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Park CE, Jo YJ, Jung DR, Park HC, Shin JH. Comparative Analysis of Gut Microbiota between Captive and Wild Long-Tailed Gorals for Ex Situ Conservation. Microorganisms 2024; 12:1419. [PMID: 39065187 PMCID: PMC11278867 DOI: 10.3390/microorganisms12071419] [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: 07/01/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The long-tailed goral is close to extinction, and ex situ conservation is essential to prevent this phenomenon. Studies on the gut microbiome of the long-tailed goral are important for understanding the ecology of this species. We amplified DNA from the 16S rRNA regions and compared the microbiomes of wild long-tailed gorals and two types of captive long-tailed gorals. Our findings revealed that the gut microbiome diversity of wild long-tailed gorals is greatly reduced when they are reared in captivity. A comparison of the two types of captive long-tailed gorals confirmed that animals with a more diverse diet exhibit greater gut microbiome diversity. Redundancy analysis confirmed that wild long-tailed gorals are distributed throughout the highlands, midlands, and lowlands. For the first time, it was revealed that the long-tailed goral are divided into three groups depending on the height of their habitat, and that the gut bacterial community changes significantly when long-tailed gorals are raised through ex situ conservation. This provides for the first time a perspective on the diversity of food plants associated with mountain height that will be available to long-tailed goral in the future.
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Affiliation(s)
- Chang-Eon Park
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (C.-E.P.); (Y.-J.J.); (D.-R.J.)
- Institute of Ornithology, Ex Situ Conservation Institution Designated by the Ministry of Environment, Gumi 39105, Republic of Korea;
| | - Young-Jae Jo
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (C.-E.P.); (Y.-J.J.); (D.-R.J.)
| | - Da-Ryung Jung
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (C.-E.P.); (Y.-J.J.); (D.-R.J.)
| | - Hee-Cheon Park
- Institute of Ornithology, Ex Situ Conservation Institution Designated by the Ministry of Environment, Gumi 39105, Republic of Korea;
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (C.-E.P.); (Y.-J.J.); (D.-R.J.)
- NGS Core Facility, Kyungpook National University, Daegu 41566, Republic of Korea
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Lee HJ, Whang KS. Oryzibacter oryziterrae gen. nov., sp. nov., isolated from rice paddy soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37737839 DOI: 10.1099/ijsem.0.006033] [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: 09/23/2023] Open
Abstract
A novel Gram-stain-negative, aerobic, motile and pleomorphic rod-shaped bacterial strain, designated COJ-58T, was isolated from rice paddy soil. Strain COJ-58T grew optimally at 20-30 °C, at pH 5.0-8.0 and with 0-1.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain COJ-58T forms a distinct lineage within the family Pleomorphomonadaceae, with highest similarity to Pleomorphomonas carboxyditropha SVCO-16T (95.9 %), Pleomorphomonas koreensis Y9T (95.8 %), Pleomorphomonas oryzae F-7T (95.7 %) and Pleomorphomonas diazotrophica R5-392T (95.6 %), respectively. The average nucleotide identity, digital DNA-DNA hybridization, average amino acid identity and percentage of conserved proteins values between the genomes of strain COJ-58T and its closely related taxa are ≤77.2 %, ≤21.6 %, ≤68.3 % and ≤61.3 %, respectively. The genome size of strain COJ-58T is 4.9 Mb and the genomic DNA G + C content is 63.7 mol%. The major fatty acids are C18 : 1 ω7c, C16 : 0 and summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I). The differential phenotypic and genotypic characteristics of strain COJ-58T indicate that it represents a novel genus and species, for which the name Oryzibacter oryziterrae gen. nov., sp. nov. is proposed, with strain COJ-58T (=KACC 22108T=JCM 34744T) as the type strain.
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Affiliation(s)
- Hyo-Jin Lee
- Institute of Microbial Ecology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
- Department of Microbial Biotechnology, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
- Department of Microbial Biotechnology, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
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Genome-based taxonomic classification of the closest-to-Comamonadaceae group supports a new family Sphaerotilaceae fam. nov. and taxonomic revisions. Syst Appl Microbiol 2022; 45:126352. [DOI: 10.1016/j.syapm.2022.126352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/06/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022]
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Jin H, Zhang D, Yan Y, Yang C, Fang B, Li X, Shao Y, Wang H, Yue J, Wang Y, Cheng H, Shi Y, Qin F. Short-term application of chicken manure under different nitrogen rates alters structure and co-occurrence pattern but not diversity of soil microbial community in wheat field. Front Microbiol 2022; 13:975571. [PMID: 36160226 PMCID: PMC9490364 DOI: 10.3389/fmicb.2022.975571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
Manure application is an effective way to improve the utilization efficiency of organic resources and alleviate the adverse effects of long-term application of chemical fertilizers. However, the impact of applying manure under different nitrogen rates on soil microbial community in wheat field remains unclear. Treatments with and without chicken manure application under three nitrogen rates (N 135, 180 and 225 kg⋅hm-2) were set in wheat field. Soil organic carbon, available nutrients, and abundance, diversity, structure and co-occurrence pattern of soil microbial community at wheat maturity were investigated. Compared with no manure application, chicken manure application increased the soil organic carbon and available phosphorus, while the effects on soil mineral nitrogen and available potassium varied with different nitrogen rates. Chicken manure application significantly increased soil bacterial abundance under the nitrogen fertilization of 135 and 225 kg⋅hm-2, increased soil fungal abundance under the nitrogen fertilization of 135 kg⋅hm-2, but decreased soil fungal abundance under the nitrogen fertilization of 180 and 225 kg⋅hm-2 (P < 0.05). There was no significant difference in alpha diversity indices of soil microbial communities between treatments with and without chicken manure application under different nitrogen rates (P > 0.05). Chicken manure application and its interaction with nitrogen rate significantly changed soil bacterial and fungal community structures (P < 0.05). There were significantly different taxa of soil microbial communities between treatments with and without chicken manure application. Chicken manure application reduced the ecological network complexity of soil bacterial community and increased that of soil fungal community. In summary, the responses of soil available nutrients and microbial abundance to applying chicken manure varied with different nitrogen rates. One growing season application of chicken manure was sufficient to alter the soil microbial community structure, composition and co-occurrence pattern, whereas not significantly affected soil microbial community diversity.
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Affiliation(s)
- Haiyang Jin
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Deqi Zhang
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yaqian Yan
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Cheng Yang
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Baoting Fang
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiangdong Li
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yunhui Shao
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hanfang Wang
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Junqin Yue
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yanjing Wang
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hongjian Cheng
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yanhua Shi
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Feng Qin
- Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
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Le VV, Ko SR, Lee SA, Kang M, Oh HM, Ahn CY. Caenimonas aquaedulcis sp. nov., Isolated from Freshwater of Daechung Reservoir during Microcystis Bloom. J Microbiol Biotechnol 2022; 32:575-581. [PMID: 35354765 PMCID: PMC9628874 DOI: 10.4014/jmb.2201.01023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/15/2022]
Abstract
A Gram-stain-negative, white-coloured, and rod-shaped bacterium, strain DR4-4T, was isolated from Daechung Reservoir, Republic of Korea, during Microcystis bloom. Strain DR4-4T was most closely related to Caenimonas terrae SGM1-15T and Caenimonas koreensis EMB320T with 98.1% 16S rRNA gene sequence similarities. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain DR4-4T and closely related type strains were below 79.46% and 22.30%, respectively. The genomic DNA G+C content was 67.5%. The major cellular fatty acids (≥10% of the total) were identified as C16:0, cyclo C17:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c), and summed feature 8 (C18:1ω7c and/or C18:1ω6c). Strain DR4-4T possessed phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol as the main polar lipids and Q-8 as the respiratory quinone. The polyamine profile was composed of putrescine, cadaverine, and spermidine. The results of polyphasic characterization indicated that the isolated strain DR4-4T represents a novel species within the genus Caenimonas, for which the name Caenimonas aquaedulcis sp. nov. is proposed. The type strain is DR4-4T (=KCTC 82470T =JCM 34453T).
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Affiliation(s)
- Ve Van Le
- Cell factory Research Centre, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea,Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - So-Ra Ko
- Cell factory Research Centre, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Sang-Ah Lee
- Environmental Safety Groups, Korea Institute of Science and Technology (KIST) Europe, Saarbrücken 66123, Germany
| | - Mingyeong Kang
- Cell factory Research Centre, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea,Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Hee-Mock Oh
- Cell factory Research Centre, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea,Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Chi-Yong Ahn
- Cell factory Research Centre, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea,Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea,Corresponding author Phone: +82-42-860-4329 Fax: +82-42-860-4594 E-mail:
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Chhetri G, Kim J, Kim I, Kang M, So Y, Seo T. Oryzicola mucosus gen. nov., sp. nov., a novel slime producing bacterium belonging to the family Phyllobacteriaceae isolated from the rhizosphere of rice plants. Antonie van Leeuwenhoek 2021; 114:1925-1934. [PMID: 34491486 DOI: 10.1007/s10482-021-01651-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
A novel Gram-stain negative, asporogenous, slimy, rod-shaped, non-motile bacterium ROOL2T was isolated from the root samples collected from a rice field located in Ilsan, South Korea. Phylogenetic analysis of the 16S rRNA sequence showed 96.5% similarity to Tianweitania sediminis Z8T followed by species of genera Mesorhizobium (96.4-95.6%), Aquabacterium (95.9-95.7%), Rhizobium (95.8%) and Ochrobactrum (95.6%). Strain ROOL2T grew optimally at 30 °C in the presence of 1-6% (w/v) NaCl and at pH 7.5. The major respiratory quinone was ubiquinone-10 and the major cellular fatty acids were C18:1ω7c, summed feature 4 (comprising iso-C17:1 I and/or anteiso-C17:1 B) and summed feature 8 (comprising C18:1ω6c and/or C18:1ω7c). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylglycerol, one unidentified aminolipid and two unidentified lipids. The assembled draft genome of strain ROOL2T had 28 contigs with N50 value of 656,326 nt, total length of 4,894,583 bp and a DNA G + C content of 61.5%. The average amino acid identity (AAI) values of strain ROOL2T against the genomes of related members belonging to the same family were below 68% and the ANI and dDDH values between the strain ROOL2T and the type strains of phylogenetically related species were 61.8-76.3% and 19.4-21.1%, respectively. Strain ROOL2T only produces carotenoid-type pigment when grown on LB agar and slime on R2A agar. In the presence of tryptophan, strain ROOL2T produced indole acetic acid (IAA), a phytohormone in plant growth and development. Gene clusters for indole-3-glycerol phosphatase and tryptophan synthase were found in the genome of strain ROOL2T. The genotypic and phenotypic characteristics indicated that strain ROOL2T represents a novel genus belonging the family Phyllobacteriaceae, for which the name Oryzicola mucosus gen. nov., sp. nov. is proposed. The type strain is ROOL2T (KCTC 82711 T = NBRC 114717 T).
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea.
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Bird LJ, Kuenen JG, Osburn MR, Tomioka N, Ishii S, Barr C, Nealson KH, Suzuki S. Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov., Serpentinimonas barnesii sp. nov. and Serpentinimonas maccroryi sp. nov., hyperalkaliphilic and facultative autotrophic bacteria isolated from terrestrial serpentinizing springs. Int J Syst Evol Microbiol 2021; 71:004945. [PMID: 34379584 PMCID: PMC8513617 DOI: 10.1099/ijsem.0.004945] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/02/2021] [Indexed: 11/18/2022] Open
Abstract
Three highly alkaliphilic bacterial strains designated as A1T, H1T and B1T were isolated from two highly alkaline springs at The Cedars, a terrestrial serpentinizing site. Cells from all strains were motile, Gram-negative and rod-shaped. Strains A1T, H1T and B1T were mesophilic (optimum, 30 °C), highly alkaliphilic (optimum, pH 11) and facultatively autotrophic. Major cellular fatty acids were saturated and monounsaturated hexadecenoic and octadecanoic acids. The genome size of strains A1T, H1T and B1T was 2 574 013, 2 475 906 and 2 623 236 bp, and the G+C content was 66.0, 66.2 and 66.1 mol%, respectively. Analysis of the 16S rRNA genes showed the highest similarity to the genera Malikia (95.1-96.4 %), Macromonas (93.0-93.6 %) and Hydrogenophaga (93.0-96.6 %) in the family Comamonadaceae. Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis based on core gene sequences revealed that the isolated strains diverged from the related species, forming a distinct branch. Average amino acid identity values of strains A1T, H1T and B1T against the genomes of related members in this family were below 67 %, which is below the suggested threshold for genera boundaries. Average nucleotide identity by blast values and digital DNA-DNA hybridization among the three strains were below 92.0 and 46.6 % respectively, which are below the suggested thresholds for species boundaries. Based on phylogenetic, genomic and phenotypic characterization, we propose Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov. (type strain A1T=NBRC 111848T=DSM 103917T), Serpentinimonas barnesii sp. nov. (type strain H1T= NBRC 111849T=DSM 103920T) and Serpentinimonas maccroryi sp. nov. (type strain B1T=NBRC 111850T=DSM 103919T) belonging to the family Comamonadaceae. We have designated Serpentinimonas raichei the type species for the genus because it is the dominant species in The Cedars springs.
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Affiliation(s)
- Lina J. Bird
- Center for Bio/Molecular Science and Engineering Naval Research Lab, 4555 Overlook Ave S.W., Washington DC 20375, USA
- Department of Earth Sciences, University of Southern California, 35 W. 37th St. SHS 560, Los Angeles, California 90089, USA
| | - J. Gijs Kuenen
- Department of Earth Sciences, University of Southern California, 35 W. 37th St. SHS 560, Los Angeles, California 90089, USA
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, Netherlands
| | - Magdalena R. Osburn
- Department of Earth and Planetary Sciences, Weinberg College of Arts & Sciences. Northwestern University Evanston, Evanston, USA
| | - Naotaka Tomioka
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe B200, Nankoku, Kochi 783-8502, Japan
| | - Shun’ichi Ishii
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe B200, Nankoku, Kochi 783-8502, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), JAMSTEC, Natsushima 2-15, Yokosuka, Kanagawa 237-0061, Japan
| | - Casey Barr
- Department of Earth Sciences, University of Southern California, 35 W. 37th St. SHS 560, Los Angeles, California 90089, USA
| | - Kenneth H. Nealson
- Department of Earth Sciences, University of Southern California, 35 W. 37th St. SHS 560, Los Angeles, California 90089, USA
| | - Shino Suzuki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe B200, Nankoku, Kochi 783-8502, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), JAMSTEC, Natsushima 2-15, Yokosuka, Kanagawa 237-0061, Japan
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), 3-1-1 Yoshinodai, Chuo-ku, Sagamihara, Kanagawa 252-5210, Japan
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