ecological functions, we investigated in greater detail the BGCs responsible for siderophore and terpenoid production in these species and their relatives. Our findings suggest that P. cryoconitis and P. lusitanus have the potential to produce novel mixtures of siderophores, involving bifunctional IucAC/AcD NIS synthetases, as well as carotenoids and squalene. This study highlights the biotechnological potential of Pedobacter spp. in medicine, agriculture and other industries, emphasizing the need for a continued exploration of its SMs and their applications.
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Affiliation(s)
| | | | | | | | | | - Tânia S. Caetano
- CESAM and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (C.C.); (G.F.); (S.M.)
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2
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Yang WL, An ML, He WH, Luo X, Zhu L, Chen GB, Zhang YT, Wang YN. Marinobacter panjinensis sp. nov., a moderately halophilic bacterium isolated from sea tidal flat environment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37167094 DOI: 10.1099/ijsem.0.005625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Two moderately halotolerant bacterium strains, designated PJ-16T and PJ-38, were isolated from a tidal flat of the red beach in Panjin City, Liaoning Province, PR China. Cells were found to be Gram-stain-negative, aerobic, motile, rod-shaped with a single polar flagellum. Optimum growth of strain PJ-16T occurred at 30 °C, pH 7.0 and 0.2-8.0 % (w/v) NaCl, and strain PJ-38 at 30 °C, pH 6.0-7.0 and 0.2-8.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PJ-16T was most closely related to Marinobacter denitrificans KCTC 62941T (99.2 % 16S rRNA gene sequence similarity), Marinobacter algicola DSM 16394T (98.6 %), Marinobacter salarius JCM 19399T (98.4 %) and Marinobacter confluentis KCTC 42705T (98.2 %), and strain PJ-38 was most closely related to M. denitrificans KCTC 62941T (99.1 %), M. algicola DSM 16394T (98.6 %), M. salarius JCM 19399T (98.4 %) and M. confluentis KCTC 42705T (98.1 %). The G+C content of the genomic DNA of strain PJ-16T based on its draft genomic sequence was 57.4 mol%. The major cellular fatty acids of strain PJ-16T were C16 : 0, C16 : 1 ω7c/C16 : 1 ω6c and C18 : 1 ω9c. The major respiratory quinone of PJ-16T was ubiquinone-9 and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The results of the phenotypic, phylogenetic and genomic analyses revealed that strains PJ-16T and PJ-38 represent a novel species of the genus Marinobacter, and the name Marinobacter panjinensis sp. nov. is proposed. The type strain is PJ-16T (= CGMCC 1.13694T= KCTC 72023T).
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Affiliation(s)
- Wen-Ling Yang
- Key Laboratory of Microbial Engineering at the Institute of Biology, Henan Academy of Sciences, Zhengzhou, 450008, PR China
| | - Ming-Li An
- Key Laboratory of Microbial Engineering at the Institute of Biology, Henan Academy of Sciences, Zhengzhou, 450008, PR China
| | - Wei-Hong He
- Key Laboratory of Microbial Engineering at the Institute of Biology, Henan Academy of Sciences, Zhengzhou, 450008, PR China
| | - Xin Luo
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450008, PR China
| | - Lin Zhu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450008, PR China
| | - Guan-Bin Chen
- School of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, 116023, PR China
| | - Ying-Tao Zhang
- Key Laboratory of Microbial Engineering at the Institute of Biology, Henan Academy of Sciences, Zhengzhou, 450008, PR China
| | - Ya-Nan Wang
- Key Laboratory of Microbial Engineering at the Institute of Biology, Henan Academy of Sciences, Zhengzhou, 450008, PR China
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3
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Bjerketorp J, Levenfors JJ, Nord C, Guss B, Öberg B, Broberg A. Selective Isolation of Multidrug-Resistant Pedobacter spp., Producers of Novel Antibacterial Peptides. Front Microbiol 2021; 12:642829. [PMID: 33717041 PMCID: PMC7947920 DOI: 10.3389/fmicb.2021.642829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/08/2021] [Indexed: 11/13/2022] Open
Abstract
Twenty-eight multidrug-resistant bacterial strains closely related or identical to Pedobacter cryoconitis, Pedobacter lusitanus and Pedobacter steynii were isolated from soil samples by selection for multidrug-resistance. Approximately 3-30% of the selected isolates were identified as Pedobacter, whereas isolation without antibiotics did not yield any isolates of this genus. Next generation sequencing data showed Pedobacter to be on 69th place among the bacterial genera (0.32% of bacterial sequences). The Pedobacter isolates produced a wide array of novel compounds when screened by UHPLC-MS/MSMS, and hierarchical cluster analysis resulted in several distinct clusters of compounds produced by specific isolates of Pedobacter, and most of these compounds were found to be peptides. The Pedobacter strain UP508 produced isopedopeptins, whereas another set of strains produced pedopeptins, which both are known cyclic lipodepsipeptides produced by Pedobacter sp. Other Pedobacter strains produced analogous peptides with a sequence variation. Further strains of Pedobacter produced additional novel antibacterial cyclic lipopeptides (ca 800 or 1400 Da in size) and/or linear lipopeptides (ca 700-960 Da in size). A 16S rRNA phylogenetic tree for the Pedobacter isolates revealed several distinct clades and subclades of isolates. One of the subclades comprised isolates producing isopedopeptin analogs, but the isopedopeptin producing isolate UP508 was clearly placed on a separate branch. We suggest that the non-ribosomal peptide synthases producing pedopeptins, isopedopeptins, and the analogous peptides, may derive from a common ancestral non-ribosomal peptide synthase gene cluster, which may have been subjected to a mutation leading to changed specificity in one of the modules and then to a modular rearrangement leading to the changed sequence found in the isopedopeptins produced by isolate UP508.
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Affiliation(s)
- Joakim Bjerketorp
- Department of Molecular Sciences, Uppsala BioCentrum, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Ultupharma AB, Uppsala, Sweden
| | - Jolanta J Levenfors
- Department of Molecular Sciences, Uppsala BioCentrum, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Ultupharma AB, Uppsala, Sweden
| | - Christina Nord
- Department of Molecular Sciences, Uppsala BioCentrum, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bengt Guss
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bo Öberg
- Ultupharma AB, Uppsala, Sweden.,Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Anders Broberg
- Department of Molecular Sciences, Uppsala BioCentrum, Swedish University of Agricultural Sciences, Uppsala, Sweden
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4
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First report on antibiotic resistance and antimicrobial activity of bacterial isolates from 13,000-year old cave ice core. Sci Rep 2021; 11:514. [PMID: 33436712 PMCID: PMC7804186 DOI: 10.1038/s41598-020-79754-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/14/2020] [Indexed: 11/24/2022] Open
Abstract
Despite the unique physiology and metabolic pathways of microbiomes from cold environments providing key evolutionary insights and promising leads for discovering new bioactive compounds, cultivable bacteria entrapped in perennial ice from caves remained a largely unexplored life system. In this context, we obtained and characterized bacterial strains from 13,000-years old ice core of Scarisoara Ice Cave, providing first isolates from perennial ice accumulated in caves since Late Glacial, and first culture-based evidences of bacterial resistome and antimicrobial compounds production. The 68 bacterial isolates belonged to 4 phyla, 34 genera and 56 species, with 17 strains representing putative new taxa. The Gram-negative cave bacteria (Proteobacteria and Bacteroidetes) were more resistant to the great majority of antibiotic classes than the Gram-positive ones (Actinobacteria, Firmicutes). More than 50% of the strains exhibited high resistance to 17 classes of antibiotics. Some of the isolates inhibited the growth of clinically important Gram-positive and Gram-negative resistant strains and revealed metabolic features with applicative potential. The current report on bacterial strains from millennia-old cave ice revealed promising candidates for studying the evolution of environmental resistome and for obtaining new active biomolecules for fighting the antibiotics crisis, and valuable cold-active biocatalysts.
