1
|
Kim W, Jang S, Chae N, Kim M, Yeh JY, Kim S, Lee YM. Hymenobacter canadensis sp. nov., isolated from freshwater of the pond in Cambridge Bay, Canada. Int J Syst Evol Microbiol 2023; 73. [PMID: 37326606 DOI: 10.1099/ijsem.0.005913] [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: 06/17/2023] Open
Abstract
A Gram-stain-negative, aerobic, reddish-coloured, rod-shaped and non-motile strain PAMC 29467T, was isolated from freshwater of the pond in Cambridge Bay, Canada. Strain PAMC 29467T was closely related to Hymenobacter yonginensis (98.1 % 16S rRNA gene similarity). Genomic relatedness analyses showed that strain PAMC 29467T is distinguishable from H. yonginensis based on average nucleotide identity (91.3 %) and digital DNA-DNA hybridization values (39.3 %). The major fatty acids (>10 %) of strain PAMC 29467T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C15 : 0 iso, C16 : 1 ω5c and summed feature 4 (C17 : 1 iso l and/or anteiso B). The major respiratory quinone was menaquinone-7. The genomic DNA G+C content was 61.5 mol%. Strain PAMC 29467T was separated from the type species in the genus Hymenobacter by its distinct phylogenetic position and some physiological characteristics. As a result, a novel species is proposed, with the name Hymenobacter canadensis sp. nov. (type strain, PAMC 29467T=KCTC 92787T=JCM 35843T).
Collapse
Affiliation(s)
- Woohyun Kim
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Seonghan Jang
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Namyi Chae
- Institutes of Life Sciences and Natural Resources, Korea University, Seoul 02841, Republic of Korea
| | - Mincheol Kim
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Jung-Yong Yeh
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Sanghee Kim
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Yung Mi Lee
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| |
Collapse
|
2
|
Ren T, Zhang C, Jin CZ, Jin FJ, Li T, Oh HM, Lee HG, Jin L. Description of Hymenobacter sediminicola sp. nov., isolated from contaminated sediment. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01846-9. [PMID: 37237242 DOI: 10.1007/s10482-023-01846-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023]
Abstract
A polyphasic taxonomic study was conducted on two Gram-negative, non-sporulating, non-motile bacterial strains, S2-20-2T and S2-21-1, isolated from a contaminated freshwater sediment in China. Comparative 16S rRNA gene sequence studies revealed a clear affiliation of two strains with Bacteroidetes, which showed the highest pairwise sequence similarities with Hymenobacter duratus BT646T (99.3%), Hymenobacter psychrotolerans Tibet-IIU11T (99.3%), Hymenobacter kanuolensis T-3T (97.6%), Hymenobacter swuensis DY53T (96.9%), Hymenobacter tenuis POB6T (96.8%), Hymenobacter seoulensis 16F7GT (96.7%), and Hymenobacter rigui KCTC 12533T (96.5%). The phylogenetic analysis based on 16S rRNA gene sequences showed that two strains formed a clear phylogenetic lineage with the genus Hymenobacter. Major fatty acids were identified as iso-C15:0, anteiso-C15:0, and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c/t) and summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B). Major cellular polar lipids were identified as phosphatidylethanolamine, three unidentified aminolipids, an unidentified aminophosopholipid and an unidentified lipid. The respiratory quinone was detected as MK-7 and the genomic DNA G + C content was determined to be 57.9% (genome) for type strain S2-20-2T and 57.7 mol% (HPLC) for strain S2-21-1. The observed ANI and dDDH values between strain S2-20-2T and its closely related strains were 75.7-91.4% and 21.2-43.9%, respectively. Based on physiological, biochemical, genetic and genomic characteristics, we propose that strains S2-20-2T and S2-21-1 represent a novel species of the genus Hymenobacter, for which the name Hymenobacter sediminicola sp. nov. is proposed. The type strain is S2-20-2T (= CGMCC 1.18734T = JCM 35801T).
Collapse
Affiliation(s)
- Tingting Ren
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Chengxiao Zhang
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Chun-Zhi Jin
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Feng-Jie Jin
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Taihua Li
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Long Jin
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
| |
Collapse
|
3
|
Kapinusova G, Jani K, Smrhova T, Pajer P, Jarosova I, Suman J, Strejcek M, Uhlik O. Culturomics of Bacteria from Radon-Saturated Water of the World's Oldest Radium Mine. Microbiol Spectr 2022; 10:e0199522. [PMID: 36000901 PMCID: PMC9602452 DOI: 10.1128/spectrum.01995-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/04/2022] [Indexed: 12/31/2022] Open
Abstract
Balneotherapeutic water springs, such as those with thermal, saline, sulfur, or any other characteristics, have recently been the subject of phylogenetic studies with a closer focus on the description and/or isolation of phylogenetically novel or biotechnologically interesting microorganisms. Generally, however, most such microorganisms are rarely obtained in pure culture or are even, for now, unculturable under laboratory conditions. In this culture-dependent study of radioactive water springs of Jáchymov (Joachimstahl), Czech Republic, we investigated a combination of classical cultivation approaches with those imitating sampling source conditions. Using these environmentally relevant cultivation approaches, over 1,000 pure cultures were successfully isolated from 4 radioactive springs. Subsequent dereplication yielded 121 unique taxonomic units spanning 44 genera and 9 taxonomic classes, ~10% of which were identified as hitherto undescribed taxa. Genomes of the latter were sequenced and analyzed, with a special focus on endogenous defense systems to withstand oxidative stress and aid in radiotolerance. Due to their origin from radioactive waters, we determined the resistance of the isolates to oxidative stress. Most of the isolates were more resistant to menadione than the model strain Deinococcus radiodurans DSM 20539T. Moreover, isolates of the Deinococcacecae, Micrococcaceae, Bacillaceae, Moraxellaceae, and Pseudomonadaceae families even exhibited higher resistance in the presence of hydrogen peroxide. In summary, our culturomic analysis shows that subsurface water springs contain diverse bacterial populations, including as-yet-undescribed taxa and strains with promising biotechnological potential. Furthermore, this study suggests that environmentally relevant cultivation techniques increase the efficiency of cultivation, thus enhancing the chance of isolating hitherto uncultured microorganisms. IMPORTANCE The mine Svornost in Jáchymov (Joachimstahl), Czech Republic is a former silver-uranium mine and the world's first and for a long time only radium mine, nowadays the deepest mine devoted to the extraction of water which is saturated with radon and has therapeutic benefits given its chemical properties. This healing water, which is approximately 13 thousand years old, is used under medical supervision for the treatment of patients with neurological and rheumatic disorders. Our culturomic approach using low concentrations of growth substrates or the environmental matrix itself (i.e., water filtrate) in culturing media combined with prolonged cultivation time resulted in the isolation of a broad spectrum of microorganisms from 4 radioactive springs of Jáchymov which are phylogenetically novel and/or bear various adaptive or coping mechanisms to thrive under selective pressure and can thus provide a wide spectrum of capabilities potentially exploitable in diverse scientific, biotechnological, or medical disciplines.
Collapse
Affiliation(s)
- Gabriela Kapinusova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Kunal Jani
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Tereza Smrhova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, Prague, Czech Republic
| | - Irena Jarosova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biotechnology, Prague, Czech Republic
| | - Jachym Suman
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Michal Strejcek
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| |
Collapse
|
4
|
Liu Y, Cui X, Yang R, Zhang Y, Xu Y, Liu G, Zhang B, Wang J, Wang X, Zhang W, Chen T, Zhang G. Genomic Insights into the Radiation-Resistant Capability of Sphingomonas qomolangmaensis S5-59 T and Sphingomonas glaciei S8-45 T, Two Novel Bacteria from the North Slope of Mount Everest. Microorganisms 2022; 10:microorganisms10102037. [PMID: 36296313 PMCID: PMC9611098 DOI: 10.3390/microorganisms10102037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
Mount Everest provides natural advantages to finding radiation-resistant extremophiles that are functionally mechanistic and possess commercial significance. (1) Background: Two bacterial strains, designated S5-59T and S8-45T, were isolated from moraine samples collected from the north slope of Mount Everest at altitudes of 5700m and 5100m above sea level. (2) Methods: The present study investigated the polyphasic features and genomic characteristics of S5-59T and S8-45T. (3) Results: The major fatty acids and the predominant respiratory menaquinone of S5-59T and S8-45T were summed as feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA sequences and average nucleotide identity values among these two strains and their reference type strains were below the species demarcation thresholds of 98.65% and 95%. Strains S5-59T and S8-45T harbored great radiation resistance. The genomic analyses showed that DNA damage repair genes, such as mutL, mutS, radA, radC, recF, recN, etc., were present in the S5-59T and S8-45T strains. Additionally, strain S5-59T possessed more genes related to DNA protection proteins. The pan-genome analysis and horizontal gene transfers revealed that strains of Sphingomonas had a consistently homologous genetic evolutionary radiation resistance. Moreover, enzymatic antioxidative proteins also served critical roles in converting ROS into harmless molecules that resulted in resistance to radiation. Further, pigments and carotenoids such as zeaxanthin and alkylresorcinols of the non-enzymatic antioxidative system were also predicted to protect them from radiation. (4) Conclusions: Type strains S5-59T (=JCM 35564T =GDMCC 1.3193T) and S8-45T (=JCM 34749T =GDMCC 1.2715T) represent two novel species of the genus Sphingomonas with the proposed name Sphingomonas qomolangmaensis sp. nov. and Sphingomonas glaciei sp. nov. The type strains, S5-59T and S8-45T, were assessed in a deeply genomic study of their radiation-resistant mechanisms and this thus resulted in a further understanding of their greater potential application for the development of anti-radiation protective drugs.
