Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil

Abstract

Background: Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems.Results: The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424 T . In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni 2+ and Zn 2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance.(Continued on next page)

Hospital sink traps as a potential source of the emerging multidrug-resistant pathogen Cupriavidus pauculus: characterization and draft genome sequence of strain MF1

“…Together, the MRGs listed in Table 1 contribute to resistance to copper, silver, magnesium, cobalt, mercury, molybdenum, arsenic, zinc, cadmium, iron, antimony and nickel. Many species of Cupriavidus including C. pauculus [76,77], C. metallidurans [78,79], C. gilardii [80], C. campinensis [81] and C. neocaledonicus [82] are considered to be metal resistant. Many of these genes confer resistance to metals by means of intracellular metal sequestration to facilitate export, as in the case of CopZ with Cu + ions [83], Ag + and Cd 2+ ions [84].…”

Genomics and transcriptomics insights into luteolin effects on the beta‐rhizobial strain Cupriavidus necator UYPR2.512

“…Comparison between the genomes of UYPR2.512, C . taiwanensis LMG19424 and the recently proposed Cupriavidus neocaledonicus STM6070 has shown that while LMG19424 and STM6070 had almost identical Sym plasmids, the UYPR2.512 strain would harbour a divergent Sym plasmid (Clerissi et al ., 2018; Klonowska et al ., 2020). However, nod , nif , fix and fdx genes are highly conserved between the analysed genomes of rhizobial Cupriavidus (Fig.…”

“…Cupriavidus rhizobia have been found associated with members of the Mimosoid clade both in species occurring in their native habitats and as invasive species (Barrett and Parker, 2006;dos Reis et al, 2010;Liu et al, 2012;Taulé et al, 2012;Gehlot et al, 2013;Platero et al, 2016). Nowadays there are two recognized Cupriavidus species containing rhizobia strains: Cupriavidus taiwanensis (Chen et al, 2001;Moulin et al, 2001;Vandamme and Coenye, 2004) and Cupriavidus necator (da Silva et al, 2012), though there is increasing evidence for the existence of additional rhizobia containing species (Platero et al, 2016;Klonowska et al, 2020).…”

Determinantes Genéticos Y Sus Mecanismos De Acción Implicados en La Resistencia Bacteriana a Metales Pesados: Una Revisión.

“…Branco y Morais (61) establecen la importancia de los genes chrC y chrF para evitar la acumulación de especies reactivas de oxígeno (ROS) en las células sometidas a estrés por cromato; además, establecen una gran similitud entre el producto génico de chrC de la cepa 5bvl1 con la Fe-SOD (ChrC) de C. metallidurans CH34. En contraste, el producto génico de chrF de Cupriavidus neocaledonicus STM 6070 aislada de un suelo rico en níquel y el producto del gen chrI de C. metallidurans CH34 han sido identificados como represores del operón chr (62,63). Sin embargo, esto difiere de otro estudio, en el cual identifican que chrF codifica para un superóxido dismutasa (Mn-SOD) (61).…”