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Zhou Y, Leung MHY, Tong X, Lai Y, Tong JCK, Ridley IA, Lee PKH. Profiling Airborne Microbiota in Mechanically Ventilated Buildings Across Seasons in Hong Kong Reveals Higher Metabolic Activity in Low-Abundance Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:249-259. [PMID: 33346641 DOI: 10.1021/acs.est.0c06201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Metabolically active bacteria within built environments are poorly understood. This study aims to investigate the active airborne bacterial microbiota and compare the total and active microbiota in eight mechanically ventilated buildings over four consecutive seasons using the 16S rRNA gene (rDNA) and the 16S rRNA (rRNA), respectively. The relative abundances of the taxa of presumptive occupants and environmental origins were significantly different between the active and total microbiota. The Sloan neutral model suggested that ecological drift and random dispersal played a smaller role in the assembly of the active microbiota than the total microbiota. The seasonal nature of the active microbiota was consistent with that of the total microbiota in both indoor and outdoor environments, while only the indoor environment was significantly affected by geography. The relative abundances of the active and total taxa were positively correlated, suggesting that the high-abundance members were also the greatest contributors to the community-level metabolic activity. Based on the rRNA/rDNA ratio, the low-abundance members consistently had a higher taxon-level metabolic activity than the high-abundance members over seasons, suggesting that the low-abundance members may have the ability to survive and thrive in the indoor environment and their impact on the health of occupants cannot be overlooked.
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Affiliation(s)
- You Zhou
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Yonghang Lai
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Jimmy C K Tong
- Building Sustainability Group, Arup, Hong Kong SAR, China
| | - Ian A Ridley
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
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6
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Kangale LJ, Raoult D, Ghigo E, Fournier PE. Pedobacter schmidteae sp. nov., a new bacterium isolated from the microbiota of the planarian Schmidtea mediterranea. Sci Rep 2020; 10:6113. [PMID: 32273530 PMCID: PMC7145819 DOI: 10.1038/s41598-020-62985-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 03/17/2020] [Indexed: 12/22/2022] Open
Abstract
Pedobacter schmidteae sp. nov. strain EGT (Collection de Souches de l'Unité des Rickettsie CSUR P6417 = Colección Española de Cultivos Tipo CECT 9771) is a new Pedobacter species isolated from the planarian Schmidtea mediterranea. Schmidtea mediterranea are flatworms living in freshwater and exhibiting an unusual ability to regenerate amputated parts. To date, the gut microbiota of Schmidtea mediterranea remains poorly studied. Here, via the culturomics strategy that consists in using diversified culture conditions, we isolated a new bacterium, strain EG, that we characterized using the taxono-genomics approach that combines phenotypic assays and genome sequencing and analysis. Strain EG exhibits a 16S rRNA sequence similarity of 98.29% with Pedobacter nyackensis strain NWG-II14T, its closest neighbour with standing in nomenclature. It is an aerobic bacterium belonging to the family Sphingobacteriaceae. Colonies are small, round, smooth and transparent. Bacterial cells are Gram-negative, rod-shaped, motile and non-spore-forming bacilli with positive catalase and oxidase activities. The genome sequence is 6,198,518 bp-long with a G + C content of 41.13%, and the Ortho-ANI and dDDH values when compared to P. nyackensis are 77.34% and 21.50%, respectively. Strain EGT exhibits unique characteristics that classify it as the type strain of new bacterial species for which we propose the name Pedobacter schmidteae sp. nov.
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Affiliation(s)
- Luis Johnson Kangale
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- IHU-Méditerranée-Infection, Marseille, France
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- TechnoJouvence, 19-21 Boulevard Jean Moulin 13385, Marseille, cedex, 05, France
| | - Eric Ghigo
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.
- IHU-Méditerranée-Infection, Marseille, France.
- TechnoJouvence, 19-21 Boulevard Jean Moulin 13385, Marseille, cedex, 05, France.
| | - Pierre-Edouard Fournier
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.
- IHU-Méditerranée-Infection, Marseille, France.
- TechnoJouvence, 19-21 Boulevard Jean Moulin 13385, Marseille, cedex, 05, France.
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7
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García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 2019; 10:2083. [PMID: 31608019 PMCID: PMC6767994 DOI: 10.3389/fmicb.2019.02083] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/23/2019] [Indexed: 11/25/2022] Open
Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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8
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Proposal of Pedobacter nototheniae sp. nov., isolated from the spleen of a black rock cod (Notothenia coriiceps, Richardson 1844) from the Chilean Antarctica. Antonie Van Leeuwenhoek 2019; 112:1465-1475. [DOI: 10.1007/s10482-019-01275-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/10/2019] [Indexed: 11/26/2022]
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9
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Mu Y, Ke Z, Feng CX, Wang XW, Wang XW, Wang HM, Chen Q, He J. Pedobacter pollutisoli sp. nov., Isolated from Tetrabromobisphenol A-Contaminated Soil. Curr Microbiol 2019; 76:442-447. [PMID: 30758644 DOI: 10.1007/s00284-019-01643-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
Abstract
A Gram-stain negative, strictly aerobic, non-spore forming, non-motile, rod-shaped bacterium, designated TBBPA-24T, was isolated from tetrabromobisphenol A-contaminated soil in China. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain TBBPA-24T was most closely related to Pedobacter nanyangensis Q4T (96.5%) and Pedobacter 'zeaxanthinifaciens' TDMA-5T (96.1%). Chemotaxonomic analysis revealed that strain TBBPA-24T possessed MK-7 as the major respiratory quinone and lipid, aminolipid, phospholipid, phosphatidylethanolamine, and phosphoaminolipid as the major polar lipid. The major fatty acids were iso-C15:0 (40.2%), summed feature 3 (C16:1ω6c and/or C16:1ω7c, 25.6%) and iso-C17:0 3-OH (16.4%). The genomic DNA G+C content of strain TBBPA-24T was 43.9 mol%. Based on the phylogenetic, phenotypic characteristics, and chemotaxonomic data, strain TBBPA-24T is considered a novel species of the genus Pedobacter, for which the name Pedobacter pollutisoli sp. nov. is proposed. The type strain TBBPA-24T (= KCTC 62314T = CCTCC AB 2017244T) is proposed.
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Affiliation(s)
- Yang Mu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Zhuang Ke
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Chen-Xi Feng
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Xiao-Wei Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Xiao-Wen Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Hong-Mei Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Qing Chen
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China. .,Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| | - Jian He
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
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Honeyman AS, Day ML, Spear JR. Regional fresh snowfall microbiology and chemistry are driven by geography in storm-tracked events, Colorado, USA. PeerJ 2018; 6:e5961. [PMID: 30498637 PMCID: PMC6252068 DOI: 10.7717/peerj.5961] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/16/2018] [Indexed: 01/15/2023] Open
Abstract
Snowfall is a global phenomenon highly integrated with hydrology and ecology. Forays into studying bioaerosols and their dependence on aeolian movement are largely constrained to either precipitation-independent analyses or in silico models. Though snowpack and glacial microbiological studies have been conducted, little is known about the biological component of meteoric snow. Through culture-independent phylogenetic and geochemical analyses, we show that the geographical location at which snow precipitates determines snowfall’s geochemical and microbiological composition. Storm-tracking, furthermore, can be used as a valuable environmental indicator to trace down what factors are influencing bioaerosols. We estimate annual aeolian snowfall deposits of up to ∼10 kg of bacterial/archaeal biomass per hectare along our study area of the eastern Front Range in Colorado. The dominant kinds of microbiota captured in an analysis of seven snow events at two different locations, one urban, one rural, across the winter of 2016/2017 included phyla Proteobacteria, Bacteroidetes, Firmicutes, and Acidobacteria, though a multitude of different kinds of organisms were found in both. Taxonomically, Bacteroidetes were more abundant in Golden (urban plain) snow while Proteobacteria were more common in Sunshine (rural mountain) samples. Chemically, Golden snowfall was positively correlated with some metals and anions. The work also hints at better informing the “everything is everywhere” hypotheses of the microbial world and that atmospheric transport of microbiota is not only common, but is capable of disseminating vast amounts of microbiota of different physiologies and genetics that then affect ecosystems globally. Snowfall, we conclude, is a significant repository of microbiological material with strong implications for both ecosystem genetic flux and general bio-aerosol theory.
