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Tizabi D, Bachvaroff T, Hill RT. Complete genome sequence of Imperialibacter roseus strain P4 T. Microbiol Resour Announc 2024; 13:e0098623. [PMID: 38780297 PMCID: PMC11237651 DOI: 10.1128/mra.00986-23] [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: 10/31/2023] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Imperialibacter roseus strain P4T is a bacterial strain isolated from Permian groundwater. The complete genome of Imperialibacter roseus strain P4T was sequenced to reveal a single circular chromosome of 6,747,663 bp with a GC content of 46.5%.
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Affiliation(s)
- Daniela Tizabi
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Tsvetan Bachvaroff
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Russell T Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
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Chen B, Zhang M, Lin D, Ye J, Tang K. Roseihalotalea indica gen. nov., sp. nov., a halophilic Bacteroidetes from mesopelagic Southwest Indian Ocean with higher carbohydrate metabolic potential. Antonie Van Leeuwenhoek 2024; 117:66. [PMID: 38607563 DOI: 10.1007/s10482-024-01965-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
The pink-colored and strictly aerobic bacterium strain, designated as TK19036T, was isolated from mesopelagic layer of the Southwest Indian Ocean. This novel isolate can grow at 10-45 °C (optimum, 30 °C), pH 6.0-8.0 (optimum, pH 7.0), and 2-14% NaCl concentrations (w/v) (optimum, 6%). The predominant respiratory quinone was Menaquinone-7. Major polar lipid profiles contained two aminolipids, aminophospholipid, two glycolipids, phosphatidylethanolamine, and three unknown polar lipids. The preponderant cellular fatty acids were iso-C15:0, C16:1 ω5c and iso-C17:0 3-OH. Phylogenetic analyses based on 16S rRNA gene sequence uncovered that the strain TK19036T pertained to the family Catalinimonadaceae under phylum Bacteroidota, and formed a distinct lineage with the closed species Tunicatimonas pelagia NBRC 107804T. The up-to-bacteria-core gene phylogenetic trees also demonstrated a deep and novel branch formed by the strain TK19036T within the family Catalinimonadaceae. Based on chemotaxonomic, phylogenetic and genomic features presented above, strain TK19036T represents a novel species from a novel genus of the family Catalinimonadaceae, for which the name Roseihalotalea indica gen. nov. sp. nov. is proposed. The type strain is TK19036T (= CGMCC 1.18940T = NBRC 116371T).
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Affiliation(s)
- Beihan Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Mingzhe Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- School of Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Dan Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Jianing Ye
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.
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Veloso S, Amouroux D, Lanceleur L, Cagnon C, Monperrus M, Deborde J, Laureau CC, Duran R. Keystone microbial taxa organize micropollutant-related modules shaping the microbial community structure in estuarine sediments. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130858. [PMID: 36706488 DOI: 10.1016/j.jhazmat.2023.130858] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/10/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
The fluctuation of environmental conditions drives the structure of microbial communities in estuaries, highly dynamic ecosystems. Microorganisms inhabiting estuarine sediments play a key role in ecosystem functioning. They are well adapted to the changing conditions, also threatened by the presence of pollutants. In order to determine the environmental characteristics driving the organization of the microbial assemblages, we conducted a seasonal survey along the Adour Estuary (Bay of Biscay, France) using 16S rRNA gene Illumina sequencing. Microbial diversity data were combined with a set of chemical analyses targeting metals and pharmaceuticals. Microbial communities were largely dominated by Proteobacteria (41 %) and Bacteroidota (32 %), showing a strong organization according to season, with an important shift in winter. The composition of microbial communities showed spatial distribution according to three main areas (upstream, middle, and downstream estuary) revealing the influence of the Adour River. Further analyses indicated that the microbial community was influenced by biogeochemical parameters (Corg/Norg and δ13C) and micropollutants, including metals (As, Cu, Mn, Sn, Ti, and Zn) and pharmaceuticals (norfloxacin, oxolinic acid and trimethoprim). Network analysis revealed specific modules, organized around keystone taxa, linked to a pollutant type, providing information of paramount importance to understand the microbial ecology in estuarine ecosystems.
