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Lee H, Chaudhary DK, Lim OB, Kim DU. Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov., isolated from forest soil. Arch Microbiol 2023; 206:42. [PMID: 38147140 DOI: 10.1007/s00203-023-03763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/27/2023]
Abstract
During the study of microbial ecology of forest soil, two circular, white-colored bacterial colonies were isolated and labeled as strains TW38T and TW40T. Both strains were catalase positive and oxidase negative. Strains TW38T and TW40T demonstrated growth within a temperature range of 10-37 °C and 18-37 °C, respectively, and thrived within a pH range of 5.5-9.0 and 6.0-8.0, respectively. Both strains grew at 0-2.0% (w/v) NaCl concentrations. The phylogenetic analysis indicated that strains TW38T and TW40T affiliated to the genus Paenibacillus, with the closest neighbors being Paenibacillus montanisoli RA17T (98.6%) and Paenibacillus arachidis E3T (95.4%), respectively. In both strains, the sole respiratory quinone was MK-7, the signature fatty acid was antiso-C15:0, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The digital DNA-DNA hybridization and the average nucleotide identity values between TW38T, TW40T, and closest reference strains were < 29.0% and < 85.0%, respectively. The DNA G+C content of TW38T and TW40T was 54.5% and 57.1%, respectively. In general, the phylogenetic, genomics, chemotaxonomic, and phenotypic data support the differentiation of TW38T and TW40T from other closest members of the genus Paenibacillus. Thus, we conclude both strains TW38T and TW40T represent novel species of the genus Paenibacillus, for which the name Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov. are proposed, respectively. The type strain of Paenibacillus silvisoli is TW38T (= KCTC 43468T = NBRC 116015T) and type strain of Paenibacillus humicola is TW40T (= KCTC 43469T = NBRC 116016T).
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Affiliation(s)
- Hyosun Lee
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, College of Science and Technology, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea
| | - Oung Bin Lim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea.
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Chhe C, Uke A, Baramee S, Tachaapaikoon C, Pason P, Waeonukul R, Ratanakhanokchai K, Kosugi A. Insulambacter thermoxylanivorax sp. nov., a thermophilic xylanolytic bacterium isolated from compost. Int J Syst Evol Microbiol 2023; 73. [PMID: 36943336 DOI: 10.1099/ijsem.0.005724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
We isolated and analysed a Gram-negative, facultatively thermophilic, xylan-degrading bacterium that we designated as strain DA-C8T. The strain was isolated from compost from Ishigaki Island, Japan, by enrichment culturing using beech wood xylan as the sole carbon source. The strain showed high xylan degradation ability under anaerobic growth conditions. The isolate grew at 37-60 °C (optimum, 55 °C) and pH 4.0-11.0 (optimum, pH 9.0). As well as xylan, strain DA-C8T could use polysaccharides such as arabinoxylan and galactan as carbon sources. Comparison of 16S rRNA gene sequences indicated that strain DA-C8T was most closely related to Paenibacillus cisolokensis LC2-13AT (93.9 %) and Paenibacillus chitinolyticus HSCC596 (93.5 %). In phylogenetic analysis, strain DA-C8T belonged to the same lineage as Xylanibacillus composti K13T (92.5 %), but there was less statistical support for branching (70 %). Digital DNA-DNA hybridization, average nucleotide identity values and average amino acid sequence identity between strain DA-C8T and P. cisolokensis LC2-13AT were 21.8, 68.3 and 58.2 %, respectively. Those between strain DA-C8T and X. composti K13 were 23.7, 67.7 and 57.6 %, respectively. The whole-genome DNA G+C content of strain DA-C8T was 52.3 mol%. The major cellular fatty acids were C16 : 0 (42.9 %), anteiso-C15 : 0 (20.0 %) and anteiso-C17 : 0 (16.7 %), the major quinone was menaquinone 7, and the major polar lipids were unidentified glycolipids. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, a novel genus is proposed-Insulambacter gen. nov.-for the novel species Insulambacter thermoxylanivorax sp. nov. The type strain is DA-C8T (=JCM 34211T=DSM 111723T).
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Affiliation(s)
- Chinda Chhe
- Faculty of Agro-Industry, Royal University of Agriculture, Phnom Penh 2695, Cambodia
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Ayaka Uke
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Sirilak Baramee
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Chakrit Tachaapaikoon
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Patthra Pason
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Rattiya Waeonukul
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Akihiko Kosugi
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
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Duhamel S, Hamilton CW, Pálsson S, Björnsdóttir SH. Microbial Response to Increased Temperatures Within a Lava-Induced Hydrothermal System in Iceland: An Analogue for the Habitability of Volcanic Terrains on Mars. ASTROBIOLOGY 2022; 22:1176-1198. [PMID: 35920884 DOI: 10.1089/ast.2021.0124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fossil hydrothermal systems on Mars are important exploration targets because they may have once been habitable and could still preserve evidence of microbial life. We investigated microbial communities within an active lava-induced hydrothermal system associated with the 2014-2015 eruption of Holuhraun in Iceland as a Mars analogue. In 2016, the microbial composition in the lava-heated water differed substantially from that of the glacial river and spring water sources that fed into the system. Several taxonomic and metabolic groups were confined to the water emerging from the lava and some showed the highest sequence similarities to subsurface ecosystems, including to the predicted thermophilic and deeply branching Candidatus Acetothermum autotrophicum. Measurements show that the communities were affected by temperature and other environmental factors. In particular, comparing glacial river water incubated in situ (5.7°C, control) with glacial water incubated within a lava-heated stream (17.5°C, warm) showed that microbial abundance, richness, and diversity increased in the warm treatment compared with the control, with the predicted major metabolism shifting from lithotrophy toward organotrophy and possibly phototrophy. In addition, thermophilic bacteria isolated from the lava-heated water and a nearby acidic hydrothermal system included the known endospore-formers Geobacillus stearothermophilus and Paenibacillus cisolokensis as well as a potentially novel taxon within the order Hyphomicrobiales. Similar lava-water interactions on Mars could therefore have generated habitable environments for microbial communities.