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Affiliation(s)
| | - Maria L Day
- Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
| | - John R Spear
- Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
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11
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Wei Y, Wang B, Zhang L, Zhang J, Chen S. Pedobacter yulinensis sp. nov., isolated from sandy soil, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2018; 68:2523-2529. [DOI: 10.1099/ijsem.0.002868] [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
Affiliation(s)
- Yahong Wei
- 1College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
- 2State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Baodan Wang
- 1College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Limei Zhang
- 1College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Jianguo Zhang
- 2State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Shaolin Chen
- 1College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
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12
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Yuan K, Cao M, Li J, Wang G. Pedobacter mongoliensis sp. nov., isolated from grassland soil. Int J Syst Evol Microbiol 2018; 68:1112-1117. [DOI: 10.1099/ijsem.0.002637] [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)
- Kai Yuan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Min Cao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Jingxin Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
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13
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Cui MD, Wang X, Jiang WK, Hu G, Yang ZG, Sun GJ, Zhu SJ, Zhou YD, Hong Q. Pedobacter agrisoli sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2018; 68:886-891. [DOI: 10.1099/ijsem.0.002604] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Meng-Di Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of life sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Xiang Wang
- College of Resource and Environment, Anhui Science and Technology University, Anhui 233100, PR China
| | - Wan-Kui Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of life sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Gang Hu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of life sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Laboratory Centre of Life Science, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Zhan-Gong Yang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of life sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Gao-Jie Sun
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of life sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Shi-Jun Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of life sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yi-Dong Zhou
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of life sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of life sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
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14
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Zhang B, Liu ZQ, Zheng YG. Pedobacter quisquiliarum sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2017; 68:438-442. [PMID: 29231155 DOI: 10.1099/ijsem.0.002531] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped, bacterium, C62-2T, was isolated from activated sludge in Fujian Province, China. Phylogenetic analysis of the 16S rRNA gene sequences showed that it was closely related to Pedobacter duraquae WB 2.1-25T (97.92 %), Pedobacter bambusae THG-G118T (97.40 %), Pedobacter cryoconitis A37T (97.37 %) and Pedobacter caeni LMG 22862T (97.3 %). Cells grew aerobically at 20-37 °C (optimum, 30 °C), pH 5.0-8.0 (optimum, pH 7.0) and in the presence of 0-3.0 % (w/v) NaCl. Strain C62-2T contained MK-7 as the major menaquinone and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1ω6c, C16 : 1ω7c) and iso-C17 : 0 3-OH. The DNA G+C content was 43.2 mol% (Tm) and DNA-DNA reassociation values were 35.4 % between strain C62-2T and P. duraquae WB 2.1-25T. On the basis of phenotypic, chemotaxonomic and phylogenetic comparisons with the closely related species and DNA-DNA relatedness values, it was concluded that strain C62-2T represents a novel species within the genus Pedobacter, for which the name Pedobacterquisquiliarum sp. nov. is proposed. The type strain is C62-2T (=CGMCC 1.15343T=NBRC 111767T).
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
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15
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Chang S, Zhang G, Chen X, Long H, Wang Y, Chen T, Liu G. The complete genome sequence of the cold adapted crude-oil degrader: Pedobacter steynii DX4. Stand Genomic Sci 2017; 12:45. [PMID: 28770030 PMCID: PMC5531107 DOI: 10.1186/s40793-017-0249-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 06/29/2017] [Indexed: 11/26/2022] Open
Abstract
Pedobacter steynii DX4 was isolated from the soil of Tibetan Plateau and it can use crude oil as sole carbon and energy source at 15 °C. The genome of Pedobacter steynii DX4 has been sequenced and served as basis for analysis its metabolic mechanism. It is the first genome of crude oil degrading strain in Pedobacter genus. The 6.58 Mb genome has an average G + C content of 41.31% and encodes 5464 genes. In addition, annotation revealed that Pedobacter steynii DX4 has cold shock proteins, abundant response regulators for cell motility, and enzymes involved in energy conversion and fatty acid metabolism. The genomic characteristics could provide information for further study of oil-degrading microbes for recovery of crude oil polluted environment.
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Affiliation(s)
- Sijing Chang
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049 China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000 China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000 China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000 China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000 China
| | - Ximing Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000 China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000 China
| | - Haozhi Long
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000 China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045 China
| | - Yilin Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045 China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000 China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000 China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000 China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000 China
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16
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Hegazi NA, Sarhan MS, Fayez M, Patz S, Murphy BR, Ruppel S. Plant-fed versus chemicals-fed rhizobacteria of Lucerne: Plant-only teabags culture media not only increase culturability of rhizobacteria but also recover a previously uncultured Lysobacter sp., Novosphingobium sp. and Pedobacter sp. PLoS One 2017; 12:e0180424. [PMID: 28686606 PMCID: PMC5501534 DOI: 10.1371/journal.pone.0180424] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 06/15/2017] [Indexed: 11/19/2022] Open
Abstract
In an effort to axenically culture the previously uncultivable populations of the rhizobacteria of Lucerne (Medicago sativa L.), we propose plant-only teabags culture media to mimic the nutritional matrix available in the rhizosphere. Here, we show that culture media prepared from Lucerne powder teabags substantially increased the cultivability of Lucerne rhizobacteria compared with a standard nutrient agar, where we found that the cultivable populations significantly increased by up to 60% of the total bacterial numbers as estimated by Quantitative Real-time Polymerase Chain Reaction (qRT-PCR). Cluster analysis of 16S rDNA Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) of cultivable Colony-Forming Units (CFUs) revealed a more distinct composition and separation of bacterial populations recovered on the plant-only teabags culture media than those developed on a standard nutrient agar. Further, the new plant medium gave preference to the micro-symbiont Sinorhizobium meliloti, and succeeded in isolating a number of not-yet-cultured bacteria, most closely matched to Novosphingobium sp., Lysobacter sp. and Pedobacter sp. The present study may encourage other researchers to consider moving from the well-established standard culture media to the challenging new plant-only culture media. Such a move may reveal previously hidden members of rhizobacteria, and help to further explore their potential environmental impacts.
