1
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Branysova T, Petru N, Lopez Marin MA, Solcova M, Demnerova K, Stiborova H. Uncovering the microbial diversity of Czech Republic archives: A study of metabolically active airborne microbes. Heliyon 2024; 10:e27930. [PMID: 38560214 PMCID: PMC10981025 DOI: 10.1016/j.heliyon.2024.e27930] [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: 11/29/2023] [Revised: 02/23/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
Despite the diligent efforts of libraries, archives, and similar institutions to preserve cultural monuments, biodeterioration continues to pose a significant threat to these objects. One of the main sources of microorganisms responsible for the biodeterioration process is the presence of airborne microorganisms. Therefore, this research aims to monitor and compare outcomes of both culture-dependent (utilising various cultivation strategies) and culture-independent approaches (RNA-based sequencing) to identifying metabolically active airborne microorganisms in archives in the Czech Republic. Through this study, several species that have the potential to pose risks to both cultural heritage objects and the health of institution employees were found. Additionally, the efficacy of different cultivation media was demonstrated to be varied across archive rooms, highlighting the necessity of employing multiple cultivation media for comprehensive analyses. Of noteworthy importance, the resuscitating-promoting factor (Rpf) proved to be a pivotal tool, increasing bacterial culturability by up to 30% when synergistically employed Reasoner's 2A agar (R2A) and R2A + Rpf media. Next, the study emphasises the importance of integrating both culture-dependent and culture-independent approaches. The overlap between genera identified by the culture-dependent approach and those identified also by the culture-independent approach varied from 33% to surpassing 94%, with the maximum alignment exceeding 94% in only one case. Our results highlight the importance of actively monitoring and assessing levels of microbial air contamination in archives to prevent further deterioration of cultural heritage objects and to promote improved conditions for employees in archives and similar institutions.
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Affiliation(s)
- Tereza Branysova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Nicole Petru
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Marco A. Lopez Marin
- Department of Water Technology and Environmental Engineering, Faculty of Environmental Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Milada Solcova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Katerina Demnerova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Hana Stiborova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
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2
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The failure on the effectiveness of formalin on cadaver disinfection and alternative methods. MARMARA MEDICAL JOURNAL 2023. [DOI: 10.5472/marumj.1244383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Objective: It was aimed to identify the contaminant and determine the alternative disinfectant detection in the microbial growth
observed in various parts of the cadaver stored in the formalin tank in the dissection laboratory of Marmara University Anatomy
Department. We also performed a literature review of this unusual pathogen.
Materials and Methods: Swab samples were inoculated on agar mediums. After incubation, matrix-assisted laser desorption ionizationtime
of flight mass spectrometry (MALDI-TOF MS) analysis was used to identify the isolate from the detected uniform colonies.
Sample solution from the cadaver tank, freshly prepared 5% formalin and 0.55% ortho-phthalaldehyde were used to determine the
disinfectant sensitivity of the isolate.
Results: According to 16s rDNA sequence analysis, it was concluded as Skermanella aerolata with 99% similarity. In the disinfectant
susceptibility test, it was observed that S. aerolata and control bacteria could grow in 5% formalin taken from the cadaver tank. No
growth was detected in other disinfectants.
Conclusion: To prevent cadaver contamination in anatomy laboratories, the quality control of the embalming solutions and indoor
air filtration of the dissection rooms should be checked at regular intervals. Members of Skermanella genus have been identified as
environmental organisms in several studies, however, recent researches reported this bacterium as a human pathogen.
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3
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Lee S, You H, Lee S, Lee Y, Kang HG, Sung HJ, Choi J, Hyun S. Individual Identification with Short Tandem Repeat Analysis and Collection of Secondary Information Using Microbiome Analysis. Genes (Basel) 2021; 13:85. [PMID: 35052425 PMCID: PMC8774430 DOI: 10.3390/genes13010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
Forensic investigation is important to analyze evidence and facilitate the search for key individuals, such as suspects and victims in a criminal case. The forensic use of genomic DNA has increased with the development of DNA sequencing technology, thereby enabling additional analysis during criminal investigations when additional legal evidence is required. In this study, we used next-generation sequencing to facilitate the generation of complementary data in order to analyze human evidence obtained through short tandem repeat (STR) analysis. We examined the applicability and potential of analyzing microbial genome communities. Microbiological supplementation information was confirmed for two of four failed STR samples. Additionally, the accuracy of the gargle sample was confirmed to be as high as 100% and was highly likely to be classified as a body fluid sample. Our experimental method confirmed that anthropological and microbiological evidence can be obtained by performing two experiments with one extraction. We discuss the advantages and disadvantages of using these techniques, explore prospects in the forensic field, and highlight suggestions for future research.