Collapse
Affiliation(s)
- Yang Liu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Xiaowen Cui
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, China
| | - Ruiqi Yang
- College of Urban Environment, Lanzhou City University, Lanzhou 730070, China
| | - Yiyang Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yeteng Xu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Binglin Zhang
- 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, Lanzhou 730000, China
| | - Jinxiu Wang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xinyue Wang
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Correspondence: (T.C.); (G.Z.)
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Correspondence: (T.C.); (G.Z.)
| |
Collapse
|
5
|
Soil substrate culturing approaches recover diverse members of Actinomycetota from desert soils of Herring Island, East Antarctica. Extremophiles 2022; 26:24. [PMID: 35829965 PMCID: PMC9279279 DOI: 10.1007/s00792-022-01271-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 06/06/2022] [Indexed: 11/12/2022]
Abstract
Antimicrobial resistance is an escalating health crisis requiring urgent action. Most antimicrobials are natural products (NPs) sourced from Actinomycetota, particularly the Streptomyces. Underexplored and extreme environments are predicted to harbour novel microorganisms with the capacity to synthesise unique metabolites. Herring Island is a barren and rocky cold desert in East Antarctica, remote from anthropogenic impact. We aimed to recover rare and cold-adapted NP-producing bacteria, by employing two culturing methods which mimic the natural environment: direct soil culturing and the soil substrate membrane system. First, we analysed 16S rRNA gene amplicon sequencing data from 18 Herring Island soils and selected the soil sample with the highest Actinomycetota relative abundance (78%) for culturing experiments. We isolated 166 strains across three phyla, including novel and rare strains, with 94% of strains belonging to the Actinomycetota. These strains encompassed thirty-five ‘species’ groups, 18 of which were composed of Streptomyces strains. We screened representative strains for genes which encode polyketide synthases and non-ribosomal peptide synthetases, indicating that 69% have the capacity to synthesise polyketide and non-ribosomal peptide NPs. Fourteen Streptomyces strains displayed antimicrobial activity against selected bacterial and yeast pathogens using an in situ assay. Our results confirm that the cold-adapted bacteria of the harsh East Antarctic deserts are worthy targets in the search for bioactive compounds.
Collapse
|
6
|
Liu J, Zhao W, Ren M, Liu Y, Xu Y, Wang J. Contrasting elevational patterns and underlying drivers of stream bacteria and fungi at the regional scale on the Tibetan Plateau. FEMS Microbiol Ecol 2022; 98:6575535. [PMID: 35482597 DOI: 10.1093/femsec/fiac050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/31/2022] [Accepted: 04/26/2022] [Indexed: 11/12/2022] Open
Abstract
Elevational gradients are the focus of development and evaluation of general theories on biodiversity. However, elevational studies of microorganisms and the underlying mechanisms remain understudied, especially at regional scales. Here, we examined stream bacterial and fungal communities along an elevational gradient of 990-4,600 m with a geographic distance up to 500 km in the southeastern Tibetan Plateau and further analyzed their elevational patterns and drivers of three biodiversity indicators, including species richness, ecological uniqueness and community composition. Bacteria and fungi showed distinct elevational trends in species richness and consistently decreasing patterns in their ecological uniqueness. The distance-decay relationships were concordant for the two microbial groups, while fungi showed higher dissimilarity and a lower turnover rate. Interestingly, bacterial and fungal compositions substantially differed between the elevations below and above 3,000 m. Climate predictors, such as the mean annual temperature and precipitation seasonality, had greater effects than local environment drivers. Notably, fungal diversity was mainly influenced by climate, while bacterial diversity was explained by the shared contributions of climate and local factors. Collectively, these findings revealed the elevational patterns of stream microbial biodiversity across mountains on a large spatial scale and highlight their underlying response mechanisms to environmental predictors.
Collapse
Affiliation(s)
- Jiawen Liu
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing 210096, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wenqian Zhao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.,University of Chinese Academy of Sciences, Beijing 1000049, China
| | - Minglei Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.,University of Chinese Academy of Sciences, Beijing 1000049, China
| | - Yongqin Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 1000049, China
| | - Yan Xu
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing 210096, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.,University of Chinese Academy of Sciences, Beijing 1000049, China
| |
Collapse
|
7
|
Park Y, Noh HJ, Hwang CY, Shin SC, Hong SG, Jin YK, Lee H, Lee YM. Hymenobacter siberiensis sp. nov., isolated from a marine sediment of the East Siberian Sea and Hymenobacter psoromatis sp. nov., isolated from an Antarctic lichen. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005290] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gram-stain-negative, strictly aerobic, red-pink-coloured, rod-shaped and non-motile bacterial strains PAMC 29290, PAMC 29294T and PAMC 29296 were isolated from marine surface sediment sampled in the East Siberian Sea and strains PAMC 26553 and PAMC 26554T were obtained from an Antarctic lichen. Strains PAMC 29290, PAMC 29294T and PAMC 29296 were closely related to
Hymenobacter artigasi
(98.8 % 16S rRNA gene similarity),
Hymenobacter antarcticus
(97.3 %) and
Hymenobacter glaciei
(96.9 %), and PAMC 26553 and PAMC 26554T showed high similarity to
Hymenobacter ginsengisoli
(97.0 %),
Hymenobacter rivuli
(96.1 %) and
Hymenobacter setariae
(95.9 %). Genomic relatedness analyses showed that strains PAMC 29290, PAMC 29294T and PAMC 29296 could be distinguished from
H. artigasi
by average nucleotide identity (ANI; 93.1–93.2 %) and digital DNA–DNA hybridization (dDDH; 50.3–51.0 %) values. Strains PAMC 26553 and PAMC 26554T could be clearly distinguished from
H. ginsengisoli
with ANI values <79.8 % and dDDH values <23.3 %. The major fatty acids of strains PAMC 29290, PAMC 29294T and PAMC 29296 were C15 : 0 iso (21.0–26.0 %), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 17.4–18.2 %), C15 : 0 anteiso (12.7–19.1 %) and summed feature 4 (C17 : 1 iso I and/or anteiso B; 8.6–16.1 %) and those of strains PAMC 26553 and PAMC 26554T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 20.7–22.2 %), C15 : 0 anteiso (17.5–19.7 %) and summed feature 4 (C17 : 1 iso I and/or anteiso B; 15.5–18.1 %). The major respiratory quinone was MK-7. The genomic DNA G+C contents were 60.6–60.8 mol%. The polar lipids of PAMC 29294T were found to consist of phosphatidylethanolamine, four unidentified aminolipids, an unidentified aminophospholipid and five unidentified lipids; those of PAMC 26554T were phosphatidylethanolamine, three unidentified aminolipids, four unidentified aminophospholipid and two unidentified lipids. The distinct phylogenetic position and some physiological characteristics distinguished the novel strains from closely related type strains in the genus
Hymenobacter
. Thus, two novel species are proposed, with the names Hymenobacter siberiensis sp. nov. (type strain, PAMC 29294T=KCTC 82466T=JCM 34574T) and Hymenobacter psoromatis sp. nov. (type strain, PAMC 26554T=KCTC 82464T=JCM 34572T), respectively.
