Draft genome sequence of the highly copper-tolerant Methylobacterium radiotolerans MLP1 isolated from the rhizosphere of grasses adjacent to mine tailings

ABSTRACT We present the genome of a highly copper-tolerant pink-pigmented facultative methylotroph isolated from the rhizosphere of grasses growing close to mine tailings. Based on whole-genome taxonomic analyses, this isolate was named Methylobacterium radiotolerans MLP1. Studies are in progress to infer its genome-based copper resistome.

T o understand how is organized the Cu-efflux resistome in bacteria thriving in Cu-rich environments, soil suspension from the rhizosphere of grasses sampled in the inactive mine "La Prieta" (Hidalgo del Parral, Chihuahua, México, 26° 56´ 27´´N, 105° 39´ 32´´W) (1) was screened for the presence of highly copper-tolerant bacteria by dilution and spread plate technique (2). After 72 h of incubation at 30°C, the most copper-tolerant isolate showed full growth on plates of succinate-ammonium mineral medium (3) supplemented with 4.0 mM CuCl 2 and total growth inhibition in 4.5 mM CuCl 2 (MIC), which falls into the range of tolerance reported for other highly Cu-tolerant species (4,5).
Its pink-pigmented phenotype and the ability to use methanol as the sole carbon source resembled pink-pigmented facultative methylotrophic bacteria (PPFM). This strain was named PPFM-MLP1. We report its genome sequence and taxonomic position.
The genome of PPFM-MLP1 was uploaded to the Type (Strain) Genome Server (TYGS) v 2022 to perform a genome-based taxonomic analysis (GBTA) based on Genome BLAST Distances Phylogeny (GBDP) using default settings (11). The comparison of query genome against type strains genomes in the TYGS database via the MASH algorithm (12) predicted that Methylobacterium radiotolerans JCM 2831 T was the type strain closest to PPFM-MLP1. A second GBTA was performed at the TYGS server adding eight genomes from M. radiotolerans strains reported in NCBI but not contained in the TYGS database. The phylogeny inferred from inter-genome distances and 16S rDNA sequences indicated the PPFM-MLP1 is part of the M. radiotolerans lineage (Fig. 1). The genomes of this cluster shared whole-genome average nucleotide identity (ANI) values >95%, digital DNA-DNA hybridizations (dDDH) values >70%, and G + C differences <1%, indicating that these genomes belong to the same species (see more details in Fig. 1). This isolate will be named M. radiotolerans MLP1.

ACKNOWLEDGMENTS
We thank Karla P. Medina Cuellar for the sample of grass rhizosphere collected in Mine "La Prieta" and for screening and storing highly copper-tolerant bacteria.

DATA AVAILABILITY
The whole-genome shotgun project was deposited in GenBank under the acces sion number JAPTHG010000000 (BioSample accession number SAMN32095585 and BioProject accession number PRJNA909792). The raw sequence reads have been deposited in the Sequence Read Archive (SRA) under the accession number SRR22690093. The GenBank assembly link is ASM2888606v1.