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Tucker SJ, Freel KC, Monaghan EA, Sullivan CES, Ramfelt O, Rii YM, Rappé MS. Spatial and temporal dynamics of SAR11 marine bacteria across a nearshore to offshore transect in the tropical Pacific Ocean. PeerJ 2021; 9:e12274. [PMID: 34760357 PMCID: PMC8572523 DOI: 10.7717/peerj.12274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 09/19/2021] [Indexed: 01/04/2023] Open
Abstract
Surveys of microbial communities across transitions coupled with contextual measures of the environment provide a useful approach to dissect the factors determining distributions of microorganisms across ecological niches. Here, monthly time-series samples of surface seawater along a transect spanning the nearshore coastal environment within Kāneʻohe Bay on the island of Oʻahu, Hawaiʻi, and the adjacent offshore environment were collected to investigate the diversity and abundance of SAR11 marine bacteria (order Pelagibacterales) over a 2-year time period. Using 16S ribosomal RNA gene amplicon sequencing, the spatiotemporal distributions of major SAR11 subclades and exact amplicon sequence variants (ASVs) were evaluated. Seven of eight SAR11 subclades detected in this study showed distinct subclade distributions across the coastal to offshore environments. The SAR11 community was dominated by seven (of 106 total) SAR11 ASVs that made up an average of 77% of total SAR11. These seven ASVs spanned five different SAR11 subclades (Ia, Ib, IIa, IV, and Va), and were recovered from all samples collected from either the coastal environment, the offshore, or both. SAR11 ASVs were more often restricted spatially to coastal or offshore environments (64 of 106 ASVs) than they were shared among coastal, transition, and offshore environments (39 of 106 ASVs). Overall, offshore SAR11 communities contained a higher diversity of SAR11 ASVs than their nearshore counterparts, with the highest diversity within the little-studied subclade IIa. This study reveals ecological differentiation of SAR11 marine bacteria across a short physiochemical gradient, further increasing our understanding of how SAR11 genetic diversity partitions into distinct ecological units.
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Affiliation(s)
- Sarah J Tucker
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Marine Biology Graduate Program, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Kelle C Freel
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States
| | - Elizabeth A Monaghan
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Marine Biology Graduate Program, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Clarisse E S Sullivan
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Oscar Ramfelt
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Yoshimi M Rii
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,He'eia National Estuarine Research Reserve, Kāne'ohe, Hawai'i, United States
| | - Michael S Rappé
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States
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2
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Gounot JS, Neuvéglise C, Freel KC, Devillers H, Piškur J, Friedrich A, Schacherer J. High Complexity and Degree of Genetic Variation in Brettanomyces bruxellensis Population. Genome Biol Evol 2021; 12:795-807. [PMID: 32302403 PMCID: PMC7313668 DOI: 10.1093/gbe/evaa077] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2020] [Indexed: 12/13/2022] Open
Abstract
Genome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype–phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms, Saccharomyces cerevisiae and Schizosaccharomyces pombe. In this context, we sought to characterize at the population level the Brettanomyces bruxellensis yeast species, which is a major cause of wine spoilage and can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53 B. bruxellensis strains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in the B. bruxellensis species. Genomes are punctuated by multiple loss-of-heterozygosity regions, whereas aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared with S. cerevisiae. The pangenome is composed of 5,409 ORFs (open reading frames) among which 5,106 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.