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Affiliation(s)
- Solip Lee
- Department of Senior Healthcare, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (H.Y.)
| | - Heesang You
- Department of Senior Healthcare, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (H.Y.)
| | - Songhee Lee
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (Y.L.)
| | - Yeongju Lee
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (Y.L.)
| | - Hee-Gyoo Kang
- Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Seongnam 13135, Korea; (H.-G.K.); (H.-J.S.)
| | - Ho-Joong Sung
- Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Seongnam 13135, Korea; (H.-G.K.); (H.-J.S.)
| | - Jiwon Choi
- Forensic DNA Analysis Division, National Forensic Service, Seoul 08636, Korea;
| | - Sunghee Hyun
- Department of Senior Healthcare, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (H.Y.)
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (Y.L.)
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4
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Li S, Shi L, Lian WH, Lin ZL, Lu CY, Xu L, Wei QC, Zhang JY, Dong L, Li WJ. Arenibaculum pallidiluteum gen. nov., sp. nov., a novel bacterium in the family Azospirillaceae, isolated from desert soil, and reclassification of Skermanella xinjiangensis to a new genus Deserticella as Deserticella xinjiangensis comb. nov., and transfer of the genera Indioceanicola and Oleisolibacter from the family Rhodospirillaceae to the family Azospirillaceae. Int J Syst Evol Microbiol 2021; 71. [PMID: 34283015 DOI: 10.1099/ijsem.0.004874] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel pale orange-coloured bacterium, designated strain SYSU D00532T, was isolated from sandy soil collected from the Gurbantunggut desert in Xinjiang, PR China. Cells of strain SYSU D00532T were found to be aerobic, Gram-stain-negative, oxidase-positive, catalase-positive, motile and rod-shaped with a single polar or subpolar flagellum. Growth occurred at 15-45 °C (optimum, 28-37 °C, pH 5.0-8.0 (optimum, pH 6.0-7.0) and with 0-1.5% NaCl (w/v; optimum, 0.5 %). The major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol. Unidentified aminolipids, unidentified polar lipids, an unidentified aminophospholipid and an unidentified phospholipid were also detected. The major respiratory quinone was ubiquinone-10 and the major fatty acids were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0 and C19:0 cyclo ω8c. The genomic DNA G+C content was 69.8 mol%. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SYSU D00532T belonged to the family Azospirillaceae and showed 93.4% (Desertibacter roseus 2622T), 93.2% (Skermanella xinjiangensis 10-1-101T), 93.2% ('Skermanella rubra' YIM 93097T) and 92.4% (Desertibacter xinjiangensis M71T) similarities. Based on the phylogenetic, phenotypic and chemotaxonomic data, strain SYSU D00532T is proposed to represent a new species of a new genus, named Arenibaculum pallidiluteum gen. nov., sp. nov., within the family Azospirillaceae. The type strain is SYSU D00532T (=KCTC 82269T=CGMCC 1.18631T=MCCC 1K04984T). We also propose the reclassification of Skermanella xinjiangensis to a new genus Deserticella as Deserticella xinjiangensis comb. nov., and the transfer of the genera Indioceanicola and Oleisolibacter from the family Rhodospirillaceae to the family Azospirillaceaewe based on the phylogenetic results.