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Affiliation(s)
- Nabil A. Hegazi
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
- * E-mail:
| | - Mohamed S. Sarhan
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohamed Fayez
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Sascha Patz
- Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/ Erfurt e.V. (IGZ), Großbeeren, Germany
| | - Brian R. Murphy
- Department of Botany, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/ Erfurt e.V. (IGZ), Großbeeren, Germany
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17
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Covas C, Caetano T, Cruz A, Santos T, Dias L, Klein G, Abdulmawjood A, Rodríguez-Alcalá LM, Pimentel LL, Gomes A, Freitas AC, Garcia-Serrano A, Fontecha J, Mendo S. Pedobacter lusitanus sp. nov., isolated from sludge of a deactivated uranium mine. Int J Syst Evol Microbiol 2017; 67:1339-1348. [DOI: 10.1099/ijsem.0.001814] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Cláudia Covas
- Biology Department and CESAM, University of Aveiro, Aveiro, Portugal
| | - Tânia Caetano
- Biology Department and CESAM, University of Aveiro, Aveiro, Portugal
| | - Andreia Cruz
- Biology Department and CESAM, University of Aveiro, Aveiro, Portugal
| | - Tiago Santos
- Biology Department and CESAM, University of Aveiro, Aveiro, Portugal
| | - Liliana Dias
- Biology Department and CESAM, University of Aveiro, Aveiro, Portugal
| | - Guenter Klein
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Luis M Rodríguez-Alcalá
- CBQF - Centro de Biotecnologia e Quı́mica Fina − Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Fábrica N∘ 1990, Segundo Piso, Santiago, Chile
| | - Lígia L Pimentel
- CBQF - Centro de Biotecnologia e Quı́mica Fina − Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Ana Gomes
- CBQF - Centro de Biotecnologia e Quı́mica Fina − Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Ana Cristina Freitas
- CBQF - Centro de Biotecnologia e Quı́mica Fina − Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Alba Garcia-Serrano
- Department of Bioactivity and Food Analysis, Group of Lipids, Instituto de Investigación en Ciencias de la Alimentación (CIAL CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 9, Madrid 28049, Spain
| | - Javier Fontecha
- Department of Bioactivity and Food Analysis, Group of Lipids, Instituto de Investigación en Ciencias de la Alimentación (CIAL CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 9, Madrid 28049, Spain
| | - Sónia Mendo
- Biology Department and CESAM, University of Aveiro, Aveiro, Portugal
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18
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Ong M, Ongkudon CM, Wong CMVL. Development of a semidefined growth medium for Pedobacter cryoconitis BG5 using statistical experimental design. Prep Biochem Biotechnol 2017; 46:657-65. [PMID: 26759918 DOI: 10.1080/10826068.2015.1135447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Pedobacter cryoconitis BG5 are psychrophiles isolated from the cold environment and capable of proliferating and growing well at low temperature regime. Their cellular products have found a broad spectrum of applications, including in food, medicine, and bioremediation. Therefore, it is imperative to develop a high-cell density cultivation strategy coupled with optimized growth medium for P. cryoconitis BG5. To date, there has been no published report on the design and optimization of growth medium for P. cryoconitis, hence the objective of this research project. A preliminary screening of four commercially available media, namely tryptic soy broth, R2A, Luria Bertani broth, and nutrient broth, was conducted to formulate the basal medium. Based on the preliminary screening, tryptone, glucose, NaCl, and K2HPO4 along with three additional nutrients (yeast extract, MgSO4, and NH4Cl) were identified to form the basal medium which was further analyzed by Plackett-Burman experimental design. Central composite experimental design using response surface methodology was adopted to optimize tryptone, yeast extract, and NH4Cl concentrations in the formulated growth medium. Statistical data analysis showed a high regression factor of 0.84 with a predicted optimum optical (600 nm) cell density of 7.5 using 23.7 g/L of tryptone, 8.8 g/L of yeast extract, and 0.7 g/L of NH4Cl. The optimized medium for P. cryoconitis BG5 was tested, and the observed optical density was 7.8. The cost-effectiveness of the optimized medium was determined as 6.25 unit prices per gram of cell produced in a 250-ml Erlenmeyer flask.
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Affiliation(s)
- Magdalena Ong
- a Biotechnology Research Institute , Universiti Malaysia Sabah , Kota Kinabalu , Sabah , Malaysia
| | - Clarence M Ongkudon
- a Biotechnology Research Institute , Universiti Malaysia Sabah , Kota Kinabalu , Sabah , Malaysia
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19
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Cho H, Ahn JH, Weon HY, Joa JH, Kwon SW, Kim SJ. Pedobacterlycopersici sp. nov., isolated from the rhizosphere of tomato plant (Solanum lycopersicum L.). Int J Syst Evol Microbiol 2016; 66:5406-5411. [PMID: 27902181 DOI: 10.1099/ijsem.0.001532] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, white bacterium, designated strain T16R-88T, was isolated from a rhizosphere soil sample collected in Buyeo-gun of Chungcheongnam-do, South Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain T16R-88T formed a lineage within the genus Pedobacter. It showed highest sequence similarities to Pedobacter ginsengisoli Gsoil 104T (97.4 %), Pedobacter nutrimenti J22T (97.2 %), Pedobacter nyackensis NWG-II14T (97.1 %), Pedobacter seoulensis THG-G12T (97.1 %) and Pedobacter panaciterrae Gsoil 042T (97.0 %). The predominant respiratory quinone was menaquinone MK-7. The major cellular fatty acids (>10 % of the total fatty acids) were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 0 3-OH and iso-C15 : 0. The polar lipids consisted of phosphatidylethanolamine, sphingolipid, one unidentified aminophospholipid, three unidentified aminolipids, three unidentified lipids and one unidentified phospholipid. DNA-DNA hybridization values between strain T16R-88T and its most closely related species were below 70 %. The DNA G+C content was 35.6 mol%. On the basis of the evidence presented in this study, strain T16R-88T represents a novel species of the genus Pedobacter, for which the name Pedobacter lycopersici sp. nov. is proposed. The type strain is T16R-88T (=KACC 18652T=NBRC 111984T).
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Affiliation(s)
- Hayoung Cho
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jae-Hyung Ahn
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jae-Ho Joa
- National Institute of Horticultural & Herbal Science, Rural Development Administration, Jeju 63240, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
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20
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Trinh H, Yi TH. Pedobacter humi sp. nov., isolated from a playground soil. Int J Syst Evol Microbiol 2016; 66:2382-2388. [PMID: 27032079 DOI: 10.1099/ijsem.0.001032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile, rod-shaped and yellow-pigmented bacterium, designated strain THG S15-2T, was isolated from playground soil in Sindorim-dong, Guro-gu, Seoul, South Korea. According to 16S rRNA gene sequence comparisons, strain THG S15-2T was found to be related most closely to Pedobacter ginsengisoli Gsoil 104T (97.5 % similarity), Pedobacter panaciterrae Gsoil 042T (97.4 %), Pedobacter seoulensis THG-G12T (97.1 %) and Pedobacter caeni LMG 22862T (97.1 %). The level of DNA-DNA relatedness between strain THG S15-2T and its phylogenetically closest neighbours was below 30.0 %. The only isoprenoid quinone detected in strain THG S15-2T was menaquinone-7. The DNA G+C content was 45.9 mol%. The major polar lipid was phosphatidylethanolamine. The major component in the polyamine pattern was sym-homospermidine. The major fatty acids were identified as summed feature 3 (C16:1ω7c and/or C16:1ω6c), iso-C15:0 and C16:0. These data supported the affiliation of strain THG S15-2T to the genus Pedobacter. Strain THG S15-2T was distinguished from related Pedobacter species by physiological and biochemical tests. Therefore, strain THG S15-2T represents a novel species, for which the name Pedobacter humi sp. nov. is proposed. The type strain is THG S15-2T (= KCTC 42735T = CCTCC AB 2015293T).