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Affiliation(s)
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Kelle C Freel
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Hugo Devillers
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jure Piškur
- Department of Biology, Lund University, Sweden
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF)
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Freel KC, Fouteau S, Roche D, Farasin J, Huber A, Koechler S, Peres M, Chiboub O, Varet H, Proux C, Deschamps J, Briandet R, Torchet R, Cruveiller S, Lièvremont D, Coppée JY, Barbe V, Arsène-Ploetze F. Effect of arsenite and growth in biofilm conditions on the evolution of Thiomonas sp. CB2. Microb Genom 2020; 6:mgen000447. [PMID: 33034553 PMCID: PMC7660254 DOI: 10.1099/mgen.0.000447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/14/2020] [Indexed: 11/30/2022] Open
Abstract
Thiomonas bacteria are ubiquitous at acid mine drainage sites and play key roles in the remediation of water at these locations by oxidizing arsenite to arsenate, favouring the sorption of arsenic by iron oxides and their coprecipitation. Understanding the adaptive capacities of these bacteria is crucial to revealing how they persist and remain active in such extreme conditions. Interestingly, it was previously observed that after exposure to arsenite, when grown in a biofilm, some strains of Thiomonas bacteria develop variants that are more resistant to arsenic. Here, we identified the mechanisms involved in the emergence of such variants in biofilms. We found that the percentage of variants generated increased in the presence of high concentrations of arsenite (5.33 mM), especially in the detached cells after growth under biofilm-forming conditions. Analysis of gene expression in the parent strain CB2 revealed that genes involved in DNA repair were upregulated in the conditions where variants were observed. Finally, we assessed the phenotypes and genomes of the subsequent variants generated to evaluate the number of mutations compared to the parent strain. We determined that multiple point mutations accumulated after exposure to arsenite when cells were grown under biofilm conditions. Some of these mutations were found in what is referred to as ICE19, a genomic island (GI) carrying arsenic-resistance genes, also harbouring characteristics of an integrative and conjugative element (ICE). The mutations likely favoured the excision and duplication of this GI. This research aids in understanding how Thiomonas bacteria adapt to highly toxic environments, and, more generally, provides a window to bacterial genome evolution in extreme environments.
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Affiliation(s)
- Kelle C. Freel
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
- Present address: Hawaiʻi Institute of Marine Biology, University of Hawaiʻi at Mānoa, Kāneʻohe, HI, USA
| | - Stephanie Fouteau
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - David Roche
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Julien Farasin
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Aline Huber
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Sandrine Koechler
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
- Present address: Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Martina Peres
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Olfa Chiboub
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Hugo Varet
- Plateforme Transcriptome et Epigenome, BioMics, Centre de Ressources et Recherches Technologiques, Institut Pasteur, Paris, France
- Hub Bioinformatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756, IP CNRS), Institut Pasteur, Paris, France
| | - Caroline Proux
- Plateforme Transcriptome et Epigenome, BioMics, Centre de Ressources et Recherches Technologiques, Institut Pasteur, Paris, France
| | - Julien Deschamps
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Rachel Torchet
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Stephane Cruveiller
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Didier Lièvremont
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Jean-Yves Coppée
- Plateforme Transcriptome et Epigenome, BioMics, Centre de Ressources et Recherches Technologiques, Institut Pasteur, Paris, France
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Florence Arsène-Ploetze
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
- Present address: Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
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Arsène-Ploetze F, Chiboub O, Lièvremont D, Farasin J, Freel KC, Fouteau S, Barbe V. Correction to: Adaptation in toxic environments: comparative genomics of loci carrying antibiotic resistance genes derived from acid mine drainage waters. Environ Sci Pollut Res Int 2018; 25:1484-1485. [PMID: 29197052 DOI: 10.1007/s11356-017-0803-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The original version of this article unfortunately contains a mistake.
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Affiliation(s)
- Florence Arsène-Ploetze
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France.
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France.
