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Kim M, Cha IT, Lee KE, Park SJ. Chryseobacterium gotjawalense sp. nov. Isolated from Soil in the Volcanic Forest Gotjawal, Jeju Island. Curr Microbiol 2024; 81:187. [PMID: 38777886 DOI: 10.1007/s00284-024-03711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/21/2024] [Indexed: 05/25/2024]
Abstract
Strain wdc7T, a rod-shaped bacterium, was isolated from soil in the Gotjawal Forest on Jeju Island, South Korea. Strain wdc7T was Gram stain-negative, facultatively anaerobic, catalase- and oxidase positive, yellow pigmented, and non-flagellated. It grew at 4-37 °C and pH 5.0-8.0 in 0-3% (w/v) NaCl. 16S rRNA gene sequencing analysis revealed that strain wdc7T belonged to the genus Chryseobacterium and was most closely related to Chryseobacterium salivictor NBC 122T, with a sequence similarity of 98.51%. Menaquinone 6 was the sole respiratory quinone, and C15:0 anteiso, C15:0 iso, and summed feature 9 were the major fatty acids. The genome length was 3.30 Mbp, with a 37% G + C content. Average amino acid identity, average nucleotide identity, and digital DNA-DNA relatedness between strain wdc7T and C. salivictor NBC 122T were 93.52%, 92.80%, and 49.7%, respectively. Digital genomic and polyphasic analyses showed that strain wdc7T likely represented a new species of the genus Chryseobacterium. We proposed the name Chryseobacterium gotjawalense sp. nov., with wdc7T (= KCTC 92440T = JCM 35602T) as the type strain.
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea
| | - In-Tae Cha
- Climate Change and Environmental Biology Research Division, National Institute of Biological Resource, Incheon, 22689, South Korea
| | - Ki-Eun Lee
- Species Diversity Research Division, National Institute of Biological Resource, Incheon, 22689, South Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea.
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Jung H, Lee D, Lee S, Kong HJ, Park J, Seo YS. Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities. Microb Genom 2023; 9:001108. [PMID: 37796250 PMCID: PMC10634447 DOI: 10.1099/mgen.0.001108] [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] [Received: 05/08/2023] [Accepted: 09/17/2023] [Indexed: 10/06/2023] Open
Abstract
Members of the genus Chryseobacterium have attracted great interest as beneficial bacteria that can promote plant growth and biocontrol. Given the recent risks of climate change, it is important to develop tolerance strategies for efficient applications of plant-beneficial bacteria in saline environments. However, the genetic determinants of plant-growth-promoting and halotolerance effects in Chryseobacterium have not yet been investigated at the genomic level. Here, a comparative genomic analysis was conducted with seven Chryseobacterium species. Phylogenetic and phylogenomic analyses revealed niche-specific evolutionary distances between soil and freshwater Chryseobacterium species, consistent with differences in genomic statistics, indicating that the freshwater bacteria have smaller genome sizes and fewer genes than the soil bacteria. Phosphorus- and zinc-cycling genes (required for nutrient acquisition in plants) were universally present in all species, whereas nitrification and sulphite reduction genes (required for nitrogen- and sulphur-cycling, respectively) were distributed only in soil bacteria. A pan-genome containing 6842 gene clusters was constructed, which reflected the general features of the core, accessory and unique genomes. Halotolerant species with an accessory genome shared a Kdp potassium transporter and biosynthetic pathways for branched-chain amino acids and the carotenoid lycopene, which are associated with countermeasures against salt stress. Protein-protein interaction network analysis was used to define the genetic determinants of Chryseobacterium salivictor NBC122 that reduce salt damage in bacteria and plants. Sixteen hub genes comprised the aromatic compound degradation and Por secretion systems, which are required to cope with complex stresses associated with saline environments. Horizontal gene transfer and CRISPR-Cas analyses indicated that C. salivictor NBC122 underwent more evolutionary events when interacting with different environments. These findings provide deep insights into genomic adaptation to dynamic interactions between plant-growth-promoting Chryseobacterium and salt stress.