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Affiliation(s)
- Sandrine Veloso
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - David Amouroux
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - Laurent Lanceleur
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Anglet, France
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - Mathilde Monperrus
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Anglet, France
| | - Jonathan Deborde
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Anglet, France; Ifremer, LITTORAL, Laboratoire Environnement Ressources des Pertuis Charentais, F-17390 La Tremblade, France
| | - Cristiana Cravo Laureau
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France.
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Wei H, He W, Li Z, Ge L, Zhang J, Liu T. Salt-tolerant endophytic bacterium Enterobacter ludwigii B30 enhance bermudagrass growth under salt stress by modulating plant physiology and changing rhizosphere and root bacterial community. FRONTIERS IN PLANT SCIENCE 2022; 13:959427. [PMID: 35982708 PMCID: PMC9380843 DOI: 10.3389/fpls.2022.959427] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Osmotic and ionic induced salt stress suppresses plant growth. In a previous study, Enterobacter ludwigii B30, isolated from Paspalum vaginatum, improved seed germination, root length, and seedling length of bermudagrass (Cynodon dactylon) under salt stress. In this study, E. ludwigii B30 application improved fresh weight and dry weight, carotenoid and chlorophyll levels, catalase and superoxide dismutase activities, indole acetic acid content and K+ concentration. Without E. ludwigii B30 treatment, bermudagrass under salt stress decreased malondialdehyde and proline content, Y(NO) and Y(NPQ), Na+ concentration, 1-aminocyclopropane-1-carboxylate, and abscisic acid content. After E. ludwigii B30 inoculation, bacterial community richness and diversity in the rhizosphere increased compared with the rhizosphere adjacent to roots under salt stress. Turf quality and carotenoid content were positively correlated with the incidence of the phyla Chloroflexi and Fibrobacteres in rhizosphere soil, and indole acetic acid (IAA) level was positively correlated with the phyla Actinobacteria and Chloroflexi in the roots. Our results suggest that E. ludwigii B30 can improve the ability of bermudagrass to accumulate biomass, adjust osmosis, improve photosynthetic efficiency and selectively absorb ions for reducing salt stress-induced injury, while changing the bacterial community structure of the rhizosphere and bermudagrass roots. They also provide a foundation for understanding how the bermudagrass rhizosphere and root microorganisms respond to endophyte inoculation.
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Affiliation(s)
- Hongjian Wei
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, South China Agricultural University, Guangzhou, China
| | - Wenyuan He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Ziji Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, South China Agricultural University, Guangzhou, China
| | - Liangfa Ge
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, South China Agricultural University, Guangzhou, China
| | - Juming Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, South China Agricultural University, Guangzhou, China
| | - Tianzeng Liu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, South China Agricultural University, Guangzhou, China
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Wang X, Guo F, Tian P, Yu S, Xue CX, Wang W, Xiao J, Niu W. Flammeovirga agarivorans sp. nov., an agar-digesting marine bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2020; 70:6060-6066. [PMID: 33095697 DOI: 10.1099/ijsem.0.004497] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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, gliding, reddish-orange-coloured, rod-shaped strain, designated SR4T, was isolated from surface seawater sampled at Luhuitou fringing reef (South China Sea). Phylogenetic analyses based on the 16S rRNA gene, phylogenomic analysis of single-copy gene families and whole genome data affiliated it to the genus Flammeovirga. It was most closely related to Flammeovirga yaeyamensis NBRC 100898T (97.99 % 16S rRNA gene similarity). The genome average nucleotide identity and DNA-DNA relatedness values between strain SR4T and its reference strains were less than 74.2 and 16.3 %, respectively. Growth occurred at 20-35 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 1-6 % (w/v) NaCl (optimum, 2-4 %). The dominant fatty acids were C16 : 0, iso-C15 : 0 and C20 : 4 ω6,9,12,15c. The polar lipid profile of strain SR4T comprised phosphatidylethanolamine, two glycolipids, two aminophospholipids and three unidentified lipids. The major respiratory quinone was MK-7. The DNA G+C content of strain SR4T was 34.20 mol%. On the basis of the polyphasic evidence, strain SR4T is proposed as representing a novel species of the genus Flammeovirga, for which the name Flammeovirga agarivorans sp. nov. is proposed. The type strain is SR4T (=KCTC 82075T=MCCC 1A17137T).
