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Zhuo Y, Jin CZ, Jin FJ, Oh HM, Lee HG, Li T, Jin L. Lacibacter sediminis sp. nov., isolated from contaminated freshwater sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37916707 DOI: 10.1099/ijsem.0.006105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Two Gram-stain-negative bacterial strains, S13-6-6 and S13-6-22T, were isolated from sediment sample collected at a water depth of 4 m from Lake Hongze, Jiangsu Province, PR China. The cells of strains S13-6-6 and S13-6-22T were non-spore-forming, aerobic, non-motile and formed orange colonies on R2A agar. Comparative 16S rRNA gene sequence studies revealed a clear affiliation of the two strains with he phylum Bacteroidota, and revealed the highest pairwise sequence similarities with Lacibacter daechungensis H32-4T (97.8 %), Lacibacter cauensis NJ-8T (97.8 %), Lacibacter luteus TTM-7T (97.4 %) and Lacibacter nakdongensis SS2-56T (97.4 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the strains formed a clear phylogenetic lineage with the genus Lacibacter. The major fatty acids were identified as iso-C15 : 1G, iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (>10 %), and the respiratory quinone was identified as menaquinone MK-7. The polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid and six unidentified lipids. The genomic DNA G+C content was determined to be 40.2 mol% (HPLC) for strain S13-6-6 and 40.3 % (genome) for strain S13-6-22T. The combined genotypic and phenotypic data indicated that strains S13-6-6 and S13-6-22T represent a novel species of the genus Lacibacter, for which the name Lacibacter sediminis sp. nov. is proposed. The type strain is S13-6-22T (=CGMCC 1.17450T =JCM 35802T).
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Affiliation(s)
- Ye Zhuo
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, PR China
- Department of Environmental biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Chun-Zhi Jin
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Feng-Jie Jin
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, PR China
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Taihua Li
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, PR China
| | - Long Jin
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, PR China
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Zhang Y, Feng S, Zhu L, Li M, Xiang X. Population dynamics of Brachionus calyciflorus driven by the associated natural bacterioplankton. Front Microbiol 2023; 13:1076620. [PMID: 36726570 PMCID: PMC9884981 DOI: 10.3389/fmicb.2022.1076620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
Zooplankton provides bacteria with a complex microhabitat richen in organic and inorganic nutrients, and the bacteria community also changes the physiochemical conditions for zooplankton, where the symbiotic relationship between them plays an important role in the nutrient cycle. However, there are few studies on the effect of associated bacteria on the population dynamics of rotifers. In order to make clear their relationships, we reconstructed the associated bacterial community in Brachionus calyciflorus culture, and examined the life history and population growth parameters, and analyzed the diversity and community composition of the associated bacteria at different growth stages of B. calyciflorus. The results showed that the addition of bacteria from natural water can promote the population growth and asexual reproduction of B. calyciflorus, but has no significant effect on sexual reproduction, exhibited by the improvement of its life expectancy at hatching, net reproduction rates and intrinsic growth rate, no significant effects on the generation time and mixis ratio of offspring. It was found that the B. calyciflorus-associated bacterial community was mainly composed of Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria and Firmicutes. Through correlation network analysis, the members of Burkholderiales, Pseudomonadales, Micrococcales, Caulobacterales and Bifidobacteriales were the keystone taxa of B. calyciflorus-associated bacteria. In addition, the relative abundance of some specific bacteria strains increased as the population density of B. calyciflorus increased, such as Hydrogenophaga, Acidovorax, Flavobacterium, Rheinheimera, Novosphingobium and Limnobacter, and their relative abundance increased obviously during the slow and exponential phases of population growth. Meanwhile, the relative abundance of adverse taxa (such as Elizabethkingia and Rickettsiales) decreased significantly with the increase in rotifer population density. In conclusion, the closely associated bacteria are not sufficient for the best growth of B. calyciflorus, and external bacterioplankton is necessary. Furthermore, the function of keystone and rare taxa is necessary for further exploration. The investigation of the symbiotic relationship between zooplankton-associated bacterial and bacterioplankton communities will contribute to monitoring their roles in freshwater ecosystems, and regulate the population dynamics of the micro-food web.