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Affiliation(s)
- Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, South Korea
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, South Korea
| | - Duyoung Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, South Korea
| | - Seungchul Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, South Korea
| | - Hee Jeong Kong
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, South Korea
| | - Jungwook Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, South Korea
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, South Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, South Korea
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Zhu GX, Chen X, Wu YJ, Wang HL, Jiao Y, Liu ZC, Zhang Y, Tang SK, Kong DJ, Cao YR. Chryseobacterium luquanense sp. nov., a casein-hydrolysing bacterium from the Jiaozi Mountain in Yunnan, PR China. Int J Syst Evol Microbiol 2023; 73. [PMID: 37728599 DOI: 10.1099/ijsem.0.006031] [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: 09/21/2023] Open
Abstract
Strain KC 927T was isolated during an investigation of the soil bacteria diversity on Jiaozi Mountain, central Yunnan, Southwest China. The strain was Gram-stain-negative, rod-shaped, non-motile, oxidase-negative, catalase-positive and aerobic. Results of 16S rRNA gene alignment and phylogenetic analysis indicated that strain KC 927T was a member of the genus Chryseobacterium and closely related to Chryseobacterium caseinilyticum GCR10T (98.4%), Chryseobacterium piscicola DSM 21068T (98.3 %) and 'Chryseobacterium formosus' CCTCC AB 2015118T (97.9 %). With a genome size of 4 348 708 bp, strain KC 927T had 33.5 mol% DNA G+C content and contained 4012 protein-coding genes and 77 RNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain KC 927T and C. caseinilyticum GCR10T, C. piscicola DSM 21068T and 'C. formosus' CCTCC AB 2015118T were 80.1, 79.6 and 90.7 %, and 25.5, 23.6 and 42.0 %, respectively. The main polar lipid of strain KC 927T was phosphatidylethanolamine and the respiratory quinone was MK-6. The major fatty acids (≥10 %) were iso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH. Evidence from phenotypic, phylogenetic and chemotaxonomic analyses support that strain KC 927T represents a new species of the genus Chryseobacterium, for which the name Chryseobacterium luquanense sp. nov. is proposed. The type strain is KC 927T (=CGMCC 1.18760T=JCM 35707T).
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Affiliation(s)
- Guo-Xing Zhu
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Xiu Chen
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
- School of Medicine, Kunming University, Kunming, Yunnan, PR China
| | - Ya-Jie Wu
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Hai-Long Wang
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Yu Jiao
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Zi-Chao Liu
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Yue Zhang
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
| | - De-Jun Kong
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, PR China
| | - Yan-Ru Cao
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
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Zhang L, Wang Y, Kong D, Ma Q, Li Y, Xing Z, Ruan Z. Chryseobacterium herbae Isolated from the Rhizospheric Soil of Pyrola calliantha H. Andres in Segrila Mountain on the Tibetan Plateau. Microorganisms 2023; 11:2017. [PMID: 37630577 PMCID: PMC10459008 DOI: 10.3390/microorganisms11082017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/22/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
A non-motile, Gram-staining-negative, orange-pigmented bacterium called herbae pc1-10T was discovered in Tibet in the soil around Pyrola calliantha H. Andres' roots. The isolate thrived in the temperature range of 10-30 °C (optimal, 25 °C), pH range of 5.0-9.0 (optimum, pH = 6.0), and the NaCl concentration range of 0-1.8% (optimal, 0%). The DNA G+C content of the novel strain was 37.94 mol%. It showed the function of dissolving organophosphorus, acquiring iron from the environment by siderophore and producing indole acetic acid. Moreover, the genome of strain herbae pc1-10T harbors two antibiotic resistance genes (IND-4 and AdeF) encoding a β-lactamase, and the membrane fusion protein of the multidrug efflux complex AdeFGH; antibiotic-resistance-related proteins were detected using the Shotgun proteomics technology. The OrthoANIu values between strains Chryseobacterium herbae pc1-10T; Chryseobacterium oleae CT348T; Chryseobacterium kwangjuense KJ1R5T; and Chryseobacterium vrystaatense R-23566T were 90.94%, 82.96%, and 85.19%, respectively. The in silico DDH values between strains herbae pc1-10T; C. oleae CT348T; C. kwangjuense KJ1R5T; and C. vrystaatense R-23566T were 41.7%, 26.6%, and 29.7%, respectively. Chryseobacterium oleae, Chryseobacterium vrystaatense, and Chryseobacterium kwangjuense, which had 16S rRNA gene sequence similarity scores of 97.80%, 97.52%, and 96.75%, respectively, were its closest phylogenetic relatives. Chryseobacterium herbae sp. nov. is proposed as the designation for the strain herbae pc1-10T (=GDMCC 1.3255 = JCM 35711), which represented a type species based on genotypic and morphological characteristics. This study provides deep knowledge of a Chryseobacterium herbae characteristic description and urges the need for further genomic studies on microorganisms living in alpine ecosystems, especially around medicinal plants.
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Affiliation(s)
- Li Zhang
- College of Life Sciences, Yantai University, Yantai 264005, China;
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (D.K.); (Q.M.)
| | - Yan Wang
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (D.K.); (Q.M.)
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China;
| | - Delong Kong
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (D.K.); (Q.M.)
| | - Qingyun Ma
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (D.K.); (Q.M.)
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Li
- College of Life Sciences, Yantai University, Yantai 264005, China;
| | - Zhen Xing
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China;
| | - Zhiyong Ruan
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (D.K.); (Q.M.)