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Affiliation(s)
- Xiaolei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Feng Guo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Peng Tian
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Shuangen Yu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Chun-Xu Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Wei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Jiaguang Xiao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Wentao Niu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
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Jeong YS, Kang W, Sung H, Lee JY, Yun JH, Shin NR, Kim HS, Lee SY, Han JE, Lee JY, Tak EJ, Kim PS, Hyun DW, Jung MJ, Whon TW, Kang MS, Lee KE, Lee BH, Bae JW. Flammeovirga pectinis sp. nov., isolated from the gut of the Korean scallop, Patinopecten yessoensis. Int J Syst Evol Microbiol 2019; 70:499-504. [PMID: 31613737 DOI: 10.1099/ijsem.0.003783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, rod-shaped, reddish-orange-coloured, gliding bacterial strain, designated L12M1T, was isolated from the gut of the Korean scallop, Patinopecten yessoensis. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain L12M1T formed a monophyletic clade with the strains in the genus Flammeovirga and showed highest 16S rRNA gene sequence similarity to Flammeovirga kamogawensis YS10T (98.66 %). The major cellular fatty acids of strain L12M1T were iso-C15 : 0 and C20 : 4ω6,9,12,15c. The predominant isoprenoid quinone was MK-7. The major polyamines were spermidine, cadaverine and the minor polyamine was putrescine. The DNA G+C content was 32.1 mol%. The phylogenetic, phenotypic, biochemical, chemotaxonomic and genotypic results indicated that strain L12M1T represents a novel species of the genus Flammeovirga, for which the name Flammeovirga pectinis sp. nov. is proposed. The type strain is L12M1T (=KCTC 62750T=JCM 33169T).
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Affiliation(s)
- Yun-Seok Jeong
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Woorim Kang
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hojun Sung
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - June-Young Lee
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Ji-Hyun Yun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Na-Ri Shin
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hyun Sik Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - So-Yeon Lee
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jeong Eun Han
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jae-Yun Lee
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Euon Jung Tak
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Pil Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Dong-Wook Hyun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Mi-Ja Jung
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Tae Woong Whon
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Myung-Suk Kang
- Biological Resources Utilization Department, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Byoung-Hee Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
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Köhler JM, Kalensee F, Cao J, Günther PM. Hadesarchaea and other extremophile bacteria from ancient mining areas of the East Harz region (Germany) suggest an ecological long-term memory of soil. SN APPLIED SCIENCES 2019. [DOI: 10.1007/s42452-019-0874-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Maejima Y, Kushimoto K, Muraguchi Y, Fukuda K, Miura T, Yamazoe A, Kimbara K, Shintani M. Proteobacteria and Bacteroidetes are major phyla of filterable bacteria passing through 0.22 μm pore size membrane filter, in Lake Sanaru, Hamamatsu, Japan. Biosci Biotechnol Biochem 2018; 82:1260-1263. [DOI: 10.1080/09168451.2018.1456317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Abstract
141 filterable bacteria that passed through a 0.22 μm pore size filter were isolated from Lake Sanaru in Hamamatsu, Japan. These belonged to Proteobacteria, Bacteroidetes, Firmicutes, or Actinobacteria among which the first two phyla comprised the majority of the isolates. 48 isolates (12 taxa) are candidates assignable to new bacterial species or genera of Proteobacteria or Bacteroidetes.
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Affiliation(s)
- Yoshiaki Maejima
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University , Hamamatsu, Japan
| | - Koya Kushimoto
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University , Hamamatsu, Japan
| | - Yusuke Muraguchi
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University , Hamamatsu, Japan
| | - Kohei Fukuda
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University , Hamamatsu, Japan
| | - Takamasa Miura
- Industrial Innovation Division, Biological Resource Center, National Institute of Technology and Evaluation , Tokyo, Japan
| | - Atsushi Yamazoe
- Industrial Innovation Division, Biological Resource Center, National Institute of Technology and Evaluation , Tokyo, Japan
| | - Kazuhide Kimbara
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University , Hamamatsu, Japan
| | - Masaki Shintani
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University , Hamamatsu, Japan
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University , Hamamatsu, Japan
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