Methylobacterium litchii sp. nov., Methylobacterium guangdongense sp. nov. and Methylorubrum subtropicum sp. nov., isolated from the phyllosphere of litchi.

Abstract

Three aerobic, pink-pigmented, Gram-negative, motile and rod-shaped bacterial strains, designated SD21^T, SI9^T and SB2^T, were isolated from the phyllosphere of healthy litchis collected from three main producing sites of Guangdong Province, PR China. The 16S rRNA gene analysis showed that strains SD21^T and SI9^T belonged to the genus Methylobacterium (Mtb.) with the highest similarity to Mtb. komagatae DSM 19563^T (98.7%) and Mtb. phyllosphaerae CBMB27^T (99.8%), respectively, while strain SB2^T belonged to the genus Methylorubrum (Mtr.) and showed the highest similarity to Mtr. suomiense DSM 14458^T (98.6%). Phylogenomic analysis based on 92 core genes clearly showed that the most closely related type strains of SD21^T, SI9^T and SB2^T were Mtb. komagatae DSM 19563^T, Mtb. phyllostachyos ICMP 17619^T and Mtr. salsuginis CGMCC 1.6474^T, respectively. The ANI and dDDH values between the three isolates and their most closely related type strains were 85.6‒90.1% and 29.5‒40.4%, respectively, much below the threshold values for species delimitation. The isolates showed clear differences from their closely related type strains in terms of growth conditions, enzyme activities, substrates assimilation and contents of the major fatty acids. They all took summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c) as the major fatty acid, ubiquinone 10 as the predominant respiratory quinone and phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine as the major polar lipids. The phenotypic, phylogenetic and chemotaxonomic analyses with genome comparison strongly support that the isolates represent three distinct novel species within the genera of Methylobacterium and Methylorubrum, for which the names Methylobacterium litchii sp. nov., Methylobacterium guangdongense sp. nov. and Methylorubrum subtropicum sp. nov. are proposed, with SD21^T (=GDMCC 1.4327^T=KCTC 8300^T), SI9^T (=GDMCC 1.4329^T=KCTC 8298^T) and SB2^T (=GDMCC 1.4328^T=KCTC 8299^T) as the type strains, respectively.