Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai

• Published in: International journal of systematic and evolutionary microbiology Vol. 67; no. 11; pp. 4507 - 4514
• Main Authors: Frindte, Katharina, Maarastawi, Sarah A., Lipski, André, Hamacher, Joachim, Knief, Claudia
• Format: Journal Article
• Language: English
• Published: England 01.11.2017
• Subjects: Bacterial Typing Techniques; Base Composition; DNA, Bacterial - genetics; Fatty Acids - chemistry; Genes, Bacterial; Methylococcaceae - classification; Methylococcaceae - genetics; Methylococcaceae - isolation & purification; Oryza - microbiology; Oxygenases - genetics; Philippines; Phylogeny; Plant Stems - microbiology; RNA, Ribosomal, 16S - genetics; Sequence Analysis, DNA; methanotroph; methane; Methyloterricola; Methylomagnum; rice
• ISSN: 1466-5026; 1466-5034; 1466-5034
• DOI: 10.1099/ijsem.0.002319

Three gammaproteobacterial methanotrophic strains (73a , 175 and 114) were isolated from stems of rice plants. All strains are Gram-negative, motile and grow on methane or methanol as sole carbon sources. They oxidize methane using the particulate methane monooxygenase. Strains 114 and 175 possess additionally a soluble methane monooxygenase. All strains contain significant amounts of the cellular fatty acids C16 : 0, C16 : 1ω6c and C16 : 1ω7c, typical for type Ib methanotrophs. Characteristic for strains 114 and 175 are high amounts of C14 : 0 and C16 : 1ω6c , while strain 73a contains high quantities of C16 : 1ω5c. 16S rRNA gene sequence analyses showed that strains 114 and 175 are most closely related to Methylomagnum ishizawai (≥99.6 % sequence identity). Strain 73a is representing a new genus within the family Methylococcaceae, most closely related to Methylococcus capsulatus (94.3 % sequence identity). Phylogenetic analysis of the PmoA sequence indicates that strain 73a represents rice paddy cluster I (RPCI), which has almost exclusively been detected in rice ecosystems. The G+C content of strain 73a is 61.0 mol%, while strains 114 and 175 have a G+C content of 63.3 mol%. Strain 73a (=LMG 29185 , =VKM B-2986 ) represents the type strain of a novel species and genus, for which the name Methyloterricola oryzae gen. nov., sp. nov. is proposed and a description is provided. Strains 175 (=LMG 28717, VKM B-2989) and 114 are members of the species Methylomagnum ishizawai. This genus was so far only represented by one isolate, so an amended description of the species is given.