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Affiliation(s)
- Solange Duhamel
- Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
- Lunar and Planetary Laboratory, University of Arizona, Tucson, Arizona, USA
- Division of Biology and Paleo Environment, Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, USA
| | | | - Snæbjörn Pálsson
- Department of Biology, University of Iceland, Reykjavík, Iceland
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Chhe C, Uke A, Baramee S, Tachaapaikoon C, Pason P, Waeonukul R, Ratanakhanokchai K, Kosugi A. Characterization of a thermophilic facultatively anaerobic bacterium Paenibacillus sp. strain DA-C8 that exhibits xylan degradation under anaerobic conditions. J Biotechnol 2021; 342:64-71. [PMID: 34688788 DOI: 10.1016/j.jbiotec.2021.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/22/2021] [Accepted: 10/13/2021] [Indexed: 10/20/2022]
Abstract
The screening, identification, and study of the functional properties of cellulolytic xylanolytic bacteria are crucial for the construction of applicable bioprocesses. The thermophilic facultatively anaerobic, xylanolytic bacterial strain DA-C8 (=JCM34211=DSM111723) exhibiting efficient xylan degradation was newly isolated from compost. Strain DA-C8 completely degraded 1% beechwood xylan within 4 days under anaerobic conditions. By 16S rRNA gene sequence homology and phylogenetic tree analysis, strain DA-C8 was closely related to Paenibacillus cisolokensis and Xylanibacillus composti; however, the average nucleotide identity and digital DNA-DNA hybridization values based on genome information and the carbon source utilization properties indicated that strain DA-C8 belongs to Paenibacillus rather than Xylanibacillus. The gene numbers of xylanase and endoglucanase of strain DA-C8 and X. composti were not different; however, strain DA-C8 had higher abundance of α-L-arabinofuranosidase, β-xylosidase, and β-glucosidase than X. composti. Strain DA-C8 showed decreased xylan and corn hull degradation abilities and growth on xylan medium under aerobic conditions. Quantitative PCR showed high expression of xylan and cellulose degradation genes under anaerobic conditions, but the genes were repressed under aerobic conditions, indicating that strain DA-C8 controls polysaccharide degradation depending on the aeration conditions. Strain DA-C8 is a new species of Paenibacillus with a unique polysaccharide degradation system.
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Affiliation(s)
- Chinda Chhe
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Faculty of Agro-Industry, Royal University of Agriculture, Phnom Penh 2695, Cambodia; Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Ayaka Uke
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Sirilak Baramee
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan; Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Khanok Ratanakhanokchai
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Akihiko Kosugi
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan.
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Uke A, Chhe C, Baramee S, Tachaapaikoon C, Pason P, Waeonukul R, Ratanakhanokchai K, Kosugi A. Draft genome sequence data of Paenibacillus cisolokensis strain LC2-13A and Xylanibacillus composti strain K-13. Data Brief 2021; 38:107361. [PMID: 34557574 PMCID: PMC8446789 DOI: 10.1016/j.dib.2021.107361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/30/2021] [Accepted: 09/06/2021] [Indexed: 11/30/2022] Open
Abstract
To discover more efficient degradation processes of lignocellulosic biomass, it is still important to analyze genomic and enzymatic data from bacteria that have strong xylanolytic ability. Here, we present the draft genome sequences of the xylanolytic bacteria Paenibacillus cisolokensis strain LC2-13A and Xylanibacillus composti strain K-13 that are closest to Paenibacillus sp. strain DA-C8, which has strong xylan degradation ability under anaerobic growth conditions. Whole-genome sequencing on the Ion GeneStudio S5 System yielded 277 contigs with total size 5,305,208 bp and G+C content 52.3 mol% for strain LC2-13A and 115 contigs with total size 4,652,266 bp and G+C content of 56.2 mol% for strain K-13. The LC2-13A genome had 5,744 protein-coding sequences (CDSs), 57 tRNAs, and 4 clustered regularly interspaced short palindromic repeats (CRISPRs), and the K-13 genome had 4,388 CDSs, 1 rRNA gene, 45 tRNAs, and 5 CRISPRs. The CDSs of LC2-13A and K-13 encoded the following carbohydrate-active enzymes: 98 and 67 glycoside hydrolases, 31 and 29 glycosyl transferases, 23 and 17 carbohydrate esterases, and 13 and 37 carbohydrate-binding modules, respectively. The whole-genome sequences of LC2-13A and K-13 have been deposited in DDBJ/ENA/GenBank under accession numbers BOVK00000000 and BOVJ00000000. The versions described in this paper are version 1.
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Affiliation(s)
- Ayaka Uke
- Japan International Research Center for Agricultural Sciences (JIRCAS), Biological Resources and Post-Harvest Division, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Chinda Chhe
- Japan International Research Center for Agricultural Sciences (JIRCAS), Biological Resources and Post-Harvest Division, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Sirilak Baramee
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Khanok Ratanakhanokchai
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Akihiko Kosugi
- Japan International Research Center for Agricultural Sciences (JIRCAS), Biological Resources and Post-Harvest Division, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Ningsih F, Sari DCAF, Rachmania MK, Yabe S, Yokota A, Oetari A, Sjamsuridzal W. Isolation and 16S rRNA gene sequences analysis of thermophilic Actinobacteria isolated from soil in Cisolok geothermal area, West Java, Indonesia. ACTA ACUST UNITED AC 2020. [DOI: 10.1088/1755-1315/457/1/012015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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