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Affiliation(s)
- Huan Trinh
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi do, 446-701, Republic of Korea
| | - Tae-Hoo Yi
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi do, 446-701, Republic of Korea
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21
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Siddiqi MZ, Liu Q, Kang MS, Kim MS, Im WT. Anseongella ginsenosidimutans gen. nov., sp. nov., isolated from soil cultivating ginseng. Int J Syst Evol Microbiol 2016; 66:1125x-1130. [DOI: 10.1099/ijsem.0.000844] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | - Qingmei Liu
- Department of Biotechnology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | - Myung-Suk Kang
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 404-708, Republic of Korea
| | - Minseok S. Kim
- Department of Biomedical Engineering, Konyang University, 121 Daehak-ro, Nonsan, Chungnam, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
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22
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Park S, Park JM, Jung YT, Won SM, Yoon JH. Pedobacter lignilitoris sp. nov., isolated from wood falls. Int J Syst Evol Microbiol 2015; 65:3481-3486. [PMID: 26296663 DOI: 10.1099/ijsem.0.000442] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterial strain, designated W-WS13T, was isolated from wood falls collected around Wando, an island in the South Sea of South Korea, and subjected to a polyphasic taxonomic study. Strain W-WS13T grew optimally at 30 °C, at pH 7.5 and in the presence of 0.5 % NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain W-WS13T belonged to the genus Pedobacter, clustering robustly with the type strain of Pedobacter arcticus, sharing 95.9 % sequence similarity. Strain W-WS13T exhibited 16S rRNA gene sequence similarity of 90.1–95.6 % to the type strains of the other species of the genus Pedobacter. Strain W-WS13T contained MK-7 as the predominant menaquinone and iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipid detected in strain W-WS13T was phosphatidylethanolamine. The DNA G+C content of strain W-WS13T was 36.9 mol%. Phylogenetic distinctiveness and differential phenotypic properties of strain W-WS13T revealed that the novel strain is separated from recognized species of the genus Pedobacter. On the basis of the data presented, strain W-WS13T is considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter lignilitoris sp. nov. is proposed. The type strain is W-WS13T ( = KCTC 42500T = CECT 8725T).
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Ji-Min Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Yong-Taek Jung
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea.,University of Science and Technology (UST), 113 Gwahak-ro, Yuseong-gu, Daejeon, South Korea
| | - Sung-Min Won
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
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23
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Abstract
A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterium, designated W-WS1T, was isolated from wood falls collected around Wando, an island located in the South Sea, Republic of Korea. Strain W-WS1T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 0–3.0 % (w/v) NaCl. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain W-WS1T belonged to the genus
Pedobacter
, clustering coherently with the type strains of
Pedobacter daechungensis
,
Pedobacter lentus
,
Pedobacter terricola
,
Pedobacter arcticus
and
Pedobacter glucosidilyticus
, showing 94.3–96.3 % sequence similarity. Strain W-WS1T exhibited 16S rRNA gene sequence similarity values of 91.2–94.0 % to the type strains of other species of the genus
Pedobacter
. Strain W-WS1T contained MK-7 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The major polar lipids detected in strain W-WS1T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain W-WS1T was 37.7 mol%. The differential phenotypic properties, together with its phylogenetic distinctiveness, revealed that strain W-WS1T is separated from recognized species of the genus
Pedobacter
. On the basis of the data presented, strain W-WS1T is considered to represent a novel species of the genus
Pedobacter
, for which the name Pedobacter silvilitoris sp. nov. is proposed. The type strain is W-WS1T ( = KCTC 42174T = CECT 8669T).
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24
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Luo YJ, Xie BS, Lv XL, Cai M, Wang YN, Cui HL, Cai H, Wu XL. Marinobacter shengliensis sp. nov., a moderately halophilic bacterium isolated from oil-contaminated saline soil. Antonie van Leeuwenhoek 2015; 107:1085-94. [PMID: 25652339 DOI: 10.1007/s10482-015-0401-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/29/2015] [Indexed: 11/29/2022]
Abstract
Two moderately halophilic strains, designated SL013A34A2(T) and SL013A24A, were isolated from oil-contaminated saline soil from Shengli Oilfield, eastern China. Cells were found to be Gram-staining negative, aerobic, rod-shaped with a single polar flagellum. The isolates were found to grow at 10-40 °C (optimum 35 °C), pH 6.0-9.0 (optimum pH 8.0), and NaCl concentrations of 0.5-18.0 % (w/v) (optimum 3.0-6.0 NaCl). The 16S rRNA gene sequence analysis indicated that the isolates belong to the genus Marinobacter. Strain SL013A34A2(T) shares the highest 16S rRNA gene sequence similarities with strain SL013A24A (99.3 %), followed by M. hydrocarbonoclasticus CGMCC 1.7683(T) (97.8 %), M. vinifirmus CGMCC 1.7265(T) (97.8 %), and M. excellens KMM 3809(T) (97.4 %), respectively, but low similarities (93.8-96.4 %) with type strains of the other numbers of genus Marinobacter. DNA-DNA relatedness values of strain SL013A34A2(T) with strains SL013A24A, M. hydrocarbonoclasticus CGMCC 1.7683(T), M. vinifirmus CGMCC 1.7265(T) and M. excellens KMM 3809(T) were 88.7, 29.2, 33.4 and 29.4 %, respectively. The major fatty acids of strain SL013A34A2(T) were identified as C18:1 ω9c, C16:0, C12:03-OH, C12:0, C16:1 ω9c and 10-methyl C18:0. The major respiratory quinone of strain SL013A34A2(T) was found to be ubiquinone-9, and its predominant polar lipids were identified as diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and unidentified glycolipid. The genomic DNA G + C content was found to be 56.1 mol %. Based on the phenotypic, genetic and chemotaxonomic characteristics, these two isolates are representatives of a novel species of the genus Marinobacter, for which the name Marinobacter shengliensis sp. nov. is proposed. The type strain is SL013A34A2(T)(=LMG 27740(T) = CGMCC 1.12758(T)).
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Affiliation(s)
- Yi-Jing Luo
- College of Engineering, Peking University, Beijing, 100871, People's Republic of China
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Ngo HTT, Kook M, Yi TH. Pedobacter ureilyticus sp. nov., isolated from tomato rhizosphere soil. Int J Syst Evol Microbiol 2015; 65:1008-1014. [PMID: 25563921 DOI: 10.1099/ijs.0.000055] [Citation(s) in RCA: 15] [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-stain-negative, strictly aerobic, rod-shaped and pinkish-yellow bacterium, which was motile by gliding and designated strain THG-T11(T), was isolated from tomato rhizosphere soil in Gyeonggi province, Republic of Korea. Based on 16S rRNA gene sequence comparisons, strain THG-T11(T) was found to be most closely related to 'Pedobacter zeaxanthinifaciens' TDMA-5 (95.9 % sequence similarity), Pedobacter agri PB92(T) (94.9 %), Pedobacter rhizosphaerae 01-96(T) (94.6 %) and Pedobacter alluvionis NWER-II11(T) (94.5 %). The DNA G+C content was 38.4 mol%. The only isoprenoid quinone detected in strain THG-T11(T) was menaquinone-7 (MK-7). The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were phosphatidylethanolamine, an unidentified phosphoglycolipid, an unidentified glycolipid, an unidentified lipid, unidentified aminophospholipids and unidentified aminolipids. The major ceramide was found to be ceramide phosphorylethanolamine. The major fatty acids were identified as iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. These data support the affiliation of strain THG-T11(T) to the genus Pedobacter. Based on phenotypic, chemotaxonomic and phylogenetic analysis, it is proposed that strain THG-T11(T) represents a novel species of the genus Pedobacter for which the name Pedobacter ureilyticus sp. nov. is proposed, with THG-T11(T) as the type strain ( = KACC 17660(T) = JCM 19461(T)).
