1
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Cho C, Lee D, Jeong D, Kim S, Kim MK, Srinivasan S. Characterization of radiation-resistance mechanism in Spirosoma montaniterrae DY10 T in terms of transcriptional regulatory system. Sci Rep 2023; 13:4739. [PMID: 36959250 PMCID: PMC10036542 DOI: 10.1038/s41598-023-31509-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/13/2023] [Indexed: 03/25/2023] Open
Abstract
To respond to the external environmental changes for survival, bacteria regulates expression of a number of genes including transcription factors (TFs). To characterize complex biological phenomena, a biological system-level approach is necessary. Here we utilized six computational biology methods to infer regulatory network and to characterize underlying biologically mechanisms relevant to radiation-resistance. In particular, we inferred gene regulatory network (GRN) and operons of radiation-resistance bacterium Spirosoma montaniterrae DY10[Formula: see text] and identified the major regulators for radiation-resistance. Our results showed that DNA repair and reactive oxygen species (ROS) scavenging mechanisms are key processes and Crp/Fnr family transcriptional regulator works as a master regulatory TF in early response to radiation.
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Affiliation(s)
- Changyun Cho
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dohoon Lee
- Bioinformatics Institute, Seoul National University, Seoul, 08826, Republic of Korea
- BK21 FOUR Intelligence Computing, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dabin Jeong
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea.
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea.
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2
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Won M, Hong SB, Han BH, Kwon SW. Spirosoma rhododendri sp. nov., isolated from a flower of royal azalea (Rhododendron schlippenbachii). Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005306] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-motile, strictly aerobic and rod- or filamentous-shaped strain, CJU-R4T, was isolated from a flower of royal azalea (Rhododendron schlippenbachii) collected in the Republic of Korea. Strain CJU-R4T was catalase-positive and oxidase-negative, and grew at 15–33 °C (optimum, 28–20 °C), at pH 5.0–8.0 (optimum, pH 7.0–8.0), and in the presence of 0–1 % NaCl (w/v; optimum, 0 %). Strain CJU-R4T had the highest 16S rRNA gene sequence similarity to
Spirosoma oryzae
RHs22T (96.6 %), revealing less than 93 % sequence similarity to other type strains. Phylogenetic and phylogenomic analysis also revealed strain CJU-R4T formed a robust cluster with
S. oryzae
RHs22T. The major fatty acids were summed feature 3 (comprising C16 : 1
ω7c and/or C16 : 1
ω6c; 33.0 %), C16 : 1
ω5c (22.1 %), iso-C15 : 0 (12.6 %) and C16 : 0 (10.7 %). The polar lipids were composed of phosphatidylethanolamine, three unidentified aminophospholipids, one unidentified phospholipid and four unidentified lipids. Menaquinone-7 was detected as the sole respiratory quinone. The genomic DNA G+C content was 55.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain CJU-R4T and
Spirosoma oryzae
DSM 28354T were 81.5 and 23.9 %, respectively. Based on the results of the phenotypic and genotypic analyses, strain CJU-R4T is considered to represent a novel species of the genus
Spirosoma
, for which the name Spirosoma rhododendri sp. nov. is proposed. The type strain is CJU-R4T (=KACC 21264T=NBRC 114513T).