| | - Olfa Chiboub
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Didier Lièvremont
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
- Institut de Chimie de Strasbourg, UMR7177, CNRS-Université de Strasbourg, Strasbourg, France
| | - Julien Farasin
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Kelle C Freel
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Stephanie Fouteau
- Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA/DRF/IBFJ/Genoscope, Evry, France
| | - Valérie Barbe
- Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA/DRF/IBFJ/Genoscope, Evry, France
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Arsène-Ploetze F, Chiboub O, Lièvremont D, Farasin J, Freel KC, Fouteau S, Barbe V. Adaptation in toxic environments: comparative genomics of loci carrying antibiotic resistance genes derived from acid mine drainage waters. Environ Sci Pollut Res Int 2018; 25:1470-1483. [PMID: 29090447 DOI: 10.1007/s11356-017-0535-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/19/2017] [Indexed: 06/07/2023]
Abstract
Several studies have suggested the existence of a close relationship between antibiotic-resistant phenotypes and resistance to other toxic compounds such as heavy metals, which involve co-resistance or cross-resistance mechanisms. A metagenomic library was previously constructed in Escherichia coli with DNA extracted from the bacterial community inhabiting an acid mine drainage (AMD) site highly contaminated with heavy metals. Here, we conducted a search for genes involved in antibiotic resistance using this previously constructed library. In particular, resistance to antibiotics was observed among five clones carrying four different loci originating from CARN5 and CARN2, two genomes reconstructed from the metagenomic data. Among the three CARN2 loci, two carry genes homologous to those previously proposed to be involved in antibiotic resistance. The third CARN2 locus carries a gene encoding a membrane transporter with an unknown function and was found to confer bacterial resistance to rifampicin, gentamycin, and kanamycin. The genome of Thiomonas delicata DSM 16361 and Thiomonas sp. X19 were sequenced in this study. Homologs of genes carried on these three CARN2 loci were found in these genomes, two of these loci were found in genomic islands. Together, these findings confirm that AMD environments contaminated with several toxic metals also constitute habitats for bacteria that function as reservoirs for antibiotic resistance genes.
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Affiliation(s)
- Florence Arsène-Ploetze
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France.
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France.
| | - Olfa Chiboub
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Didier Lièvremont
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
- Institut de Chimie de Strasbourg, UMR7177 CNRS-Université de Strasbourg, Strasbourg, France
| | - Julien Farasin
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Kelle C Freel
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Stephanie Fouteau
- Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA/DRF/IBFJ/Genoscope, Evry, France
| | - Valérie Barbe
- Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA/DRF/IBFJ/Genoscope, Evry, France
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Delhorme JB, Waissi W, Romain B, Schumacher C, Freel KC, Dufour P, Brigand C, Rohr S. Management of rectal squamous cell carcinoma. Clin Res Hepatol Gastroenterol 2017; 41:e71-e73. [PMID: 28483307 DOI: 10.1016/j.clinre.2017.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 12/30/2016] [Accepted: 03/28/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Jean-Baptiste Delhorme
- Service de chirurgie générale et digestive, Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, 2, avenue Molière, 67200 Strasbourg, France.
| | - Waisse Waissi
- Département de radiothérapie, centre Paul Strauss, 3, rue de la Porte-de-l'Hôpital, 67065 Strasbourg Cedex, France
| | - Benoit Romain
- Service de chirurgie générale et digestive, Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, 2, avenue Molière, 67200 Strasbourg, France
| | - Catherine Schumacher
- Département de radiothérapie, centre Paul Strauss, 3, rue de la Porte-de-l'Hôpital, 67065 Strasbourg Cedex, France
| | - Kelle C Freel
- Département de génétique, génomique et microbiologie, Université de Strasbourg/CNRS, UMR 7156, 28, rue Goethe, 67083 Strasbourg Cedex, France
| | - Patrick Dufour
- Département d'oncologie médicale, centre Paul Strauss, 3, rue de la Porte-de-l'Hôpital, 67065 Strasbourg Cedex, France
| | - Cécile Brigand
- Service de chirurgie générale et digestive, Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, 2, avenue Molière, 67200 Strasbourg, France
| | - Serge Rohr
- Service de chirurgie générale et digestive, Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, 2, avenue Molière, 67200 Strasbourg, France
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Delhorme JB, Severac F, Waissi W, Romain B, Antoni D, Freel KC, Schumacher C, Rohr S, Brigand C, Noël G. Surgery Is an Effective Option after Failure of Chemoradiation in Cancers of the Anal Canal and Anal Margin. Oncology 2017; 93:183-190. [PMID: 28571009 DOI: 10.1159/000475758] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 04/04/2017] [Indexed: 11/19/2022]
Abstract
BACKGROUND Surgery for anal canal cancer (ACC) and anal margin cancer (AMC) is the only curative option after failure of chemoradiotherapy (CRT). This study aimed to determine the efficacy of surgery for ACC or AMC after failed CRT. METHODS This was a single-centre, retrospective study of 161 patients initially treated with CRT. We compared the survival rates of patients successfully treated by CRT with those of patients whose CRT failed (both surgically salvaged and treated palliatively). RESULTS Thirty-one patients underwent surgery with curative intent, 20 received palliative treatment after failure of CRT, and 110 had effective CRT. The 5-year overall survival (OS) rate was significantly higher among patients with successful CRT than among patients who underwent surgery with curative intent (86 vs. 66%, p < 0.001). On the other hand, the 5-year OS of patients treated with curative surgery was significantly better than that of patients who underwent palliative treatment (66 vs. 13.5%, p < 0.001). The postoperative morbidity and mortality rates were 32 and 3%, respectively. Considering patients with failed CRT, curative surgery was the only factor prognostic of favourable OS in the multivariate analysis. CONCLUSION Curative surgery after failure of CRT for ACC or AMC remains an effective treatment to improve survival in two-thirds of cases, resulting in high but manageable morbidity.