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Affiliation(s)
- Hien T T Ngo
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do 446-701, Republic of Korea
| | - MooChang Kook
- Department of Marine Biotechnology, Anyang University, Incheon 417-833, Republic of Korea
| | - Tae-Hoo Yi
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do 446-701, Republic of Korea
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Won KH, Kook M, Yi TH. Pedobacter bambusae sp. nov., isolated from soil of a bamboo plantation. Antonie van Leeuwenhoek 2014; 107:565-73. [DOI: 10.1007/s10482-014-0352-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 12/08/2014] [Indexed: 11/29/2022]
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Zeng Y, Feng H, Huang Y. Pedobacter xixiisoli sp. nov., isolated from bank soil. Int J Syst Evol Microbiol 2014; 64:3683-3689. [DOI: 10.1099/ijs.0.065946-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, yellow, non-motile, aerobic bacterium (strain S27T) was isolated from bank soil of the Xixi wetland in Zhejiang province, PR China. Phylogenetic analysis, based on its 16S rRNA gene sequence, revealed that strain S27T could represent a novel species of the genus
Pedobacter
showing highest similarity to
Pedobacter koreensis
WPCB189T (95.45 %), followed by ‘Pedobacter zeaxanthinifaciens’ TDMA-5 (95.22 %). The temperature, pH and NaCl concentration ranges for growth were 6–37 °C (optimum 28 °C), pH 5.0–9.0 (optimum pH 7.5) and 0–3 % (w/v) [optimum 0.5 % (w/v)], respectively. The DNA G+C content was 36.1 mol%, MK-7 was the only respiratory quinone, and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) were the major fatty acids. These data all support the affiliation of strain S27T to the genus
Pedobacter
. The polar lipids of strain S27T comprised phosphatidylethanolamine, one unidentified aminophospholipid, four unidentified aminolipids and three unidentified lipids. However, strain S27T could be distinguished from other members of the genus
Pedobacter
due to its physiological and biochemical characteristics. Therefore, strain S27T represents a novel species of the genus
Pedobacter
, for which the name Pedobacter xixiisoli sp. nov. is proposed; the type strain is S27T ( = CGMCC 1.12803T = NBRC 110388T).
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Affiliation(s)
- Yanhua Zeng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Hao Feng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yili Huang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
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Ngo HTT, Son HM, Park SY, Kim KY, Yi TH. Pedobacter seoulensis sp. nov., isolated from soil of a bamboo field. Antonie van Leeuwenhoek 2014; 105:961-70. [DOI: 10.1007/s10482-014-0154-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 03/10/2014] [Indexed: 11/28/2022]
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Wilkins MJ, Kennedy DW, Castelle CJ, Field EK, Stepanauskas R, Fredrickson JK, Konopka AE. Single-cell genomics reveals metabolic strategies for microbial growth and survival in an oligotrophic aquifer. MICROBIOLOGY-SGM 2013; 160:362-372. [PMID: 24324032 DOI: 10.1099/mic.0.073965-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacteria from the genus Pedobacter are a major component of microbial assemblages at Hanford Site (a largely decommissioned nuclear production complex) in eastern Washington state, USA, and have been shown to change significantly in abundance in response to the subsurface intrusion of Columbia River water. Here we employed single-cell genomics techniques to shed light on the physiological niche of these micro-organisms. Analysis of four Pedobacter single amplified genomes (SAGs) from Hanford Site sediments revealed a chemoheterotrophic lifestyle, with the potential to exist under both aerobic and microaerophilic conditions via expression of both aa3-type and cbb3-type cytochrome c oxidases. These SAGs encoded a wide range of both intra- and extracellular carbohydrate-active enzymes, potentially enabling the degradation of recalcitrant substrates such as xylan and chitin, and the utilization of more labile sugars such as mannose and fucose. Coupled to these enzymes, a diversity of transporters and sugar-binding molecules were involved in the uptake of carbon from the extracellular local environment. The SAGs were enriched in TonB-dependent receptors, which play a key role in uptake of substrates resulting from degradation of recalcitrant carbon. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas mechanisms for resisting viral infections were identified in all SAGs. These data demonstrate the potential mechanisms utilized for persistence by heterotrophic micro-organisms in a carbon-limited aquifer, and hint at potential linkages between observed Pedobacter abundance shifts within the 300 Area (in the south-eastern corner of the site) subsurface and biogeochemical shifts associated with Columbia River water intrusion.
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Abstract
Two strains of Gram-staining-negative, rod-shaped bacteria that were motile by gliding, N7d-4T and B4a-b5, were isolated during a study of culturable bacteria in soil cultivated with potatoes. These isolates grew at 15–37 °C and at pH 6.5–7.0. The major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), anteiso-C15 : 0, iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c. The major polar lipids were phosphatidyl-N-methylethanolamine and phosphatidylethanolamine. The strains contained d-18 : 0 and d-19 : 0 sphingosines. The DNA G+C contents of strains N7d-4T and B4a-b5 were 48.5 and 46.9 mol% (HPLC), respectively. A phylogenetic analysis based on 16S rRNA gene sequences showed that strains N7d-4T and B4a-b5 were affiliated with
Pedobacter
species in the family
Sphingobacteriaceae
. Strains N7d-4T and B4a-b5 shared 99.9 % sequence similarity, and the most closely related
Pedobacter
type strains were
Pedobacter composti
TR6-06T (96.5 and 96.7 % sequence similarity, respectively),
P. oryzae
N7T (95.4 and 95.6 %) and
P. caeni
LMG 22862T (94.0 and 94.4 %). Phenotypic data and phylogenetic inference clearly distinguished the two isolates from other
Pedobacter
species. Based on these data, the isolates are considered to represent a novel species of the genus
Pedobacter
, for which the name Pedobacter luteus sp. nov. is proposed. The type strain is N7d-4T ( = KCTC 22699T = DSM 22385T).
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Urios L, Intertaglia L, Magot M. Pedobacter tournemirensis sp. nov., isolated from a fault water sample of a deep Toarcian argillite layer. Int J Syst Evol Microbiol 2013; 63:303-308. [DOI: 10.1099/ijs.0.038968-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative bacterium, designated TF5-37.2-LB10T, was isolated from subsurface water of the Toarcian geological layer of Tournemire, France. Cells were non-motile straight rods that formed cream to light pink colonies on 10-fold diluted LB agar. Strain TF5-37.2-LB10T contained menaquinone 7 and its major fatty acids were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 0 3-OH and iso-C17 : 1ω9c. The G+C content of the genomic DNA was 46 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain TF5-37.2-LB10T within the genus
Pedobacter
, family
Sphingobacteriaceae
.
Pedobacter composti
TR6-06T and
Pedobacter oryzae
DSM 19973T were the closest phylogenetic relatives (93.5 and 93.3 % 16S rRNA gene sequence similarity, respectively). On the basis of 16S rRNA gene sequence comparison and physiological and biochemical characteristics, strain TF5-37.2-LB10T represents a novel species of the genus
Pedobacter
, for which the name Pedobacter tournemirensis sp. nov. is proposed. The type strain is TF5-37.2-LB10T ( = DSM 23085T = CIP 110085T = MOLA 820T).