Collapse
Affiliation(s)
- Yerin Park
- School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Hyun-Ju Noh
- Division of Microbiology, Honam National Institute of Biological Resources, 99 Gohadoan-gil, Mokpo-si, Jeollanam-do, Republic of Korea
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Chung Yeon Hwang
- School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung Chul Shin
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Soon Gyu Hong
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Young Keun Jin
- Division of Earth-System Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Hyoungseok Lee
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Yung Mi Lee
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| |
Collapse
|
8
|
Ice Melt-Induced Variations of Structural and Functional Traits of the Aquatic Microbial Community along an Arctic River (Pasvik River, Norway). WATER 2021. [DOI: 10.3390/w13162297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The effects of climate change-induced ice melting on the microbial communities in different glacial-fed aquatic systems have been reported, but seasonal dynamics remain poorly investigated. In this study, the structural and functional traits of the aquatic microbial community were assessed along with the hydrological and biogeochemical variation patterns of the Arctic Pasvik River under riverine and brackish conditions at the beginning (May = Ice-melt (−)) and during the ice-melting season (July = Ice-melt (+)). The microbial abundance and morphometric analysis showed a spatial diversification between the riverine and brackish stations. Results highlighted different levels of microbial respiration and activities with different carbon and phosphorous utilization pathways, thus suggesting an active biogeochemical cycling along the river especially at the beginning of the ice-melting period. At Ice-melt (−), Gammaproteobacteria and Alphaproteobacteria were dominant in riverine and brackish stations, respectively. Conversely, at Ice-melt (+), the microbial community composition was more homogeneously distributed along the river (Gammaproteobacteria > Alphaproteobacteria > Bacteroidetes). Our findings provide evidence on how riverine microbial communities adapt and respond to seasonal ice melting in glacial-fed aquatic ecosystems.
Collapse
|
9
|
Hymenobacter guriensis sp. nov., and Hymenobacter duratus sp. nov., Radiation-Resistant Species Isolated from Soil in South Korea. Curr Microbiol 2021; 78:3334-3341. [PMID: 34259886 DOI: 10.1007/s00284-021-02517-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/26/2021] [Indexed: 10/20/2022]
Abstract
Two novel Gram-stain-negative, non-motile, aerobic, rod-shaped, circular, convex, red-colored and UV-tolerant strains BT594T and BT646T were isolated from soil collected in Guri city (37° 36' 0″ N, 127° 9' 0″ E) and Gwangju city (37° 22' 0″ N, 127° 17' 0″ E), respectively, South Korea. 16S rDNA sequence analysis indicated that strains BT594T and BT646T belong to a distinct lineage within the genus Hymenobacter (family Hymenobacteraceae, order Cytophagales, class Cytophagia, phylum Bacteroidetes, kingdom Bacteria). The 16S rDNA gene sequence similarity between the two strains BT594T and BT646T was 96.2%. The strain BT594T was closely related to Hymenobacter psychrotolerans Tibet-IIU11T (97.0% 16S rDNA gene similarity) and Hymenobacter tibetensis XTM003T (96.3%). The strain BT646T was closely related to Hymenobacter psychrotolerans Tibet-IIU11T (98.6%), Hymenobacter kanuolensis T-3 T (96.8%) and Hymenobacter perfusus LMG 26000 T (96.7%). The two strains were found to have the same quinone system, with MK-7 as the major respiratory quinone. The major polar lipids of strains BT594T and BT646T were phosphatidylethanolamine (PE) and aminophospholipids (APL). The major cellular fatty acids of strain BT594T were anteiso-C15:0 (17.9%), iso-C15:0 (16.1%) and summed feature 3 (C16:1 ω6c / C16:1 ω7c) (10.0%). The major cellular fatty acids of strain BT646T were summed feature 3 (C16:1 ω6c / C16:1 ω7c) (18.3%), C16:0 (17.2%) and summed feature 4 (iso-C17:1 I / anteiso-C17:1 B) (14.5%). Based on the polyphasic analysis, strains BT594T and BT646T can be suggested as two novel bacterial species within the genus Hymenobacter and the proposed names are Hymenobacter guriensis and Hymenobacter duratus, respectively. The type strain of Hymenobacter guriensis is BT594T (= KCTC 21863 T = NBRC 114853 T) and the type strain of Hymenobacter duratus is BT646T (= KCTC 21915 T = NBRC 114854 T).
Collapse
|
10
|
Sedláček I, Pantůček R, Zeman M, Holochová P, Šedo O, Staňková E, Švec P, Králová S, Vídeňská P, Micenková L, Korpole S, Lal R. Hymenobacter terrestris sp. nov. and Hymenobacter lapidiphilus sp. nov., isolated from regoliths in Antarctica. Int J Syst Evol Microbiol 2021; 70:6364-6372. [PMID: 33599603 DOI: 10.1099/ijsem.0.004540] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A group of four psychrotrophic bacterial strains was isolated on James Ross Island (Antarctica) in 2013. All isolates, originating from different soil samples, were collected from the ice-free northern part of the island. They were rod-shaped, Gram-stain-negative, and produced moderately slimy red-pink pigmented colonies on R2A agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, whole-genome sequencing, MALDI-TOF MS, rep-PCR analyses, chemotaxonomic methods and extensive biotyping was used to clarify the taxonomic position of these isolates. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates belonged to the genus Hymenobacter. The closest relative was Hymenobacter humicola CCM 8763T, exhibiting 98.3 and 98.9% 16S rRNA pairwise similarity with the reference isolates P5342T and P5252T, respectively. Average nucleotide identity, digital DNA-DNA hybridization and core gene distances calculated from the whole-genome sequencing data confirmed that P5252T and P5342T represent two distinct Hymenobacter species. The menaquinone systems of both strains contained MK-7 as the major respiratory quinone. The predominant polar lipids for both strains were phosphatidylethanolamine and one unidentified glycolipid. The major components in the cellular fatty acid composition were summed feature 3 (C16:1 ω7c/C16:1ω6c), C16:1ω5c, summed feature 4 (anteiso-C17:1 B/iso-C17:1 I), anteiso-C15:0 and iso-C15 : 0 for all isolates. Based on the obtained results, two novel species are proposed, for which the names Hymenobacter terrestris sp. nov. (type strain P5252T=CCM 8765T=LMG 31495T) and Hymenobacter lapidiphilus sp. nov. (type strain P5342T=CCM 8764T=LMG 30613T) are suggested.
Collapse
Affiliation(s)
- Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Roman Pantůček
- Department of Experimental Biology, Section of Genetics and Molecular Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michal Zeman
- Department of Experimental Biology, Section of Genetics and Molecular Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavla Holochová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petra Vídeňská
- Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lenka Micenková
- Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Suresh Korpole
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR - Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
| | - Rup Lal
- The Energy and Resources Institute, Lodhi Road, New Delhi - 110003, India
| |
Collapse
|
11
|
Spirosoma aureum sp. nov., and Hymenobacter russus sp. nov., radiation-resistant bacteria in Cytophagales order isolated from soil. Antonie Van Leeuwenhoek 2020; 113:2201-2212. [PMID: 33145621 DOI: 10.1007/s10482-020-01492-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/22/2020] [Indexed: 10/23/2022]
Abstract
A Gram-stain-negative, aerobic, nonmotile, yellow-colored strain BT328T and Gram-stain-negative, aerobic, non-motile, red-colored strain BT18T were isolated from the soil collected in Korea. Phylogenetic analyses based on 16S rRNA gene sequence revealed that strain BT328T formed a distinct lineage within the family Spirosomaceae (order Cytophagales, class Cytophagia) and was most closely related to a member of the genus Spirosoma, Spirosoma terrae 15J9-4T (95.9% 16S rRNA gene sequence similarity). Optimal growth occurred at 25 °C, pH 7.0 and in the absence of NaCl. The predominant cellular fatty acids were summed feature 3 (C16:1 ω6c/C16:1 ω7c) and C16:1 ω5c. The major respiratory quinone was MK-7. The major polar lipid was phosphatidylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BT18T formed a distinct lineage within the family Hymenobacteraceae (order Cytophagales, class Cytophagia, phylum Bacteroidetes) and was most closely related to members of the genus Hymenobacter, Hymenobacter knuensis 16F7C-2T (97.0% 16S rRNA gene sequence similarity). Optimal growth occurred at 25 °C and pH 7.0 without NaCl. The major fatty acids were iso-C15:0 and anteiso-C15:0. The major menaquinone was MK-7. The major polar lipid was phosphatidylethanolamine. Biochemical, chemotaxonomic and phylogenetic analyses indicated that strains BT328T and BT18T represents a novel bacterial species within the genus Spirosoma and Hymenobacter, respectively. For which the name Spirosoma aureum and Hymenobacter russus is proposed. The type strain of S. aureum is BT328T (=KCTC 72365T = NBRC 114506T) and the type strain of H. russus is BT18T (=KCTC 62610T = NBRC 114380T).