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Affiliation(s)
- Jean-Baptiste Delhorme
- Service de chirurgie générale et digestive, Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
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Freel KC, Charron G, Leducq JB, Landry CR, Schacherer J. Lachancea quebecensis sp. nov., a yeast species consistently isolated from tree bark in the Canadian province of Québec. Int J Syst Evol Microbiol 2016; 65:3392-3399. [PMID: 26297665 DOI: 10.1099/ijsem.0.000426] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A thorough sampling of maple, oak, birch, and apple tree bark in North America yielded a set of isolates that represent a yeast species not yet formally described. The strains obtained were all isolated from the Canadian province of Québec. These four isolates have identical electrophoretic karyotypes, distinct from other species of the genus Lachancea, and are most closely related to the formally recognized species Lachancea thermotolerans according to the D1/D2 domain of the LSU rDNA gene and 5.8S–ITS region. Previous studies revealed the existence of a population of strains closely related to L. thermotolerans, with unique D1/D2 sequences and the ability to grow on melibiose, which is also true for these isolates. The sequences obtained here (for the D1/D2, and 5.8S–ITS region) are identical among the four strains, and in a phylogenetic analysis of the D1/D2 region, the strains form a distinct clade with the previously described population closely related to L. thermotolerans, composed of isolates from Japan, as well as from the provinces of Ontario and Québec in Canada. On the basis of select physiological and phylogenetic characteristics, a novel ascosporogenous yeast species, Lachancea quebecensis sp. nov., is proposed. The type strain LL11_022T ( = CBS 14138T = CLIB 1763T = UCDFST 15-106T) was isolated from maple tree bark in the Station Duchesnay, QC region of Québec, Canada. The MycoBank number is MB811749.
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Affiliation(s)
- Kelle C Freel
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, Strasbourg, France
| | - Guillaume Charron
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO Université Laval, Québec, Canada
| | - Jean-Baptiste Leducq
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO Université Laval, Québec, Canada
| | - Christian R Landry
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO Université Laval, Québec, Canada
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, Strasbourg, France
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Freel KC, Friedrich A, Sarilar V, Devillers H, Neuvéglise C, Schacherer J. Whole-Genome Sequencing and Intraspecific Analysis of the Yeast Species Lachancea quebecensis. Genome Biol Evol 2016; 8:733-41. [PMID: 26733577 PMCID: PMC4823976 DOI: 10.1093/gbe/evv262] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The gold standard in yeast population genomics has been the model organism Saccharomyces cerevisiae. However, the exploration of yeast species outside the Saccharomyces genus is essential to broaden the understanding of genome evolution. Here, we report the analyses of whole-genome sequences of nineisolates from the recently described yeast species Lachancea quebecensis. The genome of one isolate was assembled and annotated, and the intraspecific variability within L. quebecensis was surveyed by comparing the sequences from the eight other isolates to this reference sequence. Our study revealed that these strains harbor genomes with an average nucleotide diversity of π = 2 × 10−3 which is slightly lower, although on the same order of magnitude, as that previously determined for S. cerevisiae (π = 4 × 10−3). Our results show that even though these isolates were all obtained from a relatively isolated geographic location, the same ecological source, and represent a smaller sample size than is available for S. cerevisiae, the levels of divergence are similar to those observed in this model species. This divergence is essentially linked to the presence of two distinct clusters delineated according to geographic location. However, even with relatively similar ranges of genome divergence, L. quebecensis has an extremely low global phenotypic variance of 0.062 compared with 0.59 previously determined in S. cerevisiae.