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Affiliation(s)
- Yongzhi Zhang
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, China
| | - Sen Feng
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, China
| | - Lingyun Zhu
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, China
| | - Meng Li
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, China
| | - Xianling Xiang
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, China,Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, Wuhu, Anhui, China,*Correspondence: Xianling Xiang, ✉
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Jin CZ, Wu XW, Zhuo Y, Yang Y, Li T, Jin FJ, Lee HG, Jin L. Genomic insights into a free-living, nitrogen-fixing but non nodulating novel species of Bradyrhizobium sediminis from freshwater sediment: Three isolates with the smallest genome within the genus Bradyrhizobium. Syst Appl Microbiol 2022; 45:126353. [PMID: 36030678 DOI: 10.1016/j.syapm.2022.126353] [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: 03/14/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022]
Abstract
Three bacterial strains isolated from a sediment sample collected at a water depth of 4 m from the Huaihe River in China were characterized. Phylogenetic investigation of the 16S rRNA gene and concatenated housekeeping gene sequences assigned the three novel strains in a highly supported lineage distinct from the published Bradyrhizobium species. The sequence similarities of the concatenated housekeeping genes of the three novel strains support their distinctiveness with the type strains of named species. Average nucleotide identity values of the genome sequences (79.9-82.5%) were below the threshold value of 95-96% for bacterial species circumscription. Close relatives to the novel strains are Bradyrhizobium erythrophlei, Bradyrhizobium jicamae, Bradyrhizobium lablabi, Bradyrhizobium mercantei, Bradyrhizobium elkanii and Bradyrhizobium japonicum. The complete genomes of strains S2-20-1T, S2-11-2 and S2-11-4 consist of single chromosomes of size 5.55, 5.45 and 5.47 Mb, respectively. These strains lack a symbiosis island, key nodulation and photosystem genes. Based on the data presented here, the three strains represent a novel species for which the name Bradyrhizobium sediminis sp. nov. is proposed for S2-20-1T as the type strain. Those three strains are proposed as novel species in free-living Bradyrhizobium isolates with the smallest genomes so far within the genus Bradyrhizobium. A number of functional differences between the three isolates and other published genomes indicate that the genus Bradyrhizobium is extremely heterogeneous and has roles within the community including non-symbiotic nitrogen fixation.
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Affiliation(s)
- Chun-Zhi Jin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China; Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Xue-Wen Wu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China
| | - Ye Zhuo
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China
| | - Yizi Yang
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 210-037, China
| | - Taihua Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China
| | - Feng-Jie Jin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Long Jin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China.
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Li T, Zhuo Y, Jin CZ, Wu X, Ko SR, Jin FJ, Ahn CY, Oh HM, Lee HG, Jin L. Genomic insights into a novel species Rhodoferax aquaticus sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2020; 70:4653-4660. [PMID: 32672530 DOI: 10.1099/ijsem.0.004325] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel non-phototrophic member of the genus Rhodoferax was obtained from freshwater. The purpose of this study was to analyse the genome of a nonphototrophic strain and propose a new species based on its phylogenetic, genomic, physiological and chemotaxonomic characteristics. The results of phylogenetic analysis based on 16S rRNA gene sequences supports that the strain, designated Gr-4T, has a close relationship to the genus Rhodoferax. The observed average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain Gr-4T and its closest related strains were 72.3-74.6 % and 21.9-22.8 %, respectively. These values were much lower than the species separation thresholds for ANI or dDDH of 95-96 and 70 %, respectively, and in fact fall in the intergeneric range. Strain Gr-4T does not contain RuBisCO-related genes, but does contain GS/GOGAT pathway-related genes enabling nitrate ammonification. A polyphasic study and a genomic-level investigation were done to establish the taxonomic status of strain Gr-4T. Based on the phylogenetic, genomic and physiological differences, it is proposed that the isolate be classified to the genus Rhodoferax as Rhodoferax aquaticus sp. nov. with isolate Gr-4T (=KCTC 32394T=JCM 19166T) as the type strain.