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Affiliation(s)
- Miyoung Won
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Seung-Beom Hong
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Byeong-Hak Han
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
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3
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Park Y, Ten LN, Lee YK, Jung HY, Kim MK. Larkinella humicola sp. nov., a gamma radiation-resistant bacterium isolated from soil. Arch Microbiol 2022; 204:182. [PMID: 35179646 DOI: 10.1007/s00203-022-02790-4] [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: 06/16/2021] [Revised: 01/16/2022] [Accepted: 02/01/2022] [Indexed: 11/02/2022]
Abstract
A Gram-negative, short rod-shaped, and pink-pigmented bacterial strain, designated MA1T, was isolated from a soil sample from Gijang-gun, Busan in Republic of Korea. The 16S rRNA gene sequence analysis showed that strain MA1T belonged to the genus Larkinella and was closely related to "Larkinella punicea" (97.5% similarity), Larkinella rosea 15J16-1T3AT (96.5%), and Larkinella knui 15J6-3T6T (96.2%). Polar lipid profile of strain MA1T contained phosphatidylethanolamine, two unidentified aminolipids, and three unidentified lipids. Menaquinone-7 was the only quinone and the main fatty acids were C16:1 ω5c (36.7%), iso-C15:0 (30.0%), iso-C17:0 3-OH (7.7%), and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c and/or iso-C15:0 2-OH) (7.3%). The genomic DNA G + C content was 52.3 mol% based on the whole-genome analysis. Strain MA1T exhibited a relatively low level of ANI and in silico DDH values with "Larkinella punicea" (91.9 and 47.1%, respectively), Larkinella rosea (79.7 and 23.3%), and Larkinella knui (81.9 and 25.7%). Based on its phenotypic properties and phylogenetic distinctiveness, strain MA1T should be classified in the genus Larkinella as a representative of a novel species, for which the name Larkinella humicola sp. nov. is proposed. The type strain is MA1T (= KCTC 72629T = NBRC 114191T).
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Affiliation(s)
- Yuna Park
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea
| | - Leonid N Ten
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Young Koung Lee
- Institute of Plasma Technology, Korea Institute of Fusion Energy, 37 Dongjangsan-ro, Gunsan, Jeollabuk, 54004, 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.
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea.
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4
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Liu L, Lu L, Li H, Meng Z, Dong T, Peng C, Xu X. Divergence of Phyllosphere Microbial Communities Between Females and Males of the Dioecious Populus cathayana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:351-361. [PMID: 33290085 DOI: 10.1094/mpmi-07-20-0178-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, the differentiation of phyllosphere microbiota in dioecious plants remains largely unexplored. Here, the diversity and composition of female and male Populus cathayana phyllosphere bacterial and fungal communities were investigated using 16S rRNA/ITS1 gene-based MiSeq sequencing. The divergences of bacterial and fungal community compositions occurred between females and males. Both females and males had their unique phyllosphere bacterial and fungal microbiota, such as bacterial Gemmata spp. (5.41%) and fungal Pringsheimia spp. (0.03%) in females and bacterial Chitinophaga spp. (0.009%) and fungal Phaeococcomyces spp. (0.02%) in males. Significant differences in the relative abundance of phyla Proteobacteria and Planctomycetes bacteria and phyla Ascomycota and Basidiomycota fungi (P < 0.05) were also found between females and males. Some bacterial species of genera Spirosoma and Amnibacterium and fungal genera Venturia, Suillus, and Elmerina spp. were significantly enriched in males (P < 0.05). In contrast, levels of fungal genera Phoma and Aureobasidium spp. were significantly higher in females than in males (P < 0.05). The mineral, inorganic, and organic nutrients content contributed differently to the divergence of female and male phyllosphere microbial communities, with 87.08 and 45.17% of the variations being explained for bacterial and fungal communities, respectively. These results highlight the sexual discrimination of phyllosphere microbes on the dioecious plants and provide hints on the potential host-associated species in phyllosphere environments.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Liling Liu
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- Institute of Ecology, China West Normal University, Nanchong 637009, China
| | - Lu Lu
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Huilin Li
