Methylorubrum endophytica sp. nov., a novel endophyte isolated from soybean seeds

The Methylobacteria are a genus of Rhizobiales and some species are able to create nodules and fix nitrogen in legumes. Methylobacterium species have also been isolated from other plants such as poplar trees and Arabidopsis. Our unknown endophytic strain was isolated from field grown soybean seeds at the end of the growing season 2016 in South Dakota, United States. Genome sequencing produced 123 contigs that were used to identify Methylobacterium sp. AMS5 as the closest known relative with 98.91% average nucleotide identity (ANI). Trimmed reads of Q1 were aligned with the AMS5 genome, allowing large gaps which had shown several large regions in Q1 that were deleted in relation to AMS5. Our unknown strain 123 contigs and Methylobacterium sp. AMS5 share 93.60% sequences with e-value cutoff of 1e-50 on chromosome by using Blastn and Granges. A phylogenetic tree was constructed using 16S rRNA gene sequences showing Q1 is most closely related to AMS5. The results of the genomic sequence deletions compared to AMS5, 16S phylogeny, and biochemical results suggest that the novel strain Methylorubrum sp. Q1 should be assigned to a novel species Methylorubrum soupus, as well as assign Methylobacterium sp. AMS5 to this species.