Collapse
|
12
|
Hymenobacter baengnokdamensis sp. nov., Isolated from the Soil of a Crater Lake in Korea. Curr Microbiol 2020; 77:4167-4173. [PMID: 33025184 DOI: 10.1007/s00284-020-02225-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 09/22/2020] [Indexed: 10/23/2022]
Abstract
An aerobic, Gram-stain-negative, non-motile, non-spore-forming, rod-shaped and pink-colored bacterial strain, designated BRD72T, was isolated from a crater lake (Baengnokdam) at the top of Mt. Hallasan in the Republic of Korea. Cells were catalase-positive and oxidase-negative. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the isolate was a member of the genus Hymenobacter and most closely related to Hymenobacter marinus KJ035T (96.2% similarity). The isolate was found to produce carotenoid pigment, but not flexirubin-type pigment. The predominant fatty acids of strain BRD72T were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c, 21.6%), iso-C15:0 (17.9%), anteiso-C15:0 (13.3%) and summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B, 11.3%). The major polar lipids were phosphatidylethanolamine, an unidentified amino lipid, and two unidentified aminophospholipids. The main respiratory quinone was menaquinone-7 (MK-7), and the main polyamine was homospermidine. The DNA G+C content was 59.8 mol%. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain BRD72T represents a novel species, for which the name Hymenobacter baengnokdamensis sp. nov. is proposed. The type strain is BRD72T (= KCTC 72649T = JCM 33837T).
Collapse
|
13
|
Roldán DM, Kyrpides N, Woyke T, Shapiro N, Whitman WB, Králová S, Sedláček I, Busse HJ, Menes RJ. Hymenobacter artigasi sp. nov., isolated from air sampling in maritime Antarctica. Int J Syst Evol Microbiol 2020; 70:4935-4941. [PMID: 32744985 DOI: 10.1099/ijsem.0.004362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A rod-shaped and Gram-stain-negative bacterial strain, 1BT, was isolated from an air sample collected at King George Island, maritime Antarctica. Strain 1BT is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth of strain 1BT is observed at 0-20 °C (optimum, 10 °C), pH 6.0-8.0 (optimum, pH 8.0) and in the presence of 0-1.0% NaCl (optimum, 0.5 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences places strain 1BT within the genus Hymenobacter and shows the highest similarity to Hymenobacter antarcticus VUG-A42aaT (97.5 %). The predominant menaquinone of strain 1BT is MK-7 and the major fatty acids (>10 %) comprise summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 32.5 %), iso-C15 : 0 (17.6 %) and anteiso C15 : 0 (12.3 %). The polar lipid profile consists of the major compounds phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids and one unidentified phospholipid. The DNA G+C content based on the draft genome sequence is 61.2 mol%. Based on the data from the current polyphasic study, 1BT represents a novel species of the genus Hymenobacter, for which the name Hymenobacter artigasi sp. nov. is suggested. The type strain is 1BT (=CCM 8970T=CGMCC 1.16843T).
Collapse
Affiliation(s)
- Diego M Roldán
- Laboratorio de Ecología Microbiana Medioambiental, Microbiología, Facultad de Química y Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Uruguay
| | - Nikos Kyrpides
- DOE Joint Genomics Institute, Walnut Creek, CA 94598, USA
| | - Tanja Woyke
- DOE Joint Genomics Institute, Walnut Creek, CA 94598, USA
| | - Nicole Shapiro
- DOE Joint Genomics Institute, Walnut Creek, CA 94598, USA
| | - William B Whitman
- Microbiology Department, University of Georgia, Athens, GA 30602, USA
| | - Stanislava Králová
- Czech Collection of Microorganisms, Department of Experimental Biology, Masaryk University, Brno, Czechia
| | - Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Masaryk University, Brno, Czechia
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| | - Rodolfo Javier Menes
- Laboratorio de Ecología Microbiana Medioambiental, Microbiología, Facultad de Química y Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Uruguay
| |
Collapse
|
14
|
Sedláček I, Pantůček R, Holochová P, Králová S, Staňková E, Vrbovská V, Šedo O, Švec P, Busse HJ. Hymenobacter humicola sp. nov., isolated from soils in Antarctica. Int J Syst Evol Microbiol 2019; 69:2755-2761. [PMID: 31237531 DOI: 10.1099/ijsem.0.003555] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A set of three psychrotrophic bacterial strains was isolated from different soil samples collected at the deglaciated northern part of James Ross Island (Antarctica) in 2014. All isolates were rod-shaped, Gram-stain-negative, non-motile, catalase-positive and oxidase-negative, and produced moderately slimy red-pink pigmented colonies on Reasoner's 2A (R2A) agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, whole-genome sequencing, automated ribotyping, MALDI-TOF MS, chemotaxonomy methods and extensive biotyping using conventional tests and commercial identification kits was applied to the isolates in order to clarify their taxonomic position. Phylogenetic analysis based on the 16S rRNA gene showed that all isolates belonged to the genus Hymenobacter with the closest relative being Hymenobacter aerophilus DSM 13606T, exhibiting 98.5 % 16S rRNA gene pairwise similarity to the reference isolate P6312T. Average nucleotide identity values calculated from the whole-genome sequencing data proved that P6312T represents a distinct Hymenobacter species. The major components of the cellular fatty acid composition were summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), C16 : 1 ω5c, summed feature 4 (C17 : 1 anteiso B/iso I), C15 : 0 anteiso and C15 : 0 iso. The menaquinone system of strain P6312T contained MK-7 as the major respiratory quinone. The predominant polar lipids were phosphatidylethanolamine and an unidentified phospholipid. Moderate to minor amounts of three unidentified polar lipids, four unidentified aminophospholipids, one unidentified glycolipid and one unidentified phospholipid were also present. Based on the obtained results, we propose a novel species for which the name Hymenobacterhumicola sp. nov. is suggested, with the type strain P6312T (=CCM 8763T=LMG 30612T).
Collapse
Affiliation(s)
- Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Roman Pantůček
- Section of Genetics and Molecular Biology, Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Pavla Holochová
- Czech Collection of Microorganisms, Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Stanislava Králová
- Czech Collection of Microorganisms, Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Eva Staňková
- Czech Collection of Microorganisms, Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Veronika Vrbovská
- Section of Genetics and Molecular Biology, Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pavel Švec
- Czech Collection of Microorganisms, Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| |
Collapse
|
15
|
Sedláček I, Pantůček R, Králová S, Mašlaňová I, Holochová P, Staňková E, Vrbovská V, Švec P, Busse HJ. Hymenobacter amundsenii sp. nov. resistant to ultraviolet radiation, isolated from regoliths in Antarctica. Syst Appl Microbiol 2019; 42:284-290. [DOI: 10.1016/j.syapm.2018.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 11/27/2018] [Accepted: 12/09/2018] [Indexed: 10/27/2022]
|
16
|
Sun J, Xing M, Wang W, Dai F, Liu J, Hao J. Hymenobacter profundi sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2018; 68:947-950. [PMID: 29458543 DOI: 10.1099/ijsem.0.002621] [Citation(s) in RCA: 9] [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, rod-shaped, red-pigmented, aerobic bacterium, strain M2T, was isolated from a seawater sample collected from the western Pacific Ocean at a depth of 1000 m and characterized using polyphasic taxonomy. Strain M2T was catalase-positive and oxidase-negative. Cells grew at 4-33 °C (optimum, 25 °C), at pH 6-9 (optimum, 7) and with 0-4 % (w/v) (optimum, 1 %) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain M2T was associated with the genus Hymenobacter. Strain M2T showed the highest 16S rRNA gene sequence similarities to Hymenobacter actinosclerus CCUG 39621T (95.7 %), Hymenobacter tibetensis XTM003T (95.6 %) and Hymenobacter psychrotolerans Tibet-IIU11T (95.2 %). The DNA G+C content was 59.98 mol%. Strain M2T contained C16 : 1ω5c (25.0 %), iso-C15 : 0 (23.9 %) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c, 20.4 %) as major cellular fatty acids. The major quinone of strain M2T was menaquinone 7 and the major polar lipid was phosphatidylethanolamine. The major polyamine of strain M2T was sym-homospermidine. The phylogenetic analysis and physiological and biochemical data showed that strain M2T should be classified as representing a novel species of the genus Hymenobacter, for which the name Hymenobacter profundi sp. nov. is proposed. The type strain is M2T (=CCTCC AB 2017185T=KCTC 62120T).