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Affiliation(s)
- Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lei Shi
- Division of Neurosurgical Intensive Care Unit, Department of Critical Care Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, PR China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Zhi-Liang Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Chun-Yan Lu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lu Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Qi-Chuang Wei
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Jing-Yi Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
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5
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Tang K, Yang LH, Chen YP, Tao Y, Feng FY, Meng JY. Aerophototrophica crusticola gen. nov., sp. nov., isolated from desert biocrusts. Int J Syst Evol Microbiol 2021; 71. [PMID: 33528345 DOI: 10.1099/ijsem.0.004677] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A pink-pigmented, Gram-stain-negative, rod-shaped, strictly aerobic bacterial strain MIMtkB3T, was isolated from moss crusts in Hunshandake desert of China. Cells grew at 15-45 °C (optimum of 28 °C), at pH of 6.0-8.5 (optimum of 7.0) and with 0-1.0 % (w/v) NaCl (optimum of 0 %). The strain could biosynthesize the green-coloured pigment bacteriochlorophyll a (BChl a). The respiratory quinone was ubiquinone Q-10, while C18 : 1 ω7c and C18 : 1 2OH were the major fatty acids. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid, one unidentified phospholipid, three unidentified glycolipid and one unidentified lipid were the major polar lipids. Strain MIMtkB3T was most closely related to Oleisolibacter albus NAU-10T, Niveispirillum fermenti CC-LY736T, and Rhodocista centenaria SW of the family Rhodospirillaceae with 16S rRNA gene similarities of 93.09, 92.02 and 91.73%, respectively. The genomic DNA G+C content calculated on complete genome sequencing was 69.3 mol%. The average nucleotide identity between strain MIMtkB3T and its closely related type strains in Rhodospirillaceae was below 77.96 % and digital DNA-DNA hybridization lower than 24.70 %. Full light utilization pathway of aerobic anoxygenic phototrophic bacteria was identified in the genome. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain MIMtkB3T represents a novel genus of the family Rhodospirillaceae, for which the name Aerophototrophica crusticola gen. nov., sp. nov. is proposed. The type strain is MIMtkB3T (=KCTC 42633T=MCCC 1K00570T).
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Affiliation(s)
- Kai Tang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Key Laboratory of Grassland Ecology and Restoration, Ministry of Agriculture, Hohhot 010010, PR China.,Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - Li-Hua Yang
- Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - Yu-Ping Chen
- Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - Yu Tao
- Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - Fu-Ying Feng
- Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - Jian-Yu Meng
- Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Hohhot 010018, PR China
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6
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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7
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Guo Q, Zhou Z, Zhang L, Zhang C, Chen M, Wang B, Lin M, Wang W, Zhang W, Li X. Skermanella pratensis sp. nov., isolated from meadow soil, and emended description of the genus Skermanella. Int J Syst Evol Microbiol 2020; 70:1605-1609. [DOI: 10.1099/ijsem.0.003944] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, light pink-coloured, short rod-shaped, designated strain W17T, was isolated from a meadow soil sample collected from Xinjiang, PR China. The 16S rRNA gene sequence analysis indicated that strain W17T was related most closely to
Skermanella rosea
M1T (98.72 %) and
Skermanella mucosa
8-14-6T (98.44 %). However, strain W17T showed a low level of DNA–DNA relatedness to
S. rosea
M1T (32.4±2.6 %) and
S. mucosa
8-14-6T (33.5±0.1 %). The genome size of the novel strain was 5.87 Mb and the genomic DNA G+C content was 67.27 mol%. The only respiratory quinone of strain W17T was Q-10. Diphosphatidylglycerol, phosphatidylglycerol. phosphatidylethanolamine and phosphatidylcholine were the major polar lipids. The predominant cellular fatty acids were C18 : 1ω6c and/or C18 : 1ω7c (48.53 %), C16 : 0 (20.88 %) and C18 : 0 (14.92 %). The phylogenetic, phenotypic and chemotaxonomic data showed that strain W17T represents a novel species of the genus
Skermanella
, for which the name Skermanella pratensis sp. nov. is proposed. The type strain is W17T (=GDMCC 1.1392T=KCTC 62434T).