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Zhensi Meng
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Tingfa Dong
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Chao Peng
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Xiao Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- Institute of Ecology, China West Normal University, Nanchong 637009, China
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5
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Tahon G, Lebbe L, Willems A. Spirosoma utsteinense sp. nov. isolated from Antarctic ice-free soils from the Utsteinen region, East Antarctica. Int J Syst Evol Microbiol 2021; 71. [PMID: 33729126 DOI: 10.1099/ijsem.0.004754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Between 2014 and 2016, 16 Gram-stain-negative, aerobic, rod-shaped and yellow-orange pigmented bacteria were isolated from exposed soils from the Utsteinen region, Sør Rondane Mountains, East Antarctica. Analysis of their 16S rRNA gene sequences revealed that the strains form a separate cluster in the genus Spirosoma, with Spirosoma rigui KCTC 12531T as its closest neighbour (97.8 % sequence similarity). Comparative genome analysis of two representative strains (i.e. R-68523T and R-68079) of the new group with the type strains of Spirosoma rigui (its closest neighbour) and Spirosoma linguale (type species of the genus), yielded average nucleotide identity values of 73.9-78.7 %. Digital DNA-DNA reassociation values of the two strains and these type strains ranged from 20.3 to 22.0 %. The predominant cellular fatty acids of the two novel strains were summed feature 3 (i.e. C16 : 1 ω7c and/or iso-C15 2-OH), C16 : 1 ω5c, C16 : 0 and iso-C15 : 0. The new Spirosoma strains grew with 0-0.5 % (w/v) NaCl, at pH 6.5-8.0 and displayed optimum growth between 15 and 25 °C. Based on the results of phenotypic, genomic, phylogenetic and chemotaxonomic analyses, the new strains represent a novel species of the genus Spirosoma for which the name Spirosoma utsteinense sp. nov. is proposed. The type strain is R-68523T (=LMG 31447T=CECT 9925T).
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Affiliation(s)
- Guillaume Tahon
- Present address: Laboratory of Microbiology, Agrotechnology and Food Sciences, Wageningen University, Wageningen, Netherlands.,Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Liesbeth Lebbe
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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6
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Lee JH, Jung JH, Kim MK, Choe HN, Seong CN, Lim S. Spirosoma taeanense sp. nov., a radiation resistant bacterium isolated from a coastal sand dune. Antonie van Leeuwenhoek 2021; 114:151-159. [PMID: 33449223 DOI: 10.1007/s10482-020-01508-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/27/2020] [Indexed: 11/24/2022]
Abstract
An aerobic, Gram-negative, non-motile, non-spore-forming, rod-shaped, and pale yellow-colored bacterial strain, designated TS118T, was isolated from a sand sample obtained from a coastal sand dune after exposure to 3 kGy of gamma radiation. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the genus Spirosoma and most closely related to Spirosoma metallicum PR1014kT (95.1% similarity). The genome of strain TS118T is constituted by one chromosome (5,691,492 bp) and one plasmid (28,440 bp) and has a G + C content of 52.7%. The genome contains 4641 protein coding sequences (CDSs), 38 tRNAs, and 11 rRNAs. The predominant fatty acids of strain TS118T were C16:1 ω5c, iso-C15:0, C16:0, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), and iso-C17:0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified amino lipid and an unidentified aminophospholipid. The main respiratory quinone was menaquinone-7 (MK-7). The novel strain showed resistance to gamma radiation with a D10 value (i.e., the dose required to reduce the bacterial population by tenfold) of 4.3 kGy. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain TS118T represents a novel species, for which the name Spirosoma taeanense sp. nov. is proposed. The type strain is TS118T (=KCTC 72898T =JCM 34024T).
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Affiliation(s)
- Ji Hee Lee
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Jong-Hyun Jung
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Min-Kyu Kim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Han Na Choe
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 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
| | - Sangyong Lim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea. .,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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7
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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).
