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Yabe S, Zheng Y, Wang CM, Sakai Y, Abe K, Yokota A, Donadio S, Cavaletti L, Monciardini P. Reticulibacter mediterranei gen. nov., sp. nov., within the new family Reticulibacteraceae fam. nov., and Ktedonospora formicarum gen. nov., sp. nov., Ktedonobacter robiniae sp. nov., Dictyobacter formicarum sp. nov. and Dictyobacter arantiisoli sp. nov., belonging to the class Ktedonobacteria. Int J Syst Evol Microbiol 2021; 71. [PMID: 34296987 DOI: 10.1099/ijsem.0.004883] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The aerobic, Gram-positive, mesophilic Ktedonobacteria strains, Uno17T, SOSP1-1T, 1-9T, 1-30T and 150040T, formed mycelia of irregularly branched filaments, produced spores or sporangia, and numerous secondary metabolite biosynthetic gene clusters. The five strains grew at 15-40 °C (optimally at 30 °C) and pH 4.0-8.0 (optimally at pH 6.0-7.0), and had 7.21-12.67 Mb genomes with 49.7-53.7 mol% G+C content. They shared MK9(H2) as the major menaquinone and C16 : 1-2OH and iso-C17 : 0 as the major cellular fatty acids. Phylogenetic and phylogenomic analyses showed that Uno17T and SOSP1-9T were most closely related to members of the genus Dictyobacter, with 94.43-96.21 % 16S rRNA gene similarities and 72.16-81.56% genomic average nucleotide identity. The strain most closely related to SOSP1-1T and SOSP1-30T was Ktedonobacter racemifer SOSP1-21T, with 91.33 and 98.84 % 16S rRNA similarities, and 75.13 and 92.35% average nucleotide identities, respectively. Strain 150040T formed a distinct clade within the order Ktedonobacterales, showing <90.47 % 16S rRNA gene similarity to known species in this order. Based on these results, we propose: strain 150040T as Reticulibacter mediterranei gen. nov., sp. nov. (type strain 150 040T=CGMCC 1.17052T=BCRC 81202T) within the family Reticulibacteraceae fam. nov. in the order Ktedonobacterales; strain SOSP1-1T as Ktedonospora formicarum gen. nov., sp. nov. (type strain SOSP1-1T=CGMCC 1.17205T=BCRC 81203T) and strain SOSP1-30T as Ktedonobacter robiniae sp. nov. (type strain SOSP1-30T=CGMCC 1.17733T=BCRC 81205T) within the family Ktedonobacteraceae; strain Uno17T as Dictyobacter arantiisoli sp. nov. (type strain Uno17T=NBRC 113155T=BCRC 81116T); and strain SOSP1-9T as Dictyobacter formicarum sp. nov. (type strain SOSP1-9T=CGMCC 1.17206T=BCRC 81204T) within the family Dictyobacteraceae.
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Affiliation(s)
- Shuhei Yabe
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi 980-0845, Japan
- Hazaka Plant Research Center, Kennan Eisei Kogyo Co. Ltd., Miyagi 989-1311, Japan
| | - Yu Zheng
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi 980-0845, Japan
| | - Chiung-Mei Wang
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi 980-0845, Japan
| | - Yasuteru Sakai
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi 980-0845, Japan
- Hazaka Plant Research Center, Kennan Eisei Kogyo Co. Ltd., Miyagi 989-1311, Japan
| | - Keietsu Abe
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi 980-0845, Japan
| | - Akira Yokota
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi 980-0845, Japan
| | | | - Linda Cavaletti
- FIIRV, Fondazione Istituto Insubrico di Ricerca per la Vita, Via R. Lepetit 34, 21040, Gerenzano, Varese, Italy
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Hernández M, Vera-Gargallo B, Calabi-Floody M, King GM, Conrad R, Tebbe CC. Reconstructing Genomes of Carbon Monoxide Oxidisers in Volcanic Deposits Including Members of the Class Ktedonobacteria. Microorganisms 2020; 8:microorganisms8121880. [PMID: 33260993 PMCID: PMC7761526 DOI: 10.3390/microorganisms8121880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/13/2020] [Accepted: 11/24/2020] [Indexed: 12/02/2022] Open
Abstract