Collapse
Affiliation(s)
- Jingjing Sun
- Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China.,Laboratory for Marine Drugs and Bioproducts, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| | - Mengxin Xing
- Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China.,Laboratory for Marine Drugs and Bioproducts, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| | - Wei Wang
- Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China.,Laboratory for Marine Drugs and Bioproducts, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| | - Fangqun Dai
- Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China.,Laboratory for Marine Drugs and Bioproducts, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| | - Junzhong Liu
- Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China.,Laboratory for Marine Drugs and Bioproducts, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| | - Jianhua Hao
- Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China.,Laboratory for Marine Drugs and Bioproducts, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| |
Collapse
|
17
|
Kang JW, Choi S, Choe HN, Seong CN. Hymenobacter defluvii sp. nov., isolated from wastewater of an acidic water neutralization facility. Int J Syst Evol Microbiol 2017; 68:277-282. [PMID: 29148363 DOI: 10.1099/ijsem.0.002497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A non-motile, pink-coloured and rod-shaped bacterium, designated strain POA9T, was isolated from a wastewater treatment facility, Republic of Korea. Cells were Gram-reaction-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were C16 : 1ω5c, iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and anteiso-C15 : 0. The strain contained MK-7 as the only isoprenoid quinone, phosphatidylethanolamine as the major polar lipid and sym-homospermidine as the major polyamine. The DNA G+C content was 57 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain POA9T forms a distinct evolutionary lineage within the radiation enclosing the members of the genus Hymenobacter, sharing the highest similarity with Hymenobacter actinosclerus CCUG 39621T (95.5 % sequence similarity) followed by Hymenobacterseoulensis 16F7GT (95.5 %), Hymenobactertibetensis XTM003T (95.4 %), Hymenobacterrutilus K2-33028T (95.4 %) and Hymenobacter psychrotolerans Tibet-IIU11T (94.9 %). A number of phenotypic characteristics distinguished strain POA9T from the related members of the genus Hymenobacter. On the basis of the evidence presented in this study, a novel species, Hymenobacter defluvii sp. nov., is proposed for strain POA9T (=KCTC 52270T=JCM 31658T).
Collapse
Affiliation(s)
- Joo Won Kang
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Seon Choi
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Han Na Choe
- Biological Resource Center, KRIBB, Jeongeup 56212, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| |
Collapse
|
18
|
Koskinen K, Rettberg P, Pukall R, Auerbach A, Wink L, Barczyk S, Perras A, Mahnert A, Margheritis D, Kminek G, Moissl-Eichinger C. Microbial biodiversity assessment of the European Space Agency's ExoMars 2016 mission. MICROBIOME 2017; 5:143. [PMID: 29070062 PMCID: PMC5657055 DOI: 10.1186/s40168-017-0358-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/27/2017] [Indexed: 06/01/2023]
Abstract
BACKGROUND The ExoMars 2016 mission, consisting of the Trace Gas Orbiter and the Schiaparelli lander, was launched on March 14 2016 from Baikonur, Kazakhstan and reached its destination in October 2016. The Schiaparelli lander was subject to strict requirements for microbial cleanliness according to the obligatory planetary protection policy. To reach the required cleanliness, the ExoMars 2016 flight hardware was assembled in a newly built, biocontrolled cleanroom complex at Thales Alenia Space in Turin, Italy. In this study, we performed microbiological surveys of the cleanroom facilities and the spacecraft hardware before and during the assembly, integration and testing (AIT) activities. METHODS Besides the European Space Agency (ESA) standard bioburden assay, that served as a proxy for the microbiological contamination in general, we performed various alternative cultivation assays and utilised molecular techniques, including quantitative PCR and next generation sequencing, to assess the absolute and relative abundance and broadest diversity of microorganisms and their signatures in the cleanroom and on the spacecraft hardware. RESULTS Our results show that the bioburden, detected microbial contamination and microbial diversity decreased continuously after the cleanroom was decontaminated with more effective cleaning agents and during the ongoing AIT. The studied cleanrooms and change room were occupied by very distinct microbial communities: Overall, the change room harboured a higher number and diversity of microorganisms, including Propionibacterium, which was found to be significantly increased in the change room. In particular, the so called alternative cultivation assays proved important in detecting a broader cultivable diversity than covered by the standard bioburden assay and thus completed the picture on the cleanroom microbiota. CONCLUSION During the whole project, the bioburden stayed at acceptable level and did not raise any concern for the ExoMars 2016 mission. The cleanroom complex at Thales Alenia Space in Turin is an excellent example of how efficient microbiological control is performed.
Collapse
Affiliation(s)
- Kaisa Koskinen
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Petra Rettberg
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Rüdiger Pukall
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anna Auerbach
- Department for Microbiology, University of Regensburg, Regensburg, Germany
| | - Lisa Wink
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
| | - Simon Barczyk
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Alexandra Perras
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
- Department for Microbiology, University of Regensburg, Regensburg, Germany
| | - Alexander Mahnert
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | | | - Christine Moissl-Eichinger
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| |
Collapse
|
19
|
Kang JW, Lee JH, Choe HN, Seong CN. Hymenobacter tenuis sp. nov., isolated from wastewater of an acidic water neutralization facility. Int J Syst Evol Microbiol 2017; 67:2171-2177. [PMID: 28691666 DOI: 10.1099/ijsem.0.001918] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A non-motile, red-pink-coloured, rod-shaped bacterium, designated strain POB6T, was isolated from a wastewater treatment facility, Republic of Korea. Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, C16 : 1ω5c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The strain contained menaquinone MK-7 as the only isoprenoid quinone, phosphatidylethanolamine as the major polar lipid and sym-homospermidine as the major polyamine. The DNA G+C content was 61 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain POB6T forms a distinct evolutionary lineage within the radiation enclosing the members of the genus Hymenobacter, sharing the highest similarity with Hymenobacterrigui WPCP131T (97.5 %) followed by Hymenobacter xinjiangensis X2-1gT (97.2 %), Hymenobacter perfusus A1-12T (97.2 %) and Hymenobacter gelipurpurascens Txg-1T (97.1 %). A number of phenotypic characteristics distinguished strain POB6T from related members of the genus Hymenobacter. On the basis of the evidence presented in this study, a novel species, Hymenobacter tenuis sp. nov., is proposed, with POB6T (=KCTC 52271T=JCM 31659T) as the type strain.
Collapse
Affiliation(s)
- Joo Won Kang
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Han Na Choe
- Biological Resource Center, KRIBB, Jeongeup 56212, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| |
Collapse
|
20
|
Sedláček I, Králová S, Kýrová K, Mašlaňová I, Busse HJ, Staňková E, Vrbovská V, Němec M, Barták M, Holochová P, Švec P, Pantůček R. Red-pink pigmented Hymenobacter coccineus sp. nov., Hymenobacter lapidarius sp. nov. and Hymenobacter glacialis sp. nov., isolated from rocks in Antarctica. Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001898] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stanislava Králová
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Kamila Kýrová
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ivana Mašlaňová
- Section of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Hans-Jürgen Busse
- Institut für Bakteriology, Mykology und Hygiene, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| | - Eva Staňková
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Veronika Vrbovská
- Section of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Miroslav Němec
- Section of Microbiology and Molecular Biotechnology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Miloš Barták
- Section of Plant Physiology and Anatomy, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavla Holochová
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Švec
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Roman Pantůček
- Section of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| |
Collapse
|
21
|
Lee JJ, Lee YH, Park SJ, Lee SY, Park S, Kim MK, Ten LN, Jung HY. Hymenobacter seoulensis sp. nov., isolated from river water. Int J Syst Evol Microbiol 2017; 67:596-601. [DOI: 10.1099/ijsem.0.001668] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jae-Jin Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yeon-Hee Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Su-Jin Park
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seung-Yeol Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sangkyu Park
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio and Environmental Technology, Seoul Women’s University, Seoul 01797, Republic of Korea
| | - Leonid N Ten
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hee-Young Jung
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Institute of Plant Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| |
Collapse
|
22
|
Ten LN, Lee YH, Lee JJ, Park SJ, Lee SY, Park S, Lee DS, Kang IK, Jung HY. Hymenobacter daeguensis sp. nov. isolated from river water. J Microbiol 2017; 55:253-259. [PMID: 28124781 DOI: 10.1007/s12275-017-6524-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/29/2016] [Accepted: 12/06/2016] [Indexed: 10/20/2022]
Abstract
A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, aerobic bacterial strain, designated 16F3Y-2T, was isolated from the Han River, South Korea, and was characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 16F3Y-2T belonged to the family Cytophagaceae in the phylum Bacteroidetes and was most closely related to 'Hymenobacter terrae' DG7A (98.01%), H. soli PB17T (97.26%), H. glaciei VUG-A130T (96.78%), H. antarcticus VUG-A42aaT (96.72%), H. ruber PB156T (96.61%), and H. saemangeumensis GSR0100T (95.77%). The G+C content of the genomic DNA of strain 16F3Y-2T was 62.9 mol%. The isolate contained MK-7 as the predominant respiratory quinone, and summed feature 3 (C16:1 ω7c/C16:1 ω6c; 35.5%), C15:0 iso (16.9%), C16:1 ω5c (10.9%), and C15:0 anteiso (9.9%) as major fatty acids. The major polar lipid was phosphatidylethanolamine. Phenotypic and chemotaxonomic data supported the affiliation of strain 16F3Y-2T with the genus Hymenobacter. However, strain 16F3Y-2T exhibited relatively low levels of DNA-DNA relatedness with 'H. terrae' KCTC 32554 (44.1%) and H. soli KCTC 12607T (24.3%), clearly indicating that the isolate constitutes a new genospecies. Strain 16F3Y-2T could be differentiated from its phylogenetic neighbors on the basis of several phenotypic, genotypic, and chemotaxonomic features. Therefore, strain 16F3Y-2T represents a novel species in the genus Hymenobacter, for which the name Hymenobacter daeguensis sp. nov. is proposed. The type strain is 16F3Y-2T (=KCTC 52537T =JCM 31654T).