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Affiliation(s)
- Qiannan Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Lijuan Zhang
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, PR China
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, PR China
| | - Chen Zhang
- 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
| | - Bo Wang
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, PR China
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, PR China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wei Wang
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, PR China
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, PR China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xufeng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
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8
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Microbiological Investigation of the Space Dust Collected from the External Surfaces of the International Space Station. BIONANOSCIENCE 2020. [DOI: 10.1007/s12668-019-00712-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Kim J, Jeong SE, Khan SA, Jeon CO. Hwanghaeella grinnelliae gen. nov., sp. nov., isolated from a marine red alga. Int J Syst Evol Microbiol 2019; 69:3544-3550. [DOI: 10.1099/ijsem.0.003656] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jungeun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Shehzad Abid Khan
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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10
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Liang S, Liu H, Wu S, Xu S, Jin D, Faiola F, Zhuang X, Zhuang G, Qu D, Fan H, Bai Z. Genetic diversity of diazotrophs and total bacteria in the phyllosphere of Pyrus serotina, Prunus armeniaca, Prunus avium, and Vitis vinifera. Can J Microbiol 2019; 65:642-652. [PMID: 31241350 DOI: 10.1139/cjm-2018-0588] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The phyllosphere, which supports a large number of microorganisms, represents the interface between the aboveground parts of plants and air. In this study, four nifH clone libraries were constructed from the phyllosphere of Pyrus serotina (L), Vitis vinifera (P), Prunus armeniaca (X), and Prunus avium (Y). Clones related to Skermanella (L, 12.1%; X, 15.6%; Y, 62.5%; P 70.8%), Bradyrhizobium (X, 2.1%; P, 15.1%; L, 63.7%), Erwinia (X, 68.8%), Pseudomonas (L, 3.3%; P, 7.6%), and Chroococcidiopsis (P, 0.9%; L, 4.4%, X; 5.2%, Y; 19.6%) were present at high percentages, highlighting their critical role in contributing nitrogen to the phyllosphere ecosystem. The 16S rDNA sequence analysis suggested that phyllosphere-associated bacteria were affiliated with a wide range of taxa, encompassing members from Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, Tenericutes, and Deinococcus-Thermus. Additionally, the abundance of the nifH gene and 16S rDNA was assessed with quantitative PCR. The number of copies of nifH and 16S rDNA ranged from 1.14 × 103 to 1.49 × 104 and from 3.72 × 106 to 7.02 × 107 copies/g fresh leaf sample, respectively. In conclusion, our work sheds light on the microbial communities of the phyllosphere that are important for plant growth. Moreover, we observed a unique composition of nitrogen-fixing bacteria in each phyllosphere sample, suggesting the existence of specific interactions between these functional microorganism and plants, which may provide information or be a reference for the development of bacterial fertilizers.
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Affiliation(s)
- Shengxian Liang
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.,College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Hao Liu
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Natural Resources and Environment, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Shanghua Wu
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengjun Xu
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Decai Jin
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Francesco Faiola
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoqiang Zhuang
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Qu
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Haiyan Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhihui Bai
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Heo ST, Kwon KT, Yoo JR, Choi JY, Lee KH, Ko KS. First Case of Necrotizing Fasciitis Caused by Skermanella aerolata Infection Mimicking Vibrio Sepsis. Ann Lab Med 2018; 38:604-606. [PMID: 30027706 PMCID: PMC6056393 DOI: 10.3343/alm.2018.38.6.604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 04/26/2018] [Accepted: 06/08/2018] [Indexed: 11/19/2022] Open
Affiliation(s)
- Sang Taek Heo
- Department of Infectious Disease, Jeju National University School of Medicine, Jeju, Korea
| | - Ki Tae Kwon
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Jeong Rae Yoo
- Department of Infectious Disease, Jeju National University School of Medicine, Jeju, Korea
| | - Ji Young Choi
- Department of Molecular Cell Biology and Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Keun Hwa Lee
- Department of Microbiology and Immunology, Jeju National University School of Medicine, Jeju, Korea
| | - Kwan Soo Ko
- Department of Molecular Cell Biology and Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, Korea.
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12
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Skermanella mucosa sp. nov., isolated from crude oil contaminated soil. Antonie van Leeuwenhoek 2017; 110:1053-1060. [DOI: 10.1007/s10482-017-0878-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/20/2017] [Indexed: 10/19/2022]
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13
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Kalwasińska A, Felföldi T, Szabó A, Deja-Sikora E, Kosobucki P, Walczak M. Microbial communities associated with the anthropogenic, highly alkaline environment of a saline soda lime, Poland. Antonie van Leeuwenhoek 2017; 110:945-962. [PMID: 28382378 PMCID: PMC5486852 DOI: 10.1007/s10482-017-0866-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 03/28/2017] [Indexed: 11/30/2022]
Abstract
Soda lime is a by-product of the Solvay soda process for the production of sodium carbonate from limestone and sodium chloride. Due to a high salt concentration and alkaline pH, the lime is considered as a potential habitat of haloalkaliphilic and haloalkalitolerant microbial communities. This artificial and unique environment is nutrient-poor and devoid of vegetation, due in part to semi-arid, saline and alkaline conditions. Samples taken from the surface layer of the lime and from the depth of 2 m (both having pH ~11 and ECe up to 423 dS m−1) were investigated using culture-based (culturing on alkaline medium) and culture-independent microbiological approaches (microscopic analyses and pyrosequencing). A surprisingly diverse bacterial community was discovered in this highly saline, alkaline and nutrient-poor environment, with the bacterial phyla Proteobacteria (representing 52.8% of the total bacterial community) and Firmicutes (16.6%) showing dominance. Compared to the surface layer, higher bacterial abundance and diversity values were detected in the deep zone, where more stable environmental conditions may occur. The surface layer was dominated by members of the genera Phenylobacterium, Chelativorans and Skermanella, while in the interior layer the genus Fictibacillus was dominant. The culturable aerobic, haloalkaliphilic bacteria strains isolated in this study belonged mostly to the genus Bacillus and were closely related to the species Bacillus pseudofirmus, B. cereus, B. plakortidis, B. thuringensis and B. pumilus.
