camines

• Haverkamp, Thomas Hendricus Augustus; Lossouarn, Julien; Zhaxybayeva, Olga; Lyu, Jie; Bienvenu, Nadège & Geslin, Claire [Show all 7 contributors for this article] (2021). Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing. Environmental Microbiology. ISSN 1462-2912. 23(11), p. 7105–7120. doi: 10.1111/1462-2920.15723. Full text in Research Archive Show summary

  Phylogenomic analyses of bacteria from the phylum Thermotogota have shown extensive lateral gene transfer with distantly related organisms, particularly with Firmicutes. One likely mechanism of such DNA transfer is viruses. However, to date, only three temperate viruses have been characterized in this phylum, all infecting bacteria from the Marinitoga genus. Here we report 17 proviruses integrated into genomes of bacteria belonging to eight Thermotogota genera and induce viral particle production from one of the proviruses. All except an incomplete provirus from Mesotoga fall into two groups based on sequence similarity, gene synteny and taxonomic classification. Proviruses of Group 1 are found in the genera Geotoga, Kosmotoga, Marinitoga, Thermosipho and Mesoaciditoga and are similar to the previously characterized Marinitoga viruses, while proviruses from Group 2 are distantly related to the Group 1 proviruses, have different genome organization and are found in Petrotoga and Defluviitoga. Genes carried by both groups are closely related to Firmicutes and Firmicutes (pro)viruses in phylogenetic analyses. Moreover, one of the groups show evidence of recent gene exchange and may be capable of infecting cells from both phyla. We hypothesize that viruses are responsible for a large portion of the observed gene flow between Firmicutes and Thermotogota.

• Nesbø, Camilla Lothe; Charchuk, Rhianna; Pollo, Stephen M.J.; