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Lin SY, Hameed A, Tsai CF, Tang YS, Young CC. Description of Pseudogemmobacter faecipullorum sp. nov., isolated from poultry manure. FEMS Microbiol Lett 2022; 369:6840210. [PMID: 36413463 DOI: 10.1093/femsle/fnac112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/07/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST710T, isolated from poultry manure sampled in Taiwan. Cells of strain CC-YST710T were aerobic, Gram-stain-negative, nonmotile, nonspore-forming rods, displaying positive reactions for catalase, and oxidase activities. Strain CC-YST710T was found to grow optimally at 30°C, pH 7.0, and in the presence of 2% (w/v) NaCl. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, four unidentified aminolipids, one unidentified aminophospholipid, and five unidentified lipids. The major polyamine was spermidine. The dominating cellular fatty acids (> 5%) included C16:0, C18:0, and C18:1ω7c/C18:1ω6c. Based on 16S rRNA gene analysis, this isolate showed the closest phylogenetic relationship with 'Pseudogemmobacter humicola' (97.6%), followed by Pseudogemmobacter bohemicus (97.2%) and 'Pseudogemmobacter hezensis' (97.5%). The draft genome (4.3 Mb) had 62.9 mol% G + C content. CC-YST710T can be distinguished from other Pseudogemmobacter species due to the exclusive presence of key genes encoding p-hydroxybenzoate hydroxylase, protocatechuate 3, 4-dioxygenase (α and β chain), and homogentisate 1, 2-dioxygenase involved in the degradation of phenolic compounds such as p-hydroxybenzoic acid, protocatechuate, and homogentisate, respectively. Orthologous average nucleotide identity (OrthoANI) of the isolate with the type strains of the genera Pseudogemmobacter were 77.6%‒78.0% (n = 3), followed by Tabrizicola (72.3%‒73.7%, n = 5), and Gemmobacter(72.3%‒73.5%, n = 7). Based on its distinct phylogenetic, phenotypic, and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, digital DDH, and the phylogenomic placement, strain CC-YST710T is considered to represent a novel Pseudogemmobacter species, for which the name Pseudogemmobacter faecipullorum sp. nov. (type strain CC-YST710T = BCRC 81286T = JCM 34182T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung 40227, Taiwan
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya Deemed to be University, University Road Deralakatte Mangalore 575018, Karnataka, India
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd, Taichung 40227, Taiwan
| | - Yu-Shan Tang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung 40227, Taiwan
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung 40227, Taiwan.,Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, 145, XingDa Rd., Taichung 40227, Taiwan
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Mu Y, Peng JY, Wang HP, Song Y, Wang HM, Chen Q, Chen K. Xinfangfangia pollutisoli sp. nov., Isolated from Clopyralid-Contaminated Soil. Curr Microbiol 2022; 79:255. [PMID: 35834049 DOI: 10.1007/s00284-022-02958-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/27/2022] [Indexed: 11/29/2022]
Abstract
With the aim of isolating clopyralid-degrading bacterial species for potential bioremediation, a pale-yellow, Gram-negative, rod-shaped, and non-motile designated as Clo-40T was isolated from soil which was about 10 years use of clopyralid in Zaozhuang city, Shandong province. Growth occurred within the ranges from 10 to 40 °C and 0-2.5% (w/v) NaCl. Strain could completely degrade 50 mg/L clopyralid within 2 days after induction and formed 3, 6-hydroxypicolinic acid, a major clopyralid metabolite, hydrolyze esculin, and reduce nitrates to nitrites, but could not hydrolyze gelatin. Based on phylogenetic analysis, strain clustered within the genus Xinfangfangia clade and branched with Xinfangfangia humi IMT-291T (97.6%) and Xinfangfangia soli ZQBWT (96.9%). Genome sequencing revealed a genome size of 4.41 Mbp and G + C content of 67.3%. The average nucleotide ANI values of strain with respect to X. humi IMT-291T and X. soli ZQBWT were 77.5% and 76.9%, respectively. The DDH estimated values between strain Clo-40T and X. humi IMT-291T and X. soli ZQBWT were 20.5% and 20.0%, respectively. The predominant fatty acids (> 5% of the total fatty acids) were C18:1 w7c (42.9%), C16:0 (28.8%), C17:0 cyclo (13.0%), and C14:0 (7.0%). The major polar lipids were identified as phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid, unidentified glycolipid, and unidentified lipids. The predominant respiratory quinone was Q-10. Based on data from phenotypic, chemotaxonomic, and genotypic analyses in this study, strain Clo-40T represent a novel species in the genus of Xinfangfangia, for which the name Xinfangfangia pollutisoli sp. nov. is proposed. The type strain is Clo-40T (= KCTC 92089T = GDMCC 1.2845T).
