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

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 taxo...

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Published in:	BMC genomics Vol. 21; no. 1; pp. 214 - 18
Main Authors:	Klonowska, Agnieszka, Moulin, Lionel, Ardley, Julie Kaye, Braun, Florence, Gollagher, Margaret Mary, Zandberg, Jaco Daniel, Marinova, Dora Vasileva, Huntemann, Marcel, Reddy, T B K, Varghese, Neha Jacob, Woyke, Tanja, Ivanova, Natalia, Seshadri, Rekha, Kyrpides, Nikos, Reeve, Wayne Gerald
Format:	Journal Article
Language:	English
Published:	England BioMed Central Ltd 06-03-2020 BioMed Central Springer BMC
Subjects:	Adaptation Agricultural sciences Arsenic ATPases BASIC BIOLOGICAL SCIENCES Biochemistry, Molecular Biology Biodiversity Biogeography Cadmium Cadmium - metabolism Chromosomes Cobalt Cupriavidus Cupriavidus - drug effects Cupriavidus - genetics Gene clusters Genes Genetic aspects Genomes Genomics Heavy metal efflux Heavy metal resistance Heavy metals HGT Legumes Life Sciences Metals, Heavy - toxicity Microorganisms Mimosa Mimosa - microbiology Mimosa pudica Mining industry Multigene Family New species Nickel - toxicity Nickel tolerance Novels Phylogenetics Phylogeny Physiological aspects Plant hardiness Police officers Proteins Proteobacteria Rhizobia Rhizobial biogeography Rhizobium - drug effects Rhizobium - genetics RNA, Ribosomal, 16S - genetics Silver Soil Soil Microbiology Soil study Soils Symbiosis Synteny - genetics Systematics, Phylogenetics and taxonomy Zinc - toxicity Zinc compounds United States New Caledonia Taiwan Rhizobia HGT Cupriavidus Heavy metal efflux Rhizobial biogeography Heavy metal resistance Nickel tolerance Mimosa
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Summary:	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. 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 . In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni and Zn 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. STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Curtin Univ. Sustainability Policy Inst. Murdoch Univ. AC02-05CH11231 French National Agency of Research USDOE Office of Science (SC), Biological and Environmental Research (BER)
ISSN:	1471-2164 1471-2164
DOI:	10.1186/s12864-020-6623-z