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Genome mining revealed polyhydroxybutyrate biosynthesis by Ramlibacter agri sp. nov., isolated from agriculture soil in Korea

Authors
Dahal, Ram HariKim, JungminChaudhary, Dhiraj KumarLe, Thi Tuyet NhanKim, Dong-UkJang, HyeinKim, Jaisoo
Issue Date
May-2022
Publisher
SPRINGER
Keywords
Ramlibacter agri; Agriculture soil; Polyhydroxybutyrate; Biodegradable plastics; PHB biosynthesis
Citation
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY, v.115, no.5, pp 563 - 572
Pages
10
Indexed
SCIE
SCOPUS
Journal Title
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
Volume
115
Number
5
Start Page
563
End Page
572
URI
https://scholar.korea.ac.kr/handle/2021.sw.korea/186222
DOI
10.1007/s10482-022-01721-z
ISSN
0003-6072
1572-9699
Abstract
A white-colony-forming, facultative anaerobic, motile and Gram-stain-negative bacterium, designated G-1-2-2( T) was isolated from soil of agriculture field near Kyonggi University, Republic of Korea. Strain G-1-2-2( T) synthesized the polyhydroxybutyrate and could grow at 10-35 degrees C. The phylogenetic analysis based on 16S rRNA gene sequence showed that, strain G-1-2-2( T) formed a lineage within the family Comamonadaceae and clustered as a member of the genus Ramlibacter. The 16S rRNA gene sequence of strain G-1-2-2( T) showed high sequence similarities with Ramlibacter ginsenosidimutans BXN5-27( T) (97.9%), Ramlibacter monticola G-3-2( T) (97.9%) and Ramlibacter alkalitolerans CJ661(T) (97.5%). The sole respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and an unidentified phospholipid. The principal cellular fatty acids were C-16:0, cyclo-C-17:0, summed feature 3 (C-16:1 omega 7c and/or C-16:1 omega 6c) and summed feature 8 (C-18:1 omega 7c and/or C-18:1 omega 6c). The genome of strain G-1-2-2( T) was 7,200,642 bp long with 13 contigs, 6,647 protein-coding genes, and DNA G + C content of 68.9%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain G-1-2-2( T) and close members were <= 81.2 and 24.1%, respectively. The genome of strain G-1-2-2( T) showed eight putative biosynthetic gene clusters responsible for various secondary metabolites. Genome mining revealed the presence of atoB, atoB2, phaS, phbB, phbC, and bhbD genes in the genome which are responsible for polyhydroxybutyrate biosynthesis. Based on these data, strain G-1-2-2( T) represents a novel species in the genus Ramlibacter, for which the name Ramlibacter agri sp. nov. is proposed. The type strain is G-1-2-2( T) (= KACC 21616( T) = NBRC 114389( T)).
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