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Affiliation(s)
- Agnieszka Kalwasińska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland.
| | - Tamás Felföldi
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Attila Szabó
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Edyta Deja-Sikora
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland
| | - Przemysław Kosobucki
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Toruń, Poland
| | - Maciej Walczak
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland
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14
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Subhash Y, Lee SS. Skermanella rosea sp. nov., isolated from hydrocarbon-contaminated desert sands. Int J Syst Evol Microbiol 2016; 66:3951-3956. [DOI: 10.1099/ijsem.0.001293] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Y. Subhash
- Department of Life Science, College of Natural Science, Kyonggi University, 94-6 Iui-dong Yeongtong-gu, Suwon 443-760, South Korea
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi University, 94-6 Iui-dong Yeongtong-gu, Suwon 443-760, South Korea
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15
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Zhang ZY, Gao XH, Zhang YJ, Jia M, Lu XJ, Ma YC, Tian F, Xie Q, Tang SK. Skermanella rubra sp. nov., a bacterium isolated from the desert of Xinjiang, China. Antonie van Leeuwenhoek 2015; 108:627-32. [PMID: 26122888 DOI: 10.1007/s10482-015-0518-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/23/2015] [Indexed: 11/25/2022]
Abstract
A Gram-negative, pink-coloured, rod-shaped, motile bacterium, designated YIM 93097(T), was isolated from the desert soil collected from Xinjiang province of China. Strain YIM 93097(T) was found to grow at 20-45 °C (optimum 28-37 °C), pH 5.0-7.0 (optimum pH 7.0) and 0-8 % (w/v) NaCl (optimum 1 %, w/v). Based on 16S rRNA gene sequence similarity studies, it belongs to the genus Skermanella. The 16S rRNA gene sequence similarity was identified to be 98.7 % to Skermanella xinjiangensis CCTCC AB 207153(T) while the DNA-DNA hybridization value was found to be only 48.1 %. The predominant isoprenoid quinone was determined to be Q-10. The major fatty acids were identified to be C16:0, C18:1 ω7c and summed feature 4 (consisting of C17:1 anteiso B/iso I). The major polar lipids were identified as phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, two unidentified phospholipids and one unidentified aminolipid. The DNA G+C content was found to be 67.2 mol %. The analysis of the genotypic and phenotypic data indicated that strain YIM 93097(T) belongs to a novel species of the genus Skermanella, for which the name Skermanella rubra sp. nov. is proposed. The type strain is YIM 93097(T) (=DSM 21389(T)=CCTCC AB 2015161(T)).
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Affiliation(s)
- Zheng-Yun Zhang
- Energy and Environment Science College, Yunnan Normal University, Education Ministry Key Laboratory of Renewable Energy Advanced Materials and Manufacturing Technology, Kunming, 650092, People's Republic of China
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16
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Description of Niveispirillum fermenti gen. nov., sp. nov., isolated from a fermentor in Taiwan, transfer of Azospirillum irakense (1989) as Niveispirillum irakense comb. nov., and reclassification of Azospirillum amazonense (1983) as Nitrospirillum amazonense gen. nov. Antonie van Leeuwenhoek 2014; 105:1149-62. [DOI: 10.1007/s10482-014-0176-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 04/15/2014] [Indexed: 10/25/2022]
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17
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Zhu W, Huang J, Li M, Li X, Wang G. Genomic analysis of Skermanella stibiiresistens type strain SB22 (T.). Stand Genomic Sci 2014; 9:1211-20. [PMID: 25197493 PMCID: PMC4149033 DOI: 10.4056/sigs.5751047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of genus Skermanella were described as Gram-negative, motile, aerobic, rod-shaped, obligate-heterotrophic bacteria and unable to fix nitrogen. In this study, the genome sequence of Skermanella stibiiresistens SB22(T) is reported. Phylogenetic analysis using core proteins confirmed the phylogenetic assignment based on 16S rRNA gene sequences. Strain SB22(T) has all the proteins for complete glycolysis, tricarboxylic acid cycle and pentose phosphate pathway. The RuBisCO encoding genes cbbL1S1 and nitrogenase delta subunit gene anfG are absent, consistent with its inability to fix carbon and nitrogen, respectively. In addition, the genome possesses a series of flagellar assembly and chemotaxis genes to ensure its motility.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jing Huang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mingshun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiangyang Li
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, China
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18
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Sheu SY, Chen YL, Young CC, Chen WM. Lacibacterium aquatile gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from a freshwater lake. Int J Syst Evol Microbiol 2013; 63:4797-4804. [DOI: 10.1099/ijs.0.055145-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated LTC-2T was isolated from a freshwater lake in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain LTC-2T were Gram-reaction-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile by means of a monopolar flagellum, non-spore-forming, slightly curved rods surrounded by a thick capsule and formed creamy white colonies. Growth occurred at 10–37 °C (optimum, 20–30 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0) and with 0–1.0 % NaCl (optimum, 0 %). The predominant fatty acids were C18 : 1ω7c, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-10 and the DNA G+C content was 58.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, two uncharacterized phospholipids and two uncharacterized aminophospholipids. The major polyamines were putrescine, homospermidine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain LTC-2T forms a distinct lineage with respect to closely related genera in the family
Rhodospirillaceae
, most closely related to the genera
Elstera
and
Dongia
, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera were less than 94 %. On the basis of the genotypic and phenotypic data, strain LTC-2T represents a novel genus and species of the family
Rhodospirillaceae
, for which the name Lacibacterium aquatile gen. nov., sp. nov. is proposed. The type strain is LTC-2T ( = BCRC 80445T = LMG 26999T = KCTC 32017T).
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Affiliation(s)
- Shih-Yi Sheu
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Yi-Ling Chen
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Chiu-Chung Young
- College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Wen-Ming Chen
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
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19
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Amoozegar MA, Makhdoumi-Kakhki A, Ramezani M, Nikou MM, Fazeli SAS, Schumann P, Ventosa A. Limimonas halophila gen. nov., sp. nov., an extremely halophilic bacterium in the family Rhodospirillaceae. Int J Syst Evol Microbiol 2012; 63:1562-1567. [PMID: 22904212 DOI: 10.1099/ijs.0.041236-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, Gram-staining-negative, non-pigmented, rod-shaped, strictly aerobic, extremely halophilic bacterium, designated strain IA16(T), was isolated from the mud of the hypersaline Lake Aran-Bidgol, in Iran. Cells of strain IA16(T) were not motile. Growth occurred with 2.5-5.2 M NaCl (optimum 3.4 M), at pH 6.0-8.0 (optimum pH 7.0) and at 30-50 °C (optimum 40 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IA16(T) belonged in the family Rhodospirillaceae and that its closest relatives were Rhodovibrio sodomensis DSM 9895(T) (91.6 % sequence similarity), Rhodovibrio salinarum NCIMB 2243(T) (91.2 %), Pelagibius litoralis CL-UU02(T) (88.9 %) and Fodinicurvata sediminis YIM D82(T) (88.7 %). The novel strain's major cellular fatty acids were C19 : 0 cyclo ω7c and C18 : 0 and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, four unidentified phospholipids, three unidentified aminolipids and two other unidentified lipids. The cells of strain IA16(T) contained the ubiquinone Q-10. The G+C content of the novel strain's genomic DNA was 67.0 mol%. The physiological, biochemical and phylogenetic differences between strain IA16(T) and other previously described taxa indicate that the strain represents a novel species in a new genus within the family Rhodospirillaceae, for which the name Limimonas halophila gen. nov., sp. nov. is proposed. The type strain of Limimonas halophila is IA16(T) ( = IBRC-M 10018(T) = DSM 25584(T)).
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Affiliation(s)
- Mohammad Ali Amoozegar
- Microorganisms Bank, Iranian Biological Resource Centre, Academic Centre for Education, Culture and Research, Tehran, Iran.,Extremophiles Laboratory, Department of Microbiology, Faculty of Biology, and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Ali Makhdoumi-Kakhki
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohadaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre, Academic Centre for Education, Culture and Research, Tehran, Iran
| | - Mahdi Moshtaghi Nikou
- Microorganisms Bank, Iranian Biological Resource Centre, Academic Centre for Education, Culture and Research, Tehran, Iran
| | | | - Peter Schumann
- Genetic Department, Rojan Insititute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Antonio Ventosa
- Leibniz-Institut-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
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20
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Luo G, Shi Z, Wang H, Wang G. Skermanella stibiiresistens sp. nov., a highly antimony-resistant bacterium isolated from coal-mining soil, and emended description of the genus
Skermanella. Int J Syst Evol Microbiol 2012; 62:1271-1276. [DOI: 10.1099/ijs.0.033746-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, motile, rod-shaped, antimony-resistant bacterium, designated strain SB22T, was isolated from soil of Jixi coal mine, China. The major cellular fatty acids (>5 %) were C18 : 1ω7c (63.5 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I, 10.8 %) and C16 : 0 (9.9 %). The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unknown aminolipid. The genomic DNA G+C content was 69.6 mol% and Q-10 was the major respiratory quinone. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SB22T was most closely related to
Skermanella aerolata
5416T-32T (97.3 %),
Skermanella parooensis
ACM 2042T (95.8 %) and
Skermanella xinjiangensis
10-1-101T (92.9 %). The DNA–DNA hybridization value between strain SB22T and
S. aerolata
KACC 11604T ( = 5416T-32T) was 43.3 %. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics of strain SB22T and related species, it is considered that the isolate represents a novel species of the genus
Skermanella
, for which the name Skermanella stibiiresistens sp. nov. is proposed. The type strain is SB22T ( = CGMCC 1.10751T = KCTC 23364T). An emended description of the genus Skermanella is provided.
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Affiliation(s)
- Guosheng Luo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Zunji Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Hui Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
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21
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Yamada K, Fukuda W, Kondo Y, Miyoshi Y, Atomi H, Imanaka T. Constrictibacter antarcticus gen. nov., sp. nov., a cryptoendolithic micro-organism from Antarctic white rock. Int J Syst Evol Microbiol 2011; 61:1973-1980. [DOI: 10.1099/ijs.0.026625-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-spore-forming, ovoid to rod-shaped aerobic or microaerobic bacterium, strain 262-8T, was isolated from a cavity within white rock collected in Antarctica. Strain 262-8T grew at 5–30 °C (optimum 25 °C), at pH 6–8 (optimum approximately pH 7) and with 0.1–2.0 % (w/v) NaCl (optimum 0.5 % NaCl). The addition of tryptone or yeast extract was essential for growth. Strain 262-8T was able to utilize organic compounds such as ribose, pyruvate and succinate in the presence of a low concentration of tryptone. Ubiquinone 10 was the major respiratory quinone. The major fatty acids were C18 : 1, C16 : 0 and C18 : 0. The G+C content of the genomic DNA was 69.8 mol%. Comparative analyses of 16S rRNA gene sequences and physiological characteristics indicated that strain 262-8T was a phylogenetically novel bacterium that should be classified in a new genus of the family Rhodospirillaceae, for which the name Constrictibacter antarcticus gen. nov., sp. nov. is proposed. The type strain of the type species is 262-8T ( = JCM 16422T = ATCC BAA-1906T).
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Affiliation(s)
- Kozo Yamada
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Wakao Fukuda
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Yuka Kondo
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuki Miyoshi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tadayuki Imanaka
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
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Desertibacter roseus gen. nov., sp. nov., a gamma radiation-resistant bacterium in the family Rhodospirillaceae, isolated from desert sand. Int J Syst Evol Microbiol 2011; 61:1109-1113. [DOI: 10.1099/ijs.0.021246-0] [Citation(s) in RCA: 19] [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 Gram-negative, rod-shaped, strictly aerobic bacterium, strain 2622T, was isolated from gamma-irradiated soil sampled from the Taklimakan desert in Xinjiang, China. Phylogenetic analyses showed that strain 2622T formed a distinct lineage in the family Rhodospirillaceae and shared 91.7 and 90.1 % 16S rRNA gene sequence similarity with its closest relatives, the type strains of Skermanella xinjiangensis and Skermanella aerolata, respectively. The DNA G+C content of strain 2622T was 71.4 mol% and the isoprenoid quinone was ubiquinone Q-10. Based on phenotypic and chemotaxonomic data and phylogenetic analysis, strain 2622T is considered to represent a novel species of a new genus in the family Rhodospirillaceae, for which the name Desertibacter roseus gen. nov., sp. nov. is proposed. The type strain of Desertibacter roseus is strain 2622T ( = CCTCC AB 208152T = KCTC 22436T).