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Affiliation(s)
- Yang Mu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.,Taizhou Center for Disease Prevention and Control, Taizhou, 225300, People's Republic of China
| | - Jia-Yi Peng
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Hui-Ping Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Yue Song
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Hong-Mei Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Qing Chen
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China.
| | - Kai Chen
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
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Ma T, Xue H, Piao C, Liu C, Yang M, Bian D, Li Y. Reclassification of 11 Members of the Family Rhodobacteraceae at Genus and Species Levels and Proposal of Pseudogemmobacter hezensis sp. nov. Front Microbiol 2022; 13:849695. [PMID: 35495672 PMCID: PMC9044078 DOI: 10.3389/fmicb.2022.849695] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, motile bacterial strain, D13-10-4-6T, was isolated from the bark sample of Populus × euramericana. The strain could grow at 15-35°C, at pH 6-10 and in 0-4% (w/v) NaCl, and the strain tested positive for oxidase and catalase activities. The main polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The main respiratory quinone was Q-10, and the predominant fatty acid was C18:1 ω7c. The phylogenetic analyses showed that the strain belonged to the genus Pseudogemmobacter of the family Rhodobacteraceae. The family Rhodobacteraceae is an ecologically diverse group that includes bacteria from aquatic to terrestrial ecosystems. As a consequence, the classification of the family Rhodobacteraceae is difficult, not least when the early taxonomy work relied heavily on 16S rRNA gene analysis. Recently, the taxonomic status of many members of the family has been revised based on the genome analysis; however, there are still some classification conflicts due to the lack of genome sequences and parallel publication time. In this study, phylogenetic trees based on 16S rRNA gene, gyrB gene, and 120 concatenated proteins, the average amino acid identity (AAI) and percentage of conserved proteins (POCP) have been used for the analysis of strain D13-10-4-6T and other members of 15 genera within the family to further clarify their taxonomic relationships. For the data of phylogeny, AAI, and POCP, the taxonomic proposals are (1) reclassification of Rhodobacter tardus as the type species of a novel genus, Stagnihabitans gen. nov., as Stagnihabitans tardus comb. nov.; (2) reclassification of Tabrizicola alkalilacus, Tabrizicola sediminis, Tabrizicola algicola into a novel genus, Pseudotabrizicola gen. nov., as Pseudotabrizicola alkalilacus comb. nov., Pseudotabrizicola sediminis comb. nov., Pseudotabrizicola algicola comb. nov.; (3) reclassification of Rhodobacter sediminicola into the genus Cereibacter as Cereibacter sediminicola comb. nov.; (4) reclassification of Rhodobacter flagellatus, Rhodobacter thermarum, and Xinfangfangia soli into the genus Tabrizicola as Tabrizicola flagellatus comb. nov., Tabrizicola thermarum comb. Nov., and Tabrizicola soli comb. nov.; (5) reclassification of Xinfangfangia humi into the genus Pseudogemmobacter as Pseudogemmobacter humicola comb. nov.; (6) classification of strain D13-10-4-6T as a novel species of the genus Pseudogemmobacter, for which the name P. hezensis sp. nov. is proposed, the type strain is D13-10-4-6T (= CFCC 12033T = KCTC 82215T).
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Affiliation(s)
- Tengfei Ma
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Han Xue
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Chungen Piao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Chengyi Liu
- Panzhihua City Academy of Agricultural and Forest Sciences, Panzhihua, China
| | - Mei Yang
- Panzhihua City Academy of Agricultural and Forest Sciences, Panzhihua, China
| | - Danran Bian
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
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Muramatsu S, Hirose S, Iino T, Ohkuma M, Hanada S, Haruta S. Neotabrizicola shimadae gen. nov., sp. nov., an aerobic anoxygenic phototrophic bacterium harbouring photosynthetic genes in the family Rhodobacteraceae, isolated from a terrestrial hot spring. Antonie van Leeuwenhoek 2022; 115:731-740. [PMID: 35380297 DOI: 10.1007/s10482-022-01728-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 03/06/2022] [Indexed: 11/27/2022]
Abstract
A bacteriochlorophyll-containing bacterium, designated as strain N10T, was isolated from a terrestrial hot spring in Nagano Prefecture, Japan. Gram-stain-negative, oxidase- and catalase-positive and ovoid to rod-shaped cells showed the features of aerobic anoxygenic phototrophic bacteria, i.e., strain N10T synthesised bacteriochlorophylls under aerobic conditions and could not grow anaerobically even under illumination. Genome analysis found genes for bacteriochlorophyll and carotenoid biosynthesis, light-harvesting complexes and type-2 photosynthetic reaction centre in the chromosome. Phylogenetic analyses based on the 16S rRNA gene sequence and 92 core proteins revealed that strain N10T was located in a distinct lineage near the type species of the genera Tabrizicola and Xinfangfangia and some species in the genus Rhodobacter (e.g., Rhodobacter blasticus). Strain N10T shared < 97.1% 16S rRNA gene sequence identity with those species in the family Rhodobacteraceae. The digital DNA-DNA hybridisation, average nucleotide identity and average amino acid identity values with the relatives, Tabrizicola aquatica RCRI19T (an aerobic anoxygenic phototrophic bacterium), Xinfangfangia soli ZQBWT and R. blasticus ATCC 33485T were 19.9-20.7%, 78.2-79.1% and 69.1-70.1%, respectively. Based on the phenotypic features, major fatty acid and polar lipid compositions, genome sequence and phylogenetic position, a novel genus and species are proposed for strain N10T, to be named Neotabrizicola shimadae (= JCM 34381T = DSM 112087T). Strain N10T which is phylogenetically located among aerobic anoxygenic phototrophic bacteria (Tabrizicola), bacteriochlorophyll-deficient bacteria (Xinfangfangia) and anaerobic anoxygenic phototrophic bacteria (Rhodobacter) has great potential to promote studies on the evolution of photosynthesis in Rhodobacteraceae.