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8
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Antonelli F, Esposito A, Calvo L, Licursi V, Tisseyre P, Ricci S, Romagnoli M, Piazza S, Guerrieri F. Characterization of black patina from the Tiber River embankments using Next-Generation Sequencing. PLoS One 2020; 15:e0227639. [PMID: 31917800 PMCID: PMC6952188 DOI: 10.1371/journal.pone.0227639] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/23/2019] [Indexed: 11/19/2022] Open
Abstract
Black patinas are very common biological deterioration phenomena on lapideous artworks in outdoor environments. These substrates, exposed to sunlight, and atmospheric and environmental agents (i.e. wind and temperature changes), represent extreme environments that can only be colonized by highly versatile and adaptable microorganisms. Black patinas comprise a wide variety of microorganisms, but the morphological plasticity of most of these microorganisms hinders their identification by optical microscopy. This study used Next-Generation Sequencing (NGS) (including shotgun and amplicon sequencing) to characterize the black patina of the travertine embankments (muraglioni) of the Tiber River in Rome (Italy). Overall, the sequencing highlighted the rich diversity of bacterial and fungal communities and allowed the identification of more than one hundred taxa. NGS confirmed the relevance of coccoid and filamentous cyanobacteria observed by optical microscopy and revealed an informative landscape of the fungal community underlining the presence of microcolonial fungi and phylloplane yeasts. For the first time high-throughput sequencing allowed the exploration of the expansive diversity of bacteria in black patina, which has so far been overlooked in routine analyses. Furthermore, the identification of euendolithic microorganisms and weathering agents underlines the biodegradative role of black patina, which has often been underestimated. Therefore, the use of NGS to characterize black patinas could be useful in choosing appropriate conservation treatments and in the monitoring of stone colonization after the restoration interventions.
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Affiliation(s)
- Federica Antonelli
- Department of Innovation of Biological Systems, Food and Forestry (DIBAF), Tuscia University, Viterbo, Italy
| | - Alfonso Esposito
- Department of Cellular, Computational and Integrative Biology–CIBIO, University of Trento, Trento, Italy
| | - Ludovica Calvo
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Valerio Licursi
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | | | - Sandra Ricci
- Biology Laboratory, Istituto Superiore per la Conservazione e per il Restauro (ISCR), Rome, Italy
| | - Manuela Romagnoli
- Department of Innovation of Biological Systems, Food and Forestry (DIBAF), Tuscia University, Viterbo, Italy
| | - Silvano Piazza
- Department of Cellular, Computational and Integrative Biology–CIBIO, University of Trento, Trento, Italy
| | - Francesca Guerrieri
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- Epigenetics and epigenomic of hepatocellular carcinoma, U1052, Cancer Research Center of Lyon (CRCL), Lyon, France
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9
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Li W, Ten LN, Lee SY, Kang IK, Jung HY. Spirosoma horti sp. nov., isolated from apple orchard soil. Int J Syst Evol Microbiol 2018; 68:930-935. [DOI: 10.1099/ijsem.0.002614] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Weilan Li
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Leonid N. Ten
- 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
| | - In-Kyu Kang
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hee-Young Jung
- Institute of Plant Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
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10
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Okiria J, Ten LN, Park SJ, Lee SY, Lee DH, Kang IK, Lee DS, Jung HY. Spirosoma migulaei sp. nov., isolated from soil. J Microbiol 2017; 55:927-932. [DOI: 10.1007/s12275-017-7377-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 12/12/2022]
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11
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Ten LN, Okiria J, Lee JJ, Lee SY, Park S, Lee DS, Kang IK, Kim MK, Jung HY. Spirosoma terrae sp. nov., Isolated from Soil from Jeju Island, Korea. Curr Microbiol 2017; 75:492-498. [DOI: 10.1007/s00284-017-1408-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/29/2017] [Indexed: 12/11/2022]
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12
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Spirosoma jeollabukense sp. nov., isolated from soil. Arch Microbiol 2017; 200:431-438. [DOI: 10.1007/s00203-017-1453-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/25/2017] [Accepted: 11/13/2017] [Indexed: 02/06/2023]
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13
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Active microorganisms thrive among extremely diverse communities in cloud water. PLoS One 2017; 12:e0182869. [PMID: 28792539 PMCID: PMC5549752 DOI: 10.1371/journal.pone.0182869] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 07/25/2017] [Indexed: 12/27/2022] Open
Abstract