Microorganisms can potentially colonise volcanic rocks using the chemical energy in reduced gases such as methane, hydrogen (H2) and carbon monoxide (CO). In this study, we analysed soil metagenomes from Chilean volcanic soils, representing three different successional stages with ages of 380, 269 and 63 years, respectively. A total of 19 metagenome-assembled genomes (MAGs) were retrieved from all stages with a higher number observed in the youngest soil (1640: 2 MAGs, 1751: 1 MAG, 1957: 16 MAGs). Genomic similarity indices showed that several MAGs had amino-acid identity (AAI) values >50% to the phyla Actinobacteria, Acidobacteria, Gemmatimonadetes, Proteobacteria and Chloroflexi. Three MAGs from the youngest site (1957) belonged to the class Ktedonobacteria (Chloroflexi). Complete cellular functions of all the MAGs were characterised, including carbon fixation, terpenoid backbone biosynthesis, formate oxidation and CO oxidation. All 19 environmental genomes contained at least one gene encoding a putative carbon monoxide dehydrogenase (CODH). Three MAGs had form I coxL operon (encoding the large subunit CO-dehydrogenase). One of these MAGs (MAG-1957-2.1, Ktedonobacterales) was highly abundant in the youngest soil. MAG-1957-2.1 also contained genes encoding a [NiFe]-hydrogenase and hyp genes encoding accessory enzymes and proteins. Little is known about the Ktedonobacterales through cultivated isolates, but some species can utilise H2 and CO for growth. Our results strongly suggest that the remote volcanic sites in Chile represent a natural habitat for Ktedonobacteria and they may use reduced gases for growth.
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Affiliation(s)
- Marcela Hernández
- Johann Heinrich von Thünen Institut, Institut für Biodiversität, 50, 38116 Braunschweig, Germany;
- School of Environmental Sciences, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany;
- Correspondence:
| | - Blanca Vera-Gargallo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain;
| | | | - Gary M. King
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany;
| | - Christoph C. Tebbe
- Johann Heinrich von Thünen Institut, Institut für Biodiversität, 50, 38116 Braunschweig, Germany;
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Geng YH, He XY, Li N, Li J, Gu TJ, Sun XM, Song XY, Chen XL, Zhang YZ, Qin QL, Zhang XY. Vibrio algicola sp. nov., isolated from the surface of coralline algae. Int J Syst Evol Microbiol 2020; 70:5149-5155. [PMID: 32812859 DOI: 10.1099/ijsem.0.004394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, oxidase- and catalase-positive, facultative anaerobic and rod-shaped bacterium, designated strain SM1977T, was isolated from the surface of coralline algae collected from the intertidal zone at Qingdao, PR China. The strain grew at 10-35 °C, pH 4.5-8.5 and with 1-8.5% (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 20 and DNA. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1977T was affiliated with the genus Vibrio, having the highest sequence similarity (97.6 %) to the type strain of Vibrio casei, followed by those of another five species (95.6-97.6 %) in the Rumoiensis clade of the genus Vibrio. However, the in silico DNA-DNA hybridization (75.3-75.9 %) and average nucleotide identity (21.6-22.8 %) values of SM1977T against these close relatives were all below the corresponding thresholds to discriminate bacterial species. The major fatty acids were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and summed feature 8 (C18:1 ω6c and /or C18:1 ω7c). The predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The sole respiratory quinone was Q-8. The genomic DNA G+C content of strain SM1977T, determined from the obtained whole genomic sequence, was 42.3 mol%. On the basis of the polyphasic results obtained in this study, strain SM1977T is considered to represent a novel species within the genus Vibrio, for which the name Vibrio algicola sp. nov. is proposed. The type strain is SM1977T (=MCCC 1K04351T=KCTC 72847T).
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Affiliation(s)
- Yu-Hui Geng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xiao-Yan He
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Na Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Jian Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Tie-Ji Gu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xiao-Meng Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xiu-Lan Chen
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Qi-Long Qin
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xi-Ying Zhang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
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