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Affiliation(s)
- So Muramatsu
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Setsuko Hirose
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Takao Iino
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-0856, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan.
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Chen WM, Chang TH, Yang CC, Sheu DS, Jheng LC, Sheu SY. Rhodobacter amnigenus sp. nov. and Rhodobacter ruber sp. nov., isolated from freshwater habitats. Int J Syst Evol Microbiol 2021; 71. [PMID: 34904946 DOI: 10.1099/ijsem.0.005150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains, designated HSP-20T and CCP-1T, isolated from freshwater habitats in Taiwan, were characterized by polyphasic taxonomy. Both strains were Gram-stain-negative, aerobic, non-motile and rod-shaped. Cells of strains HSP-20T and CCP-1T formed pink and dark red coloured colonies, respectively. Both strains contained bacteriochlorophyll a, and showed optimum growth under anaerobic conditions by photoheterotrophy, but no growth by photoautotrophy. Phylogenetic analyses based on 16S rRNA gene and whole-genome sequences indicated that both strains belonged to the genus Rhodobacter. Analysis of 16S rRNA gene sequences showed that strains HSP-20T and CCP-1T shared 98.3 % sequence similarity and were closely related to Rhodobacter tardus CYK-10T (96.0 %) and Rhodobacter flagellatus SYSU G03088T (96.0 %), respectively. Both strains shared common chemotaxonomic characteristics including Q-10 as the major isoprenoid quinone, C18 : 1 ω7c as the predominant fatty acid, and phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as the main polar lipids. The DNA G+C content of both strains was 66.2 mol%. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95-96, 90 and 70 %, respectively, used for species demarcation. On the basis of phenotypic and genotypic properties and phylogenetic inference, both strains should be classified as novel species within the genus Rhodobacter, for which the names Rhodobacter amnigenus sp. nov. (=BCRC 81193T=LMG 31334T) and Rhodobacter ruber sp. nov. (=BCRC 81189T=LMG 31335T) are proposed.
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Affiliation(s)
- Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan, ROC
| | - Ting-Hsuan Chang
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan, ROC
| | - Che-Chia Yang
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan, ROC
| | - Der-Shyan Sheu
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan, ROC
| | - Li-Cheng Jheng
- Department of Chemical and Materials Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City 807, Taiwan, ROC
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan, ROC
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Shi L, Mo K, Bao S, Wu Q, Xue C, Huang H. Mangrovicoccus algicola sp. nov., an alginate lyase - producing marine bacterium. Int J Syst Evol Microbiol 2021; 71. [PMID: 34662266 DOI: 10.1099/ijsem.0.004844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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, non-motile, ellipsoid bacterium, designated HB182678T, was isolated from brown alga collected from Hainan province, PR China. Growth was observed at 10-50 °C (optimum 37-40 °C), at pH 6-10 (optimum pH 8) and in the presence of 0.5-13% (w/v) NaCl (optimum, 2-4%). The predominant isoprenoid quinone was Q-10 and the major fatty acids were C18 : 1 ω7c, C16 : 0, C18 : 0 and C19 : 0 cyclo ω8c. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, an unidentified phospholipid, two unidentified glycolipids and three unidentified aminophospholipids. The size of the draft genome was 4.40 Mbp with G+C content 68.8 mol%. Phylogenetic analysis of 16S rRNA gene sequence indicated that strain HB182678T belonged to the genus Mangrovicoccus, and the closest phylogenetically related species was Mangrovicoccus ximenensis T1lg56T (with the similarity of 96.3%). Whole genome average nucleotide identity (ANI) value between them was 84.3% and in silico DNA-DNA hybridization value was 27.2%. The combined phylogenetic relatedness, phenotypic and genotypic features supported the conclusion that strain HB182678T represents a novel species of the genus Mangrovicoccus, for which the name Mangrovicoccus algicola sp. nov. is proposed. The type strain is HB182678T (=MCCC 1K04624T=KCTC 82318T).
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Affiliation(s)
- Lei Shi
- College of Life Sciences, Jiamusi University, Jiamusi 154007, PR China
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou 571101, PR China
| | - Kunlian Mo
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou 571101, PR China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou 571101, PR China
| | - Shixiang Bao
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou 571101, PR China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou 571101, PR China
| | - Qingjuan Wu
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou 571101, PR China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou 571101, PR China
| | - Chunmei Xue
- College of Life Sciences, Jiamusi University, Jiamusi 154007, PR China
| | - Huiqin Huang
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou 571101, PR China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou 571101, PR China
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