Collapse
Affiliation(s)
- Leonid N Ten
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yeon-Hee Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jae-Jin Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Su-Jin Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung-Yeol Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sangkyu Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dae Sung Lee
- Department of Environmental Engineering, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - In-Kyu Kang
- Department of Horticultural Science, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hee-Young Jung
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea. .,Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea.
| |
Collapse
|
23
|
Liu K, Liu Y, Wang N, Gu Z, Shen L, Xu B, Zhou Y, Liu H, Jiao N. Hymenobacter glacieicola sp. nov., isolated from glacier ice. Int J Syst Evol Microbiol 2016; 66:3793-3798. [DOI: 10.1099/ijsem.0.001266] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Keshao Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Beijing 100101, PR China
| | - Yongqin Liu
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, PR China
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Beijing 100101, PR China
| | - Ninglian Wang
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, PR China
- Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Zhengquan Gu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Beijing 100101, PR China
| | - Liang Shen
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Beijing 100101, PR China
| | - Baiqing Xu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Beijing 100101, PR China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yuguang Zhou
- Institute of Microbiology, China General Microbiological Culture Collection Center, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hongcan Liu
- Institute of Microbiology, China General Microbiological Culture Collection Center, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, PR China
| |
Collapse
|
24
|
Kang JW, Baik KS, Im WT, Seong CN. Hymenobacter coalescens sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 2016; 66:3546-3551. [DOI: 10.1099/ijsem.0.001226] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Joo Won Kang
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Keun Sik Baik
- Department of Food Science and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyoung National University, Anseong 17579, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| |
Collapse
|
25
|
A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city. Sci Rep 2016; 6:29235. [PMID: 27378552 PMCID: PMC4932501 DOI: 10.1038/srep29235] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/13/2016] [Indexed: 12/03/2022] Open
Abstract
Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels’ surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation.
Collapse
|
26
|
Kang JW, Lee JH, Baik KS, Lee SS, Seong CN. Hymenobacter wooponensis sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 2015; 65:1871-1876. [PMID: 25766109 DOI: 10.1099/ijs.0.000187] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A non-motile and rod-shaped bacterium, designated strain WM78T, was isolated from freshwater collected from the Woopo wetland (Republic of Korea). Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were iso-C15:0, anteiso-C15:0, C16:1ω7c and/or C16:1ω6c and iso-C17:1 I and/or anteiso-C17:1 B. The strain contained MK-7 as the major isoprenoid quinone, phosphatidylethanolamine as the major polar lipid and sym-homospermidine as the major polyamine. The genomic DNA G+C content was 62 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain WM78T forms evolutionary lineage within the radiation comprising members of the genus Hymenobacter with Hymenobacter gelipurpurascens Txg1T (97.7 % sequence similarity) as its nearest neighbour. A number of phenotypic characteristics distinguished strain WM78T from related members of the genus Hymenobacter. The evidence presented in this study support the designation of strain WM78T as a representative of a novel species in the genus Hymenobacter for which the name Hymenbactor wooponensis sp. nov. is proposed. The type strain is WM78T ( = KCTC 32528T = JCM 19491T).
Collapse
Affiliation(s)
- Joo Won Kang
- Department of Biology, College of life science and Natural Resources, Sunchon National University, Suncheon 540-950, Republic of Korea
| | - Ji Hee Lee
- Department of Biology, College of life science and Natural Resources, Sunchon National University, Suncheon 540-950, Republic of Korea
| | - Keun Sik Baik
- Department of Food Science and Technology, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Sang Suk Lee
- Department of Animal Science and Technology, College of life science and Natural Resources, Sunchon National University, Suncheon 540-950, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of life science and Natural Resources, Sunchon National University, Suncheon 540-950, Republic of Korea
| |
Collapse
|
27
|
Hu W, Zhang Q, Li D, Cheng G, Mu J, Wu Q, Niu F, An L, Feng H. Diversity and community structure of fungi through a permafrost core profile from the Qinghai-Tibet Plateau of China. J Basic Microbiol 2014; 54:1331-41. [DOI: 10.1002/jobm.201400232] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 05/18/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Weigang Hu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences; Lanzhou University; Lanzhou China
| | - Qi Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences; Lanzhou University; Lanzhou China
| | - Dingyao Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences; Lanzhou University; Lanzhou China
| | - Gang Cheng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences; Lanzhou University; Lanzhou China
| | - Jing Mu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences; Lanzhou University; Lanzhou China
| | - Qingbai Wu
- State Key Laboratory of Frozen Soil Engineering (SKLFSE), Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI); Chinese Academy of Sciences; Lanzhou China
| | - Fujun Niu
- State Key Laboratory of Frozen Soil Engineering (SKLFSE), Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI); Chinese Academy of Sciences; Lanzhou China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences; Lanzhou University; Lanzhou China
| | - Huyuan Feng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences; Lanzhou University; Lanzhou China
| |
Collapse
|
28
|
Chang X, Zheng J, Jiang F, Liu P, Kan W, Qu Z, Fang C, Peng F. Hymenobacter arcticus sp. nov., isolated from glacial till. Int J Syst Evol Microbiol 2014; 64:2113-2118. [DOI: 10.1099/ijs.0.060251-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, red–pink-pigmented strain, designated R2-4T, was isolated from a till sample near Ny-Alesund, Svalbard Archipelago, Norway. Cells were aerobic, Gram-stain-negative and rod-shaped. Growth occurred at 4–30 °C (optimum, 20–22 °C), at pH 6.0–9.0 (optimum, pH 7.0) and with 0–1 % NaCl added to R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R2-4T belonged to the genus
Hymenobacter
. 16S rRNA gene sequence similarity between strain R2-4T and the type strains of related species of the genus ranged from 94.51 to 96.05 %. Strain R2-4T contained iso-C15 : 0, anteiso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 4 (C17 : 1 anteiso B and/or iso I) and C16 : 1ω5c as the major cellular fatty acids, MK-7 as the major respiratory quinone, and phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids and unknown lipids as the main polar lipids. The polyamine was sym-homospermidine. The DNA G+C content of strain R2-4T was 61.6 mol%. On the basis of phylogenetic, physiological and chemotaxonomic data, strain R2-4T is considered to represent a novel species of the genus
Hymenobacter
, for which the name Hymenobacter arcticus sp. nov. is proposed. The type strain is R2-4T ( = CCTCC AB 2012104T = KACC 16881T).