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Affiliation(s)
- Taihua Li
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210-037, PR China
| | - Ye Zhuo
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210-037, PR China
| | - Chun-Zhi Jin
- Industrial Biomaterial Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.,Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Xuewen Wu
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210-037, PR China
| | - So-Ra Ko
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Feng-Jie Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210-037, PR China
| | - Chi-Yong Ahn
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Long Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210-037, PR China
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Yang Y, Jin CZ, Jin FJ, Li T, Lee JM, Kim CJ, Lee HG, Jin L. Caulobacter soli sp. nov., isolated from soil sampled at Jiri Mountain, Republic of Korea. Int J Syst Evol Microbiol 2020; 70:4158-4164. [PMID: 32525471 DOI: 10.1099/ijsem.0.004264] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, yellow-pigmented, aerobic, non-spore-forming, motile with a single polar flagellum and rod-shaped bacterium, Ji-3-8T, was isolated from a soil sample taken from Jiri Mountain, Republic of Korea. Comparative 16S rRNA gene sequence studies showed the isolate had clear affiliation with Alphaproteobacteria and the closest relatedness to Caulobacter rhizosphaerae KCTC 52515T, Caulobacter henricii ATCC 15253T, Caulobacter segnis ATCC 21756T, Caulobacter hibisci THG-AG3.4T, Caulobacter flavus RHGG3T and Caulobacter vibrioides CB51T showing 99.1, 98.9, 97.7, 97.6, 97.5 and 97.4 % 16S rRNA gene sequence similarity, respectively, and 94.7-96.5 % to the remaining species of genus Caulobacter. The predominant ubiquinone was Q-10 and the major fatty acids were C18 : 1 ω7c 11-methyl, C16 : 0, summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). The major polar lipids were found to be phosphatidylglycerol, two unidentified phosphoglycolipid and two unidentified glycolipids. The G+C content of the genomic DNA of strain Ji-3-8T was 68.1 mol%. Average nucleotide identity and digital DNA-DNA hybridization values of strain Ji-3-8T with C. rhizosphaerae KCTC 52515T, C. henricii ATCC 15253T, C. segnis ATCC 21756T, C. flavus RHGG3T and C. vibrioides were 79.7-87.7% and 23.0-34.3%, respectively. Based on the polyphasic evidence, it is proposed that strain Ji-3-8T forms a novel species in the genus Caulobacter, for which the name Caulobacter soli sp. nov. is proposed. The type strain is Ji-3-8T (=CCTCC AB 2019389T=KCTC 72990T).
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Affiliation(s)
- Yuanyuan Yang
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China
| | - Chun-Zhi Jin
- Industrial Biomaterial Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Feng-Jie Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China
| | - Taihua Li
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China
| | - Jong-Min Lee
- Industrial Biomaterial Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Chang-Jin Kim
- Industrial Biomaterial Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Long Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China
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Genomic and Metabolic Insights into Denitrification, Sulfur Oxidation, and Multidrug Efflux Pump Mechanisms in the Bacterium Rhodoferax sediminis sp. nov. Microorganisms 2020; 8:microorganisms8020262. [PMID: 32075304 PMCID: PMC7074706 DOI: 10.3390/microorganisms8020262] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/05/2020] [Accepted: 02/13/2020] [Indexed: 12/31/2022] Open
Abstract
This genus contains both phototrophs and nonphototrophic members. Here, we present a high-quality complete genome of the strain CHu59-6-5T, isolated from a freshwater sediment. The circular chromosome (4.39 Mbp) of the strain CHu59-6-5T has 64.4% G+C content and contains 4240 genes, of which a total of 3918 genes (92.4%) were functionally assigned to the COG (clusters of orthologous groups) database. Functional genes for denitrification (narGHJI, nirK and qnor) were identified on the genomes of the strain CHu59-6-5T, except for N2O reductase (nos) genes for the final step of denitrification. Genes (soxBXAZY) for encoding sulfur oxidation proteins were identified, and the FSD and soxF genes encoding the monomeric flavoproteins which have sulfide dehydrogenase activities were also detected. Lastly, genes for the assembly of two different RND (resistance-nodulation division) type efflux systems and one ABC (ATP-binding cassette) type efflux system were identified in the Rhodoferax sediminis CHu59-6-5T. Phylogenetic analysis based on 16S rRNA sequences and Average Nucleotide Identities (ANI) support the idea that the strain CHu59-6-5T has a close relationship to the genus Rhodoferax. A polyphasic study was done to establish the taxonomic status of the strain CHu59-6-5T. Based on these data, we proposed that the isolate be classified to the genus Rhodoferax as Rhodoferax sediminis sp. nov. with isolate CHu59-6-5T.
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