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Affiliation(s)
- Laurent Urios
- Université de Pau et des Pays de l’Adour, IPREM UMR 5254, Equipe Environnement et Microbiologie, IBEAS, 64013 Pau, France
| | - Laurent Intertaglia
- Observatoire Océanologique, Laboratoire d’Océanographie Biologique de Banyuls, Université Pierre et Marie Curie (Paris VI), Institut National des Sciences de l’Univers (INSU), CNRS UMS 2348, 66651 Banyuls-sur-Mer, France
| | - Michel Magot
- Université de Pau et des Pays de l’Adour, IPREM UMR 5254, Equipe Environnement et Microbiologie, IBEAS, 64013 Pau, France
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Zhou Z, Jiang F, Wang S, Peng F, Dai J, Li W, Fang C. Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus
Pedobacter
,
Pedobacter heparinus
,
Pedobacter daechungensis
,
Pedobacter terricola
,
Pedobacter glucosidilyticus
and
Pedobacter lentus. Int J Syst Evol Microbiol 2012; 62:1963-1969. [DOI: 10.1099/ijs.0.031104-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, short rod-shaped, motile (by gliding) bacterial strain, designated A12T, was isolated from tundra soil collected from Ny-Ålesund, in the Arctic region of Norway. The temperature, NaCl and pH ranges for growth were 4–25 °C (optimum, 18 °C), 0–2 % (optimum, 0 %) and pH 6–9 (optimum, pH 7). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the Arctic isolate belonged to the genus
Pedobacter
and showed highest sequence similarity (94.4 %) to
Pedobacter daechungensis
KCTC 12637T. The DNA G+C content (38.3 mol%), polar lipid profile, presence of sphingolipid, MK-7 as the only respiratory quinone, and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH as major fatty acids supported the allocation of strain A12T to the genus
Pedobacter
as a representative of a novel species, for which the name Pedobacter
arcticus sp. nov. is proposed. The type strain is A12T ( = CCTCC AB 2010223T = NRRL B-59457T). Emended descriptions of the genus
Pedobacter
and of
Pedobacter heparinus
,
Pedobacter daechungensis
,
Pedobacter terricola
,
Pedobacter glucosidilyticus
and
Pedobacter lentus
are also given.
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Affiliation(s)
- Zhichao Zhou
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Fan Jiang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Shaohua Wang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Jun Dai
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Wenxin Li
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Chengxiang Fang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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Cai M, Wang L, Cai H, Li Y, Wang YN, Tang YQ, Wu XL. Salinarimonas ramus sp. nov. and Tessaracoccus oleiagri sp. nov., isolated from a crude oil-contaminated saline soil. Int J Syst Evol Microbiol 2011; 61:1767-1775. [DOI: 10.1099/ijs.0.025932-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four bacterial strains, SL014B-41A4T, SL014B-20A1T, SL014B-76A1 and SL014B-79A, isolated from a crude oil-contaminated saline soil of Shengli Oilfield, China, were investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SL014B-41A4T belonged to the genus Salinarimonas in the order Rhizobiales, with the highest sequence similarity with Salinarimonas rosea YIM YD3T (98.3 %). The DNA–DNA relatedness of strain SL014B-41A4T to S. rosea YIM YD3T was 27.03±3.0 %. Strain SL014B-41A4T was Gram-negative staining, facultatively anaerobic and produced deep red pigment in artificial seawater medium. Cells of strain SL014B-41A4T were rod-shaped (0.6–4.0×1.25–25 µm), motile with a single polar flagellum and often formed branches. The strain contained Q-10 as the predominant respiratory ubiquinone and C18 : 1ω7c (57.5 %), C16 : 0 (16.4 %) and 10-methyl C19 : 0 (9.1 %) as the major fatty acids. Strains SL014B-20A1T, SL014B-76A1 and SL014B-79A were actinobacteria and belonged to the genus Tessaracoccus in the family Propionibacteriaceae of the order Actinomycetales with the highest 16S rRNA gene sequence similarities with Tessaracoccus flavescens SST-39T (96.4 %), Tessaracoccus lubricantis KISS-17SeT (96.2 %) and Tessaracoccus bendigoensis Ben 106T (94.7 %). Strains SL014B-20A1T, SL014B-76A1 and SL014B-79A were Gram-positive staining, facultatively anaerobic, non-endospore-forming, non-motile, acid-fast and oval to rod-shaped (0.48×0.5–1.0 µm). These three novel strains had ll-diaminopimelic acid (DAP) as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-9(H4) as the only menaquinone and anteiso-C15 : 0 (67.11–76.14 %) as the major cellular fatty acid. The G+C contents of the genomic DNA of strain SL014B-41A4T and strains SL014B-20A1T, SL014B-76A1 and SL014B-79A were 67.68 mol% and 65.65–67.17 mol%, respectively. Based on phenotypic and genotypic characteristics, strain SL014B-41A4T represents a novel species of the genus Salinarimonas, for which the name Salinarimonas ramus is proposed, with strain SL014B-41A4T ( = DSM 22962T = CGMCC 1.9161T) as the type strain. Strains SL014B-20A1T, SL014B-76A1 and SL014B-79A represent a novel species of the genus Tessaracoccus, for which the name Tessaracoccus oleiagri is proposed, with strain SL014B-20A1T ( = DSM 22955T = CGMCC 1.9159T) as the type strain.
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Affiliation(s)
- Man Cai
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, PR China
| | - Lu Wang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, PR China
| | - Hua Cai
- Department of Environmental Science and Engineering, Tsinghua University, Beijing 100081, PR China
| | - Yan Li
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, PR China
| | - Ya-Nan Wang
- Department of Environmental Science and Engineering, Tsinghua University, Beijing 100081, PR China
| | - Yue-Qin Tang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, PR China
| | - Xiao-Lei Wu
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, PR China
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Arp G, Bissett A, Brinkmann N, Cousin S, De Beer D, Friedl T, Mohr KI, Neu TR, Reimer A, Shiraishi F, Stackebrandt E, Zippel B. Tufa-forming biofilms of German karstwater streams: microorganisms, exopolymers, hydrochemistry and calcification. ACTA ACUST UNITED AC 2010. [DOI: 10.1144/sp336.6] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractTo understand mechanisms of tufa biofilm calcification, selected karstwater stream stromatolites in Germany have been investigated with regard to their hydrochemistry, biofilm community, exopolymers, physicochemical microgradients, calcification pattern and lamination. In stream waters, CO2 degassing drives the increase in calcite saturation to maximum values of approximately 10-fold, independent from the initial Ca2+/alkalinity ratio. For the cyanobacteria of tufa biofilms, a culture-independent molecular approach showed that microscopy of resin-embedded biofilm thin sections underestimated the actual diversity of cyanobacteria, i.e. the six cyanobacteria morphotypes were opposed to nine different lineages of the 16S rDNA phylogeny. The same morphotype may even represent two genetically distant cyanobacteria and the closest relatives of tufa biofilm cyanobacteria may be from quite different habitats. Diatom diversity was even higher in the biofilm at the studied exemplar site than that of the cyanobacteria, i.e. 13 diatom species opposed to 9 cyanobacterial lineages. The non-phototrophic prokaryotic biofilm community is clearly different from the soil-derived community of the stream waters, and largely composed of flavobacteria, firmicutes, proteobacteria and actinobacteria. The exopolymeric biofilm matrix can be divided into three structural domains by fluorescence lectin-binding analysis. Seasonal and spatial variability of these structural EPS domains is low in the investigated streams. As indicated by microsensor data, biofilm photosynthesis is the driving mechanism in tufa stromatolite formation. However, photosynthesis-induced biofilm calcification accounts for only 10–20% of the total Ca2+ loss in the streams, and occurs in parallel to inorganic precipitation driven by CO2-degassing within the water column and on biofilm-free surfaces. Annual stromatolite laminae reflect seasonal changes in temperature and light supply. The stable carbon isotope composition of the laminae is not affected by photosynthesis-induced microgradients, but mirrors that of the bulk water body only reflecting climate fluctuations. Tufa stromatolites with their cyanobacterial–photosynthesis-related calcification fabrics form an analogue to porostromate cyanobacterial stromatolites in fossil settings high in CaCO3 mineral supersaturation but comparatively low in dissolved inorganic carbon. Here, the sum-effect of heterotrophic exopolymer-degradation and secondary Ca2+-release rather decreases calcite saturation, contrary to settings high in dissolved inorganic carbon such as soda lakes.