Collapse
Affiliation(s)
- Xulu Chang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Jingli Zheng
- 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
| | - Ping Liu
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Wenjing Kan
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Zhihao Qu
- 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
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| |
Collapse
|
29
|
Han L, Wu SJ, Qin CY, Zhu YH, Lu ZQ, Xie B, Lv J. Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter. Antonie van Leeuwenhoek 2014; 105:971-8. [PMID: 24677143 DOI: 10.1007/s10482-014-0155-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 03/11/2014] [Indexed: 11/30/2022]
Abstract
A red-pink, Gram-negative, rod-shaped, non-motile, non-spore-forming bacterium, designated strain DK6-37 was isolated from the permafrost region of Qilian Mountains in northwest of China. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that this isolate represents a novel member of the genus Hymenobacter, with low sequence similarities (<97 %) to recognized Hymenobacter species. Optimum growth was observed at 28 °C, pH 7.0 and 0 % NaCl. The strain was found to contain MK-7 as the predominant menaquinone. The polar lipids were identified as phosphatidylethanolanmine, two unknown aminophospholipids, one unknown aminolipid and three unknown polar lipids. The major fatty acids were identified as summed feature 3 (C16:1 ω7c/C16:1 ω6c as defined by MIDI), summed feature 4 (anteiso-C17:1 B/iso-C17:1 I), C16:1 ω5c, iso-C17:0 3-OH, iso-C15:0 and C18:0. The DNA G + C content was determined to be 67.4 mol %. On the basis of the polyphasic evidence presented, it is proposed that strain DK6-37 represents a novel species of the genus Hymenobacter, for which the name Hymenobacter qilianensis sp. nov. is proposed. The type strain is DK6-37(T) (= CGMCC 1.12720(T) = JCM 19763(T)).
Collapse
Affiliation(s)
- Lu Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
30
|
Su S, Chen M, Teng C, Jiang S, Zhang C, Lin M, Zhang W. Hymenobacter kanuolensis sp. nov., a novel radiation-resistant bacterium. Int J Syst Evol Microbiol 2014; 64:2108-2112. [PMID: 24682704 DOI: 10.1099/ijs.0.051680-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, rod-shaped, non-motile, red-pigmented, radiation-resistant, aerobic bacterium designated T-3(T) was isolated from a soil sample from the Qinghai-Tibet Plateau in Tibet, China, after exposure to 10 kGy gamma radiation. Phylogenetic analysis based on 16S rRNA sequences indicated that this isolate represented a novel member of the genus Hymenobacter. Sequence identities of the 16S rRNA gene of strain T-3(T) with the type strains of species of the genus Hymenobacter with validly published names range from 89% to 97%, and the most closely related species is Hymenobacter psychrotolerans Tibet-IIU11(T) (97%). The DNA-DNA relatedness between strain T-3(T) and H. psychrotolerans is 59.10%. The major fatty acids of strain T-3(T) were iso-C(15 : 0) (27.66%), summed feature 4 (iso-C(17 : 1)I and/or anteiso-C(17 : 1)B, 15.84%), anteiso-C(15 : 0) (14.08%) and summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c, 12.38%). The major menaquinone of strain T-3(T) was MK-7. Phosphatidylethanolamine (PE) was predominant in the polar lipid profile. The G+C content of the DNA of strain T-3(T) was 69.17 mol%. On the basis of the results of the polyphasic characterization presented in this study, it is concluded that strain T-3(T) represents a novel species of the genus Hymenobacter, for which the name Hymenobacter kanuolensis is proposed. The type strain is T-3(T) ( = ACCC 05760(T) = KCTC 32407(T)).
Collapse
Affiliation(s)
- Shiyou Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Chao Teng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Shijie Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Chen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| |
Collapse
|
31
|
Reddy GSN, Garcia-Pichel F. Description of Hymenobacter arizonensis sp. nov. from the southwestern arid lands of the United States of America. Antonie van Leeuwenhoek 2012; 103:321-30. [PMID: 22987249 DOI: 10.1007/s10482-012-9812-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Accepted: 09/07/2012] [Indexed: 11/25/2022]
Abstract
Strain OR362-8(T) was isolated from a biological soil crust sample collected from the southwestern arid lands of the United States of America, using BG11-PGY medium. Cells of OR362-8(T) were found to be rod shaped; occur singly, as pairs and in groups; non-motile; positive for catalase, oxidase, phosphatase and gelatinase; hydrolyze starch; contain iso-C(15:0), anteiso-C(15:0), iso-C(15:1)G, C(16:1ω5c) and summed feature 3 (C(16:1(ω7c))/iso-C(15:0) 2OH as defined by the MIDI system) as the major fatty acids; and MK-7 as the sole respiratory quinone. A BLAST sequence similarity search using 16S rRNA gene sequence of OR362-8(T) identified Hymenobacter as the nearest genus with a similarity of 90.4-96.9 %. The phylogenetic analyses based on the phenetic methods UPGMA, NJ, ME and DNA parsimony resulted in the clustering of OR362-8(T) with Clade 1 Hymenobacter species represented by Hymenobacter glaciei, Hymenobacter antarcticus, Hymenobacter flocculans, Hymenobacter metalli and Hymenobacter soli with the closest being the Hymenobacter glaciei (96.9 % 16S rRNA gene sequence similarity). Besides the strong phylogentic affiliation, OR362-8(T) also exhibited significant phenotypic and chemotaxonomic differences with the members of Clade 1 Hymenobacter spp. More importantly, the DNA G+C content (mol%) of OR362-8(T) is very high (70 %) compared to the nearest species identified by phylogenetic analysis. Based on the phylogenetic, phenotypic and chemotaxonomic characteristics, OR362-8(T) was assigned to a novel species for which we propose here the name Hymenobacter arizonensis sp. nov., with OR362-8(T) (=ATCC BAA 1266(T) = DSM 17860(T) = JCM 13504(T)) as the type strain.
Collapse
Affiliation(s)
- Gundlapally S N Reddy
- School of Life Sciences, Arizona State University, Main Campus, Tempe, AZ 85287-4501, USA.
| | | |
Collapse
|
32
|
Hoang VA, Kim YJ, Nguyen NL, Yang DC. Hymenobacter ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2012; 63:661-666. [PMID: 22544792 DOI: 10.1099/ijs.0.039719-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, red bacterium, designated DCY57(T), was isolated from soil of a ginseng field in a mountainous region of Chungnam province in South Korea. Strain DCY57(T) grew with 0-1 % (w/v) NaCl and the optimum temperature for growth was 30 °C. Strain DCY57(T) contained MK-7 as the predominant menaquinone. The polyamine was sym-homospermidine. The major fatty acids were C(16:1)ω5c, iso-C(15:0), anteiso-C(15:0) and summed feature 3 (containing C(16:1)ω7c and/or C(16:1)ω6c). The major polar lipids were phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids and unknown lipids. The DNA G+C content was 58.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DCY57(T) was most closely related to members of the genus Hymenobacter. The isolate exhibited 91.7 % 16S rRNA gene sequence similarity with H. soli PB17(T), 94.5 % with H. flocculans A2-50A(T) and 95.8 % with H. metalli A2-91(T). On the basis of the evidence presented in this study, strain DCY57(T) represents a novel species within the genus Hymenobacter, for which the name Hymenobacter ginsengisoli sp. nov. is proposed. The type strain is DCY57(T) ( = KCTC 23674(T) = JCM 17841(T)).
Collapse
Affiliation(s)
- Van-An Hoang
- Korean Ginseng Center and Ginseng Genetic Recourses Bank, Kyung Hee University, Seocheon-dong, Giheung-guYongin-si, Gyeonggi-do 449-701, Republic of Korea
| | - Yeon-Ju Kim
- Korean Ginseng Center and Ginseng Genetic Recourses Bank, Kyung Hee University, Seocheon-dong, Giheung-guYongin-si, Gyeonggi-do 449-701, Republic of Korea
| | - Ngoc Lan Nguyen
- Korean Ginseng Center and Ginseng Genetic Recourses Bank, Kyung Hee University, Seocheon-dong, Giheung-guYongin-si, Gyeonggi-do 449-701, Republic of Korea
| | - Deok-Chun Yang
- Korean Ginseng Center and Ginseng Genetic Recourses Bank, Kyung Hee University, Seocheon-dong, Giheung-guYongin-si, Gyeonggi-do 449-701, Republic of Korea
| |
Collapse
|
33
|
Abaydulla G, Luo X, Shi J, Peng F, Liu M, Wang Y, Dai J, Fang C. Rufibacter tibetensis gen. nov., sp. nov., a novel member of the family Cytophagaceae isolated from soil. Antonie van Leeuwenhoek 2011; 101:725-31. [DOI: 10.1007/s10482-011-9686-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 12/11/2011] [Indexed: 10/14/2022]
|
34
|
Joung Y, Cho SH, Kim H, Kim SB, Joh K. Hymenobacter yonginensis sp. nov., isolated from a mesotrophic artificial lake. Int J Syst Evol Microbiol 2011; 61:1511-1514. [DOI: 10.1099/ijs.0.024588-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A non-motile, red-pigmented bacterium, designated strain HMD1010T, was isolated from an artificial lake located within the campus of Hankuk University of Foreign Studies, Yongin, Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD1010T formed a lineage within the genus Hymenobacter and was closely related to the type strains of Hymenobacter rigui (96.7 % sequence similarity) and H. gelipurpurascens (95.6 %). The major fatty acids were C16 : 1ω5c (21.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c; 17.2 %), iso-C15 : 0 (14.5 %) and summed feature 4 (anteiso-C17 : 1 B and/or iso-C17 : 1 I; 11.9 %). The DNA G+C content was 60.4 mol%. On the basis of the evidence presented in this study, strain HMD1010T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter yonginensis sp. nov. was proposed. The type strain is HMD1010T ( = KCTC 22745T = CECT 7546T).