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Pan S, Zhang W, Li Y, Zhou P, Zhang H, Niu L, Wang L. Understanding the ecological processes governing hydrophyte-associated bacterial communities involved in hydrophyte growth and development. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 312:114952. [PMID: 35339791 DOI: 10.1016/j.jenvman.2022.114952] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/11/2022] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
Maintaining hydrophyte growth has been a major focus of aquatic ecological research. The hydrophyte microbiome plays a key role in the growth and health of hydrophytes, but the ecological processes regulating the assembly and function of hydrophyte microbial communities remain unclear. This knowledge gap limits the efficacy of managing microbiomes to enhance the capacity of hydrophytes to restore the aquatic environment. Here, we sampled three typical hydrophytes (Ceratophyllum demersum, Nymphoides peltatum, and Potamogeton crispus) to study the ecological process governing hydrophyte-associated bacterial communities. The results demonstrated that hydrophyte-associated bacterial communities were affected more by the hydrophyte host species (HEEI = 2.40) than by the environment (HEEI = 1.00). The hydrophyte host species not only affected bacterial community assembly, but reduced the diversity and network complexity of the bacterial community relative to that of the environment. Furthermore, the core taxa of two hydrophytes were identified. Chryseobacterium was the core taxon of N. peltatum, and Burkholderia-Caballeronia-Paraburkholderia, Pseudolabrys, and Pajaroellobacter were the core taxa of P. crispus. The core taxa of P. crispus were closely related to potential denitrification-related functions of bacteria and revealed that P. crispus played a role in denitrification during aquatic ecological restoration. Overall, the results of this study highlight the need to develop approaches employing hydrophyte-associated bacteria to promote the development of hydrophytes, which will be essential for increasing the utility of hydrophyte microbiomes in the future and enhancing aquatic ecological restoration.
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Affiliation(s)
- Shenyang Pan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Pengcheng Zhou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
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Park H, Seo SI, Lim JH, Song J, Seo JH, Kim PI. Screening of Carbofuran-Degrading Bacteria Chryseobacterium sp. BSC2-3 and Unveiling the Change in Metabolome during Carbofuran Degradation. Metabolites 2022; 12:metabo12030219. [PMID: 35323662 PMCID: PMC8950912 DOI: 10.3390/metabo12030219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 02/01/2023] Open
Abstract
Carbofuran is one of the most commonly used N-methylcarbamate-based pesticides and is excellent for controlling pests; however, carbofuran also causes soil and water pollution. Although various studies have been conducted on the bioremediation of pesticide-contaminated soil, the changes occurring in the metabolome during the bioremediation of carbofuran are not fully understood. In this study, the intracellular and extracellular metabolites of the Chryseobacterium sp. BSC2-3 strain were analysed during carbofuran degradation by using a liquid chromatography–mass spectrometry-based metabolomics approach. We found that the BSC2-3 strain extracellularly transformed carbofuran into 3-hydroxycarbofuran. Intracellular metabolite analysis revealed that carbofuran mainly affected aminobenzoate degradation, ubiquinone and terpenoid-quinone biosynthesis, and arginine and proline metabolism. Carbofuran especially affected the metabolic pathway for the degradation of naphthalene and aminobenzoate. Metabolomics additionally revealed that the strain produces disease resistance inducers and plant growth regulators. We also identified the genes involved in the production of indole-3-acetic acid, which is one of the most active auxins. Overall, we identified the metabolic changes induced in carbofuran-degrading bacteria and the genes predicted to be responsible for the degradation of carbofuran.
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Affiliation(s)
- Haeseong Park
- Center for Industrialization of Agricultural and Livestock Microorganisms, 241 Cheomdangwahak-ro, Jeongeup-si 56212, Korea; (H.P.); (S.I.S.); (J.-H.L.)
| | - Sun Il Seo
- Center for Industrialization of Agricultural and Livestock Microorganisms, 241 Cheomdangwahak-ro, Jeongeup-si 56212, Korea; (H.P.); (S.I.S.); (J.-H.L.)
| | - Ji-Hwan Lim
- Center for Industrialization of Agricultural and Livestock Microorganisms, 241 Cheomdangwahak-ro, Jeongeup-si 56212, Korea; (H.P.); (S.I.S.); (J.-H.L.)
| | - Jaekyeong Song
- Division of Agricultural Microbiology, National Academy of Agricultural Science, 166 Nongsaengmyeong-ro, Wanju-gun 55365, Korea;
| | - Joo-Hyun Seo
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul 02707, Korea
- Correspondence: (J.-H.S.); (P.I.K.); Tel.: +82-63-536-6001 (P.I.K.)
| | - Pyoung Il Kim
- Center for Industrialization of Agricultural and Livestock Microorganisms, 241 Cheomdangwahak-ro, Jeongeup-si 56212, Korea; (H.P.); (S.I.S.); (J.-H.L.)
- Correspondence: (J.-H.S.); (P.I.K.); Tel.: +82-63-536-6001 (P.I.K.)
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Oren A, Garrity GM. List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication. Int J Syst Evol Microbiol 2020; 70:4844-4847. [PMID: 32993851 DOI: 10.1099/ijsem.0.004366] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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