Clouds are key components in Earth’s functioning. In addition of acting as obstacles to light radiations and chemical reactors, they are possible atmospheric oases for airborne microorganisms, providing water, nutrients and paths to the ground. Microbial activity was previously detected in clouds, but the microbial community that is active in situ remains unknown. Here, microbial communities in cloud water collected at puy de Dôme Mountain’s meteorological station (1465 m altitude, France) were fixed upon sampling and examined by high-throughput sequencing from DNA and RNA extracts, so as to identify active species among community members. Communities consisted of ~103−104 bacteria and archaea mL-1 and ~102−103 eukaryote cells mL-1. They appeared extremely rich, with more than 28 000 distinct species detected in bacteria and 2 600 in eukaryotes. Proteobacteria and Bacteroidetes largely dominated in bacteria, while eukaryotes were essentially distributed among Fungi, Stramenopiles and Alveolata. Within these complex communities, the active members of cloud microbiota were identified as Alpha- (Sphingomonadales, Rhodospirillales and Rhizobiales), Beta- (Burkholderiales) and Gamma-Proteobacteria (Pseudomonadales). These groups of bacteria usually classified as epiphytic are probably the best candidates for interfering with abiotic chemical processes in clouds, and the most prone to successful aerial dispersion.
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14
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2017; 67:1095-1098. [PMID: 28581921 DOI: 10.1099/ijsem.0.001986] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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15
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Jeon SH, Kang MS, Joo ES, Kim EB, Lim S, Jeong SW, Jung HY, Srinivasan S, Kim MK. Deinococcus persicinus sp. nov., a radiation-resistant bacterium from soil. Int J Syst Evol Microbiol 2016; 66:5077-5082. [DOI: 10.1099/ijsem.0.001473] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Seon Hwa Jeon
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Myung-Suk Kang
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 404-107, Republic of Korea
| | - Eun Sun Joo
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Eun Bit Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Sangyong Lim
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Sun-wook Jeong
- Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Hee-Young Jung
- College of Agricultural and Life Sciences, Kyungpook National University, Daegu 702-701, Republic of Korea
- Institute of Plant Medicine, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 139-774, Republic of Korea
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16
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Oh YJ, Lee HW, Lim SK, Kwon MS, Lee J, Jang JY, Park HW, Nam YD, Seo MJ, Choi HJ. Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi. J Microbiol 2016; 54:588-593. [PMID: 27572507 DOI: 10.1007/s12275-016-6349-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/03/2016] [Accepted: 08/06/2016] [Indexed: 10/21/2022]
Abstract
A novel halophilic bacterium, strain K7(T), was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0-25.0% (w/v) NaCl (optimum 10-15% NaCl), pH 5.5-8.5 (optimum pH 7.0-7.5), and 15-42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone-7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio-C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7(T) and Gracilibacillus orientalis XH-63(T) (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7(T) is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7(T) (KACC 18669(T); JCM 31344(T)).
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Affiliation(s)
- Young Joon Oh
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hae-Won Lee
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Seul Ki Lim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Min-Sung Kwon
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Jieun Lee
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Ja-Young Jang
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hae Woong Park
- Advanced Process Technology Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Young-Do Nam
- Research Group of Gut Microbiome, Korea Food Research Institute, Seongnam, 13539, Republic of Korea
| | - Myung-Ji Seo
- Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Hak-Jong Choi
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
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17
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Spirosoma fluminis sp. nov., a Gamma–Radiation Resistant Bacterium Isolated from Sediment of the Han River in South Korea. Curr Microbiol 2016; 73:689-695. [DOI: 10.1007/s00284-016-1114-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/01/2016] [Indexed: 10/21/2022]
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18
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Lee JJ, Joo ES, Lee DH, Jung HY, Kim MK. Phylogenetic diversity and UV resistance analysis of radiation-resistant bacteria isolated from the water in Han River. ACTA ACUST UNITED AC 2016. [DOI: 10.7845/kjm.2016.6015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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