Collapse
Affiliation(s)
- Yochan Joung
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Wangsan, Yongin, Gyeonggi 449-791, Republic of Korea
| | - Sung-Heun Cho
- Department of Microbiology, School of Bioscience and Biotechnology, Chungnam National University, 220 Gung-dong, Yuseong, Daejeon 305-764, Republic of Korea
| | - Haneul Kim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Wangsan, Yongin, Gyeonggi 449-791, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology, School of Bioscience and Biotechnology, Chungnam National University, 220 Gung-dong, Yuseong, Daejeon 305-764, Republic of Korea
| | - Kiseong Joh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Wangsan, Yongin, Gyeonggi 449-791, Republic of Korea
| |
Collapse
|
35
|
Klassen JL, Foght JM. Characterization of Hymenobacter isolates from Victoria Upper Glacier, Antarctica reveals five new species and substantial non-vertical evolution within this genus. Extremophiles 2010; 15:45-57. [PMID: 21104190 DOI: 10.1007/s00792-010-0336-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 11/01/2010] [Indexed: 11/26/2022]
Abstract
We isolated several Hymenobacter-like strains from Victoria Upper Glacier, Antarctica, basal ice that diverged substantially from currently defined Hymenobacter species according to their 16S rRNA and gyrB gene phylogenies. All strains were psychrotolerant, heterotrophic aerobes which grew preferentially on low salt and low nutrient strength agar. Further phenotypic and chemotaxonomic characterization of these isolates supported their assignment as five novel species: H. algoricola sp. nov., H. antarcticus sp. nov., H. elongatus sp. nov., H. fastidiosus sp. nov., and H. glaciei sp. nov. Remarkable among these data was the prevalence of horizontal gene transfers and phenotypic variation, even between apparently closely related strains. These results suggest extensive non-vertical evolution within the genus Hymenobacter, and may reflect evolutionary trajectories resulting from dormancy, e.g., during interment in glacial ice.
Collapse
Affiliation(s)
- Jonathan L Klassen
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | | |
Collapse
|
36
|
Hymenobacter perfusus sp. nov., Hymenobacter flocculans sp. nov. and Hymenobacter metalli sp. nov. three new species isolated from an uranium mine waste water treatment system. Syst Appl Microbiol 2010; 33:436-43. [PMID: 21051170 DOI: 10.1016/j.syapm.2010.09.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 09/29/2010] [Accepted: 09/30/2010] [Indexed: 11/23/2022]
Abstract
Three red-pink pigmented strains, designated A1-12(T), A2-50A(T) and A2-91(T), were recovered from two different sites in a uranium mine. For all strains, the optimum growth temperature was 25°C, the optimum pH was 6.0-6.5 and the DNA G+C contents were between 60 and 63.4 mol%. The major respiratory quinone was menaquinone 7 (MK-7) and the fatty acid profiles contained iso- and anteiso-branched C15 fatty acids, summed feature 3 (16:1 ω6c and/or ω7c and/or 15:0 iso 2-OH), summed feature 4 (17:1 anteiso B and/or iso I) and the unsaturated fatty acid 16:1 ω5c as the major components. Phylogenetic analysis of the 16S rRNA gene sequences showed that these organisms represented three distinct branches within the family Flexibacteraceae most closely related to the members of the genus Hymenobacter. Strain A1-12(T) formed a distinct phylogenetic line along with H. rigui KCTC 12533(T) and they shared approximately 98.9% 16S rRNA gene sequence similarity. However, these two strains shared only 14.7% pairwise similarity in their genomic DNA. Strains A2-50A(T) and A2-91(T) formed two distinct lineages, related to the species H. soli KCTC 12607(T), sharing about 95.5% 16S rRNA gene sequence similarity between themselves, and 88.3 and 92.0% with other members of the genus Hymenobacter. Based on the phylogenetic analysis and physiological and biochemical characteristics, these isolates were considered to represent three novel species for which we propose the names Hymenobacter perfusus for strain A1-12(T) (=CIP 110166=LMG 26000), Hymenobacter flocculans for strain A2-50A(T) (=CIP 110139=LMG 25699) and Hymenobacter metalli for strain A2-91(T) (=CIP 110140=LMG 25700).
Collapse
|
37
|
Zhang DC, Busse HJ, Liu HC, Zhou YG, Schinner F, Margesin R. Hymenobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 2010; 61:859-863. [PMID: 20495040 DOI: 10.1099/ijs.0.023465-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A non-motile, rod-shaped, red-pigmented bacterium, designated strain BZ33r(T), was isolated from soil of an industrial site. Cells stained Gram-negative and were aerobic and psychrophilic, showing good growth at 1-20 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ33r(T) was related to members of the genus Hymenobacter and had highest sequence similarity with Hymenobacter aerophilus DSM 13606(T) (97.5 %). The predominant cellular fatty acids were anteiso-C(15 : 0) (20.3 %), summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH; 20.2 %), iso-C(15 : 0) (20.0 %), summed feature 4 (iso-C(17 : 1) I and/or anteiso-C(17 : 1) B; 8.2 %) and C(16 : 1)ω5c (7.9 %). Strain BZ33r(T) had MK-7 as the major menaquinone. The polyamine pattern contained sym-homospermidine as the major compound with moderate amounts of spermidine. Phosphatidylethanolamine, three unknown aminophospholipids, two unknown aminolipids, two unknown glycolipids and five unknown polar lipids were present in the polar lipid profile. The G+C content of the DNA was 61.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain BZ33r(T) is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter psychrophilus sp. nov. is proposed. The type strain is BZ33r(T) ( = DSM 22290(T) = CGMCC 1.8975(T) = LMG 25548(T)).
Collapse
Affiliation(s)
- De-Chao Zhang
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Hans-Jürgen Busse
- Institute of Bacteriology, Mycology and Hygiene, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Franz Schinner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| |
Collapse
|
38
|
Fujii M, Takano Y, Kojima H, Hoshino T, Tanaka R, Fukui M. Microbial community structure, pigment composition, and nitrogen source of red snow in Antarctica. MICROBIAL ECOLOGY 2010; 59:466-75. [PMID: 19847476 PMCID: PMC4261141 DOI: 10.1007/s00248-009-9594-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 09/19/2009] [Indexed: 05/03/2023]
Abstract
"Red snow" refers to red-colored snow, caused by bloom of cold-adapted phototrophs, so-called snow algae. The red snow found in Langhovde, Antarctica, was investigated from several viewpoints. Various sizes of rounded red cells were observed in the red snow samples under microscopy. Pigment analysis demonstrated accumulation of astaxanthin in the red snow. Community structure of microorganisms was analyzed by culture-independent methods. In the analyses of small subunit rRNA genes, several species of green algae, fungus, and various phylotypes of bacteria were detected. The detected bacteria were closely related to psychrophilic or psychrotolerant heterotrophic strains, or sequences detected from low-temperature environments. As predominant lineage of bacteria, members of the genus Hymenobacter were consistently detected from samples obtained in two different years. Nitrogen isotopic compositions analysis indicated that the red snow was significantly 15N-enriched. Based on an estimation of trophic level, it was suggested that primary nitrogen sources of the red snow were supplied from fecal pellet of seabirds including a marine top predator of Antarctica.
Collapse
Affiliation(s)
- Masanori Fujii
- />The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819 Japan
| | - Yoshinori Takano
- />Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, 237-0061 Japan
| | - Hisaya Kojima
- />The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819 Japan
| | - Tamotsu Hoshino
- />Institute for Biological Resources and Function, National Institute of Advanced Industrial Science and Technology, 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517 Japan
| | - Ryouichi Tanaka
- />The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819 Japan
| | - Manabu Fukui
- />The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819 Japan
| |
Collapse
|
39
|
2′-Methyl and 1′-xylosyl derivatives of 2′-hydroxyflexixanthin are major carotenoids of Hymenobacter species. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.03.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
40
|
Zhang L, Dai J, Tang Y, Luo X, Wang Y, An H, Fang C, Zhang C. Hymenobacter deserti sp. nov., isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 2009; 59:77-82. [DOI: 10.1099/ijs.0.000265-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|