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23
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Kim SJ, Kim YS, Weon HY, Anandham R, Noh HJ, Kwon SW. Xenophilus aerolatus sp. nov., isolated from air. Int J Syst Evol Microbiol 2010; 60:327-330. [DOI: 10.1099/ijs.0.013185-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel aerobic, Gram-negative, motile, rod-shaped bacterial strain designated 5516S-2T was isolated from an air sample taken in Suwon, Republic of Korea. Colonies were yellow-pigmented and circular with entire margins. 16S rRNA gene sequence analysis showed that strain 5516S-2T was closely related to Xylophilus ampelinus DSM 7250T (97.6 % sequence similarity), Variovorax soli KACC 11579T (97.5 %) and Xenophilus azovorans DSM 13620T (97.1 %). However, the phylogenetic tree indicated that strain 5516S-2T formed a separate clade from Xenophilus azovorans. Strain 5516S-2T displayed 42, 31 and 30 % DNA–DNA relatedness to the type strains of Xenophilus azovorans, Xylophilus ampelinus and V. soli, respectively. The major fatty acids (>10 % of total fatty acids) were C16 : 0 (33.3 %), C17 : 0 cyclo (18.8 %), C18 : 1
ω7c (17.5 %) and summed feature 3 (comprising C16 : 1
ω7c and/or iso-C15 : 0 2-OH; 13.0 %). The DNA G+C content was 69 mol%. The major quinone was ubiquinone Q-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unknown aminophospholipids. Genotypic and phenotypic characteristics clearly distinguished strain 5516S-2T from closely related species and indicated that it represents a novel species within the genus Xenophilus, for which the name Xenophilus aerolatus sp. nov. is proposed. The type strain is 5516S-2T (=KACC 12602T=DSM 19424T).
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Affiliation(s)
- Soo-Jin Kim
- Korean Agricultural Culture Collection (KACC), National Agrobiodiversity Center, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Yi-Seul Kim
- Korean Agricultural Culture Collection (KACC), National Agrobiodiversity Center, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Hang-Yeon Weon
- Korean Agricultural Culture Collection (KACC), National Agrobiodiversity Center, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Rangasamy Anandham
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Madurai, India
| | - Hyung-Jun Noh
- Mushroom Research Division, National Institute of Horticultural & Medicinal Crop, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection (KACC), National Agrobiodiversity Center, Rural Development Administration, Suwon 441-707, Republic of Korea
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24
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An H, Zhang L, Tang Y, Luo X, Sun T, Li Y, Wang Y, Dai J, Fang C. Skermanella xinjiangensis sp. nov., isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 2009; 59:1531-4. [DOI: 10.1099/ijs.0.003350-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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25
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Choi DH, Hwang CY, Cho BC. Pelagibius litoralis gen. nov., sp. nov., a marine bacterium in the family Rhodospirillaceae isolated from coastal seawater. Int J Syst Evol Microbiol 2009; 59:818-23. [DOI: 10.1099/ijs.0.002774-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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26
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Lladó S, Jiménez N, Viñas M, Solanas AM. Microbial populations related to PAH biodegradation in an aged biostimulated creosote-contaminated soil. Biodegradation 2009; 20:593-601. [PMID: 19153811 DOI: 10.1007/s10532-009-9247-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 01/06/2009] [Indexed: 11/26/2022]
Abstract
A previous bioremediation survey on a creosote-contaminated soil showed that aeration and optimal humidity promoted depletion of three-ringed polycyclic aromatic hydrocarbons (PAHs), but residual concentrations of four-ringed benzo(a)anthracene (B(a)A) and chrysene (Chry) remained. In order to explain the lack of further degradation of heavier PAHs such as four-ringed PAHs and to analyze the microbial population responsible for PAH biodegradation, a chemical and microbial molecular approach was used. Using a slurry incubation strategy, soil in liquid mineral medium with and without additional B(a)A and Chry was found to contain a powerful PAH-degrading microbial community that eliminated 89% and 53% of the added B(a)A and Chry, respectively. It is hypothesized that the lack of PAH bioavailability hampered their further biodegradation in the unspiked soil. According to the results of the culture-dependent and independent techniques Mycobacterium parmense, Pseudomonas mexicana, and Sphingobacterials group could control B(a)A and Chry degradation in combination with several microorganisms with secondary metabolic activity.
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Affiliation(s)
- Salvador Lladó
- Department of Microbiology, University of Barcelona, Diagonal 645, E-08028, Barcelona, Spain
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