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Affiliation(s)
- Gernot Arp
- University of Göttingen, Geoscience Centre, Goldschmidtstraße 3, D-37077 Göttingen, Germany
| | - Andrew Bissett
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, D-28359 Bremen, Germany
- Present address: CSIRO, Plant Industry, P. O. Box 1600, Canberra, ACT 2601, Australia
| | - Nicole Brinkmann
- University of Göttingen, Albrecht-von-Haller-Institute for Plant Sciences, Experimental Phycology and Culture Collection of Algae (SAG), Nikolausberger Weg 18, D-37073 Göttingen
| | - Sylvie Cousin
- German Collection of Microorganisms and Cell Cultures DSMZ, Inhoffenstraße 7 B, D-38124 Braunschweig, Germany
- Institut Pasteur, Genopole de l'Ile de France, PF1, Paris, France
| | - Dirk De Beer
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, D-28359 Bremen, Germany
| | - Thomas Friedl
- University of Göttingen, Albrecht-von-Haller-Institute for Plant Sciences, Experimental Phycology and Culture Collection of Algae (SAG), Nikolausberger Weg 18, D-37073 Göttingen
| | - Kathrin I. Mohr
- University of Göttingen, Albrecht-von-Haller-Institute for Plant Sciences, Experimental Phycology and Culture Collection of Algae (SAG), Nikolausberger Weg 18, D-37073 Göttingen
- Present address: Helmholtz Centre for Infection Research, Inhoffenstraße 7, D-38124 Braunschweig, Germany
| | - Thomas R. Neu
- Helmholtz Centre for Environmental Research UFZ, Department of River Ecology, Brückstraße 3a, D-39114 Magdeburg, Germany
| | - Andreas Reimer
- University of Göttingen, Geoscience Centre, Goldschmidtstraße 3, D-37077 Göttingen, Germany
| | - Fumito Shiraishi
- University of Göttingen, Geoscience Centre, Goldschmidtstraße 3, D-37077 Göttingen, Germany
- Present address: Division of Evolution of Earth Environment, Graduate School of Social and Cultural Studies, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Erko Stackebrandt
- German Collection of Microorganisms and Cell Cultures DSMZ, Inhoffenstraße 7 B, D-38124 Braunschweig, Germany
| | - Barbara Zippel
- Helmholtz Centre for Environmental Research UFZ, Department of River Ecology, Brückstraße 3a, D-39114 Magdeburg, Germany
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Ali Z, Cousin S, Fruhling A, Brambilla E, Schumann P, Yang Y, Stackebrandt E. Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet. Int J Syst Evol Microbiol 2009; 59:2610-7. [DOI: 10.1099/ijs.0.008771-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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36
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Stackebrandt E, Verbarg S, Frühling A, Busse HJ, Tindall BJ. Dissection of the genus Methylibium: reclassification of Methylibium fulvum as Rhizobacter fulvus comb. nov., Methylibium aquaticum as Piscinibacter aquaticus gen. nov., comb. nov. and Methylibium subsaxonicum as Rivibacter subsaxonicus gen. nov., comb. nov. and emended descriptions of the genera Rhizobacter and Methylibium. Int J Syst Evol Microbiol 2009; 59:2552-60. [PMID: 19622640 DOI: 10.1099/ijs.0.008383-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
16S rRNA gene sequenced-based phylogeny indicates that Rhizobacter dauci ATCC 43778(T) branches within the radiation of Methylibium type strains. A comparative chemotaxonomic study including fatty acid methyl esters, polar lipids and polyamines reveals significant differences that, in combination with the topology of phylogenetic trees, support a dissection of the genus Methylibium. The proposals of this study include the transfer of Methylibium fulvum to the genus Rhizobacter as Rhizobacter fulvus comb. nov. (type strain Gsoil 322(T) =KCTC 12591(T) =DSM 19916(T)) and the reclassification of Methylibium aquaticum as Piscinibacter aquaticus gen. nov., comb. nov. (the type strain of Piscinibacter aquaticus is IMCC1728(T) =KCCM 42364(T) =NBRC 102349(T) =DSM 19915(T)) and of Methylibium subsaxonicum as Rivibacter subsaxonicus gen. nov., comb. nov. (the type strain of Rivibacter subsaxonicus is BF49(T) =DSM 19570(T) =CIP 109700(T)). As a consequence of these reclassifications, emended descriptions of the genera Methylibium and Rhizobacter are provided.
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Affiliation(s)
- Erko Stackebrandt
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstr. 7B, D-38124 Braunschweig, Germany.
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Jeon Y, Kim JM, Park JH, Lee SH, Seong CN, Lee SS, Jeon CO. Pedobacter oryzae sp. nov., isolated from rice paddy soil. Int J Syst Evol Microbiol 2009; 59:2491-5. [DOI: 10.1099/ijs.0.005710-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Weon HY, Kim BY, Lee CM, Hong SB, Jeon YA, Koo BS, Kwon SW. Solitalea koreensis gen. nov., sp. nov. and the reclassification of [Flexibacter] canadensis as Solitalea canadensis comb. nov. Int J Syst Evol Microbiol 2009; 59:1969-75. [DOI: 10.1099/ijs.0.007278-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Gordon NS, Valenzuela A, Adams SM, Ramsey PW, Pollock JL, Holben WE, Gannon JE. Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil. Int J Syst Evol Microbiol 2009; 59:1720-6. [PMID: 19542109 DOI: 10.1099/ijs.0.000158-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Nathan S Gordon
- Microbial Ecology Program, Division of Biological Sciences, The University of Montana, Missoula, MT 59812-1006, USA.
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Verbarg S, Frühling A, Cousin S, Brambilla E, Gronow S, Lünsdorf H, Stackebrandt E. Biostraticola tofi gen. nov., spec. nov., a novel member of the family Enterobacteriaceae. Curr Microbiol 2008; 56:603-8. [PMID: 18324435 DOI: 10.1007/s00284-008-9133-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Accepted: 01/21/2008] [Indexed: 10/22/2022]
Abstract
Bacterial strain BF36T, isolated from the biofilm of a tufa deposit in a hard water rivulet, was characterized by a polyphasic taxonomic approach. Cells of these organisms were Gram-negative, motile, nonpigmented, rod-shaped, non-endospore-forming, and facultatively anaerobic. Cells, organized in loose consortia, were coated by a massive slime layer. Phylogenetic analyses using 16S rRNA gene sequences showed that strain BF36T was a member of the family Enterobacteriaceae, class Gammaproteobacteria, displaying a moderate degree of relationship (96.5% sequence similarity) to Sodalis glossinidius and "Sodalis pallipedes," intracellular symbionts of the tsetse fly Glossinis morsitans morsitans. Dendrograms of relationship generated by different algorithms consistently grouped isolate BF36T with Sodalis glossinidius, Pragia fontium, Budvicia aquatica, Serratia rubideae, and Brenneria spp (94.7-95.8% similarity) which also share many common metabolic properties. Differences between strain BF36T and Sodalis glossinidius DSM 13495T are seen in motility and in the pattern of substrates utilized. Membership to the family was also confirmed by a fatty acid profile consisting of major amounts of C16:0)and C16:1omega7, by the presence of isoprenoids of the ubiquinone Q8 and menaquinone MK8 types and a DNA G + C content of 54.2 mol%. The decision to classify strain BF36T into a new genus Biostraticola gen. nov. is based on its distant phylogenetic position as compared to any other representative of the family and the significant phenotypic differences to its nearest phylogenetic neighbor, Sodalis glossinidius. BF36T represents the type species, for which the name Biostraticola tofi sp. nov. is proposed. The type strain is BF36T (DSM 19580T; CIP109699T).
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Affiliation(s)
- Susanne Verbarg
- DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7B, 38124, Braunschweig, Germany
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Methylibium subsaxonicum spec. nov., a Betaproteobacterium Isolated from a Hardwater Rivulet. Curr Microbiol 2008; 56:298-305. [DOI: 10.1007/s00284-007-9095-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 11/23/2007] [Indexed: 10/22/2022]
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