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
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 a...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Journal Article |
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2020
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| Subjects: | |
| Online Access: | http://hdl.handle.net/20.500.11937/78245 |
| _version_ | 1848763944527724544 |
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| author | Klonowska, Agnieszka Moulin, Lionel Ardley, Julie Kaye Braun, Florence Gollagher, Margaret Mary Zandberg, Jaco Daniel Marinova, Dora Huntemann, Marcel Reddy, T.B.K. Varghese, Neha Jacob Woyke, Tanja Ivanova, Natalia Seshadri, Rekha Kyrpides, Nikos Reeve, Wayne Gerald |
| author_facet | Klonowska, Agnieszka Moulin, Lionel Ardley, Julie Kaye Braun, Florence Gollagher, Margaret Mary Zandberg, Jaco Daniel Marinova, Dora Huntemann, Marcel Reddy, T.B.K. Varghese, Neha Jacob Woyke, Tanja Ivanova, Natalia Seshadri, Rekha Kyrpides, Nikos Reeve, Wayne Gerald |
| author_sort | Klonowska, Agnieszka |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | 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 19424T
. In contrast to the nickel and
zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ 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. |
| first_indexed | 2025-11-14T11:11:30Z |
| format | Journal Article |
| id | curtin-20.500.11937-78245 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T11:11:30Z |
| publishDate | 2020 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-782452020-05-27T08:27:23Z 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 Klonowska, Agnieszka Moulin, Lionel Ardley, Julie Kaye Braun, Florence Gollagher, Margaret Mary Zandberg, Jaco Daniel Marinova, Dora Huntemann, Marcel Reddy, T.B.K. Varghese, Neha Jacob Woyke, Tanja Ivanova, Natalia Seshadri, Rekha Kyrpides, Nikos Reeve, Wayne Gerald 1205 - Urban and Regional Planning 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 19424T . In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ 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. 2020 Journal Article http://hdl.handle.net/20.500.11937/78245 10.1186/s12864-020-6623-z http://creativecommons.org/licenses/by/4.0/ fulltext |
| spellingShingle | 1205 - Urban and Regional Planning Klonowska, Agnieszka Moulin, Lionel Ardley, Julie Kaye Braun, Florence Gollagher, Margaret Mary Zandberg, Jaco Daniel Marinova, Dora Huntemann, Marcel Reddy, T.B.K. Varghese, Neha Jacob Woyke, Tanja Ivanova, Natalia Seshadri, Rekha Kyrpides, Nikos Reeve, Wayne Gerald 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 |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | 1205 - Urban and Regional Planning |
| url | http://hdl.handle.net/20.500.11937/78245 |