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Affiliation(s)
- Kelle C Freel
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
| | - Véronique Sarilar
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Hugo Devillers
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Cécile Neuvéglise
- INRA, UMR1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, Jouy-en-Josas, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, UMR7156, University of Strasbourg - CNRS, Strasbourg, France
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10
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Freel KC, Krueger MC, Farasin J, Brochier-Armanet C, Barbe V, Andrès J, Cholley PE, Dillies MA, Jagla B, Koechler S, Leva Y, Magdelenat G, Plewniak F, Proux C, Coppée JY, Bertin PN, Heipieper HJ, Arsène-Ploetze F. Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas. PLoS One 2015; 10:e0139011. [PMID: 26422469 PMCID: PMC4589449 DOI: 10.1371/journal.pone.0139011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/07/2015] [Indexed: 11/19/2022] Open
Abstract
Acid mine drainage (AMD) is a highly toxic environment for most living organisms due to the presence of many lethal elements including arsenic (As). Thiomonas (Tm.) bacteria are found ubiquitously in AMD and can withstand these extreme conditions, in part because they are able to oxidize arsenite. In order to further improve our knowledge concerning the adaptive capacities of these bacteria, we sequenced and assembled the genome of six isolates derived from the Carnoulès AMD, and compared them to the genomes of Tm. arsenitoxydans 3As (isolated from the same site) and Tm. intermedia K12 (isolated from a sewage pipe). A detailed analysis of the Tm. sp. CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs) were found in each of these three genomes. We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7). Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments.
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Affiliation(s)
- Kelle C. Freel
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Département Microorganismes, Génomes, Environnement, Equipe Ecophysiologie Moléculaire des Microorganismes, Institut de Botanique, Strasbourg, France
| | - Martin C. Krueger
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Julien Farasin
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Département Microorganismes, Génomes, Environnement, Equipe Ecophysiologie Moléculaire des Microorganismes, Institut de Botanique, Strasbourg, France
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, Villeurbanne, France
| | - Valérie Barbe
- Laboratoire de Biologie Moléculaire pour l’Etude des Génomes, (LBioMEG), CEA-IG-Genoscope, Evry, France
| | - Jeremy Andrès
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Département Microorganismes, Génomes, Environnement, Equipe Ecophysiologie Moléculaire des Microorganismes, Institut de Botanique, Strasbourg, France
| | - Pierre-Etienne Cholley
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Département Microorganismes, Génomes, Environnement, Equipe Ecophysiologie Moléculaire des Microorganismes, Institut de Botanique, Strasbourg, France
| | - Marie-Agnès Dillies
- Plate-Forme Transcriptome et Epigénome, Centre d'Innovation et de Recherche Technologique—Département Génomes et Génétique, Institut Pasteur, Paris, France
| | - Bernd Jagla
- Plate-Forme Transcriptome et Epigénome, Centre d'Innovation et de Recherche Technologique—Département Génomes et Génétique, Institut Pasteur, Paris, France
| | - Sandrine Koechler
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Département Microorganismes, Génomes, Environnement, Equipe Ecophysiologie Moléculaire des Microorganismes, Institut de Botanique, Strasbourg, France
| | - Yann Leva
- Université de Haute-Alsace, Biopôle–LVBE, Colmar, France
| | - Ghislaine Magdelenat
- Laboratoire de Biologie Moléculaire pour l’Etude des Génomes, (LBioMEG), CEA-IG-Genoscope, Evry, France
| | - Frédéric Plewniak
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Département Microorganismes, Génomes, Environnement, Equipe Ecophysiologie Moléculaire des Microorganismes, Institut de Botanique, Strasbourg, France
| | - Caroline Proux
- Plate-Forme Transcriptome et Epigénome, Centre d'Innovation et de Recherche Technologique—Département Génomes et Génétique, Institut Pasteur, Paris, France
| | - Jean-Yves Coppée
- Plate-Forme Transcriptome et Epigénome, Centre d'Innovation et de Recherche Technologique—Département Génomes et Génétique, Institut Pasteur, Paris, France
| | - Philippe N. Bertin
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Département Microorganismes, Génomes, Environnement, Equipe Ecophysiologie Moléculaire des Microorganismes, Institut de Botanique, Strasbourg, France
| | - Hermann J. Heipieper
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Florence Arsène-Ploetze
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Département Microorganismes, Génomes, Environnement, Equipe Ecophysiologie Moléculaire des Microorganismes, Institut de Botanique, Strasbourg, France
- * E-mail:
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Abstract
Mitochondria are important organelles that harbor their own genomes encoding a key set of proteins that ensure respiration and provide the eukaryotic cell with energy. Recent advances in high-throughput sequencing technologies present a unique opportunity to explore mitochondrial (mt) genome evolution. The Saccharomycotina yeasts have proven to be the leading organisms for mt comparative and population genomics. In fact, the explosion of complete yeast mt genome sequences has allowed for a broader view of the mt diversity across this incredibly diverse subphylum, both within and between closely related species. Here, we summarize the present state of yeast mitogenomics, including the currently available data and what it reveals concerning the diversity of content, organization, structure and evolution of mt genomes.
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Affiliation(s)
- Kelle C Freel
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156 Strasbourg 67083, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156 Strasbourg 67083, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156 Strasbourg 67083, France
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12
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Freel KC, Friedrich A, Hou J, Schacherer J. Population genomic analysis reveals highly conserved mitochondrial genomes in the yeast species Lachancea thermotolerans. Genome Biol Evol 2014; 6:2586-94. [PMID: 25212859 PMCID: PMC4224330 DOI: 10.1093/gbe/evu203] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The increasing availability of mitochondrial (mt) sequence data from various yeasts provides a tool to study genomic evolution within and between different species. While the genomes from a range of lineages are available, there is a lack of information concerning intraspecific mtDNA diversity. Here, we analyzed the mt genomes of 50 strains from Lachancea thermotolerans, a protoploid yeast species that has been isolated from several locations (Europe, Asia, Australia, South Africa, and North / South America) and ecological sources (fruit, tree exudate, plant material, and grape and agave fermentations). Protein-coding genes from the mtDNA were used to construct a phylogeny, which reflected a similar, yet less resolved topology than the phylogenetic tree of 50 nuclear genes. In comparison to its sister species Lachancea kluyveri, L. thermotolerans has a smaller mt genome. This is due to shorter intergenic regions and fewer introns, of which the latter are only found in COX1. We revealed that L. kluyveri and L. thermotolerans share similar levels of intraspecific divergence concerning the nuclear genomes. However, L. thermotolerans has a more highly conserved mt genome with the coding regions characterized by low rates of nonsynonymous substitution. Thus, in the mt genomes of L. thermotolerans, stronger purifying selection and lower mutation rates potentially shape genome diversity in contract to what was found for L. kluyveri, demonstrating that the factors driving mt genome evolution are different even between closely related species.
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Affiliation(s)
- Kelle C Freel
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, France
| | - Jing Hou
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR7156, France
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13
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Becerril-Espinosa A, Freel KC, Jensen PR, Soria-Mercado IE. Marine Actinobacteria from the Gulf of California: diversity, abundance and secondary metabolite biosynthetic potential. Antonie Van Leeuwenhoek 2012; 103:809-19. [PMID: 23229438 DOI: 10.1007/s10482-012-9863-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 12/01/2012] [Indexed: 12/30/2022]
Abstract
The Gulf of California is a coastal marine ecosystem characterized as having abundant biological resources and a high level of endemism. In this work we report the isolation and characterization of Actinobacteria from different sites in the western Gulf of California. We collected 126 sediment samples and isolated on average 3.1-38.3 Actinobacterial strains from each sample. Phylogenetic analysis of 136 strains identified them as members of the genera Actinomadura, Micromonospora, Nocardiopsis, Nonomuraea, Saccharomonospora, Salinispora, Streptomyces and Verrucosispora. These strains were grouped into 26-56 operational taxonomic units (OTUs) based on 16S rRNA gene sequence identities of 98-100 %. At 98 % sequence identity, three OTUs appear to represent new taxa while nine (35 %) have only been reported from marine environments. Sixty-three strains required seawater for growth. These fell into two OTUs at the 98 % identity level and include one that failed to produce aerial hyphae and was only distantly related (≤95.5 % 16S identity) to any previously cultured Streptomyces sp. Phylogenetic analyses of ketosynthase domains associated with polyketide synthase genes revealed sequences that ranged from 55 to 99 % nucleotide identity to experimentally characterized biosynthetic pathways suggesting that some may be associated with the production of new secondary metabolites. These results indicate that marine sediments from the Gulf of California harbor diverse Actinobacterial taxa with the potential to produce new secondary metabolites.
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Affiliation(s)
- Amayaly Becerril-Espinosa
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, km 103 Carretera Tijuana- Ensenada, 22830, Ensenada, Baja California, Mexico
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14
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Abstract
In July of 2006 and January of 2008, a total of 671 marine sediment samples were collected at depths from 5 to 2012 m throughout the Fijian islands and selectively processed for the cultivation of marine actinomycetes belonging to the genus Salinispora. The primary objectives were to assess the diversity, distribution and phylogeny of 'S. pacifica', the least well studied of the three species in the genus. Employing a sequential screening method based on antibiotic sensitivity, RFLP patterns, and 16S rRNA and ITS sequence analyses, 42 of 750 isolates with Salinispora-like features were identified as 'S. pacifica'. These strains represent the first report of 'S. pacifica' from Fiji and include 15 representatives of 4 new 'S. pacifica' 16S rRNA sequence types. Among the 'S. pacifica' strains isolated, little evidence for geographical isolation emerged based on 16S, ITS or secondary metabolite biosynthetic gene fingerprinting. The inclusion of isolates from additional collection sites and other Salinispora spp. revealed a high degree of dispersal among 'S. pacifica' populations and phylogenetic support for the delineation of this lineage as a third species.
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Affiliation(s)
- Kelle C Freel
- Scripps Institution of Oceanography, Center for Marine Biotechnology and Biomedicine, University of California-San Diego, La Jolla, CA 92093, USA
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15
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Asolkar RN, Freel KC, Jensen PR, Fenical W, Kondratyuk TP, Park EJ, Pezzuto JM. Arenamides A-C, cytotoxic NFkappaB inhibitors from the marine actinomycete Salinispora arenicola. J Nat Prod 2009; 72:396-402. [PMID: 19117399 PMCID: PMC2837138 DOI: 10.1021/np800617a] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Three new cyclohexadepsipeptides, arenamides A-C (1-3), were isolated from the fermentation broth of a marine bacterial strain identified as Salinispora arenicola. The planar structures of these compounds were assigned by detailed interpretation of NMR and MS/MS spectroscopic data. The absolute configurations of the amino acids, and those of the chiral centers on the side chain, were established by application of the Marfey and modified Mosher methods. The effect of arenamides A and B on NFkappaB activity was studied with stably transfected 293/NFkappaB-Luc human embryonic kidney cells induced by treatment with tumor necrosis factor (TNF). Arenamides A (1) and B (2) blocked TNF-induced activation in a dose- and time-dependent manner with IC(50) values of 3.7 and 1.7 microM, respectively. In addition, the compounds inhibited nitric oxide (NO) and prostaglandin E(2) (PGE(2)) production with lipopolysaccharide (LPS)-induced RAW 264.7 macrophages. Moderate cytotoxicity was observed with the human colon carcinoma cell line HCT-116, but no cytotoxic effect was noted with cultured RAW cells. Taken together, these data suggest that the chemoprevention and anti-inflammatory characteristics of arenamides A and B warrant further investigation.
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Affiliation(s)
| | | | | | - William Fenical
- To whom correspondence should be addressed. Phone: 858-534-2133. Fax: 858-558-3702. E-mail:
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