Genome sequence-based identification of bacteria nodulating Mimosa pudica growing in the Eastern Himalayas and Western Ghats of India and description of Cupriavidus mimosae sp. nov. and Cupriavidus gehlotii sp. nov.

Mimosa pudica is an invasive weed widespread in India's tropical regions and is nodulated by beta-rhizobia belonging to the genera Cupriavidus and Paraburkholderia. In this study, we characterized three bacterial strains isolated from root nodules of M. pudica collected from the Eastern Himalayan (EH) and Western Ghats (WG) regions of India. Whole-genome sequencing was performed for strain SKND8 (EH), and strains WGtm5T and WGlv3T (WG). Core-gene phylogeny based on the bac120 gene set placed strain SKND8 with Paraburkholderia caribensis, and average nucleotide identity (ANI) values above 96% and digital DNA-DNA hybridization (dDDH) values above 70% confirmed its identification as P. caribensis. In contrast, strains WGtm5T and WGlv3T clustered within the Cupriavidus taiwanensis species complex and shared ANI and dDDH values below 96% and 65.5%, respectively, with all validly published Cupriavidus species. ANI values below 95.9% and dDDH below 64.5% between WGtm5T and WGlv3T indicated that they represent two distinct novel species. The major fatty acids of both strains included C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). Analysis of the symbiotic genes nifH and nodC indicated that strain SKND8 carries symbiosis genes characteristic of symbiovar (sv.) tropicalis, whereas WGtm5T and WGlv3T share an undescribed Cupriavidus symbiovar common to members of the C. taiwanensis species complex. Based on the genome-based phylogenetic, genomic relatedness and phenotypic data, we propose two new species: Cupriavidus mimosae sp. nov. for strain WGtm5T (= MCC 4888T = KACC 22828T) and Cupriavidus gehlotii sp. nov. for strain WGlv3T (= MCC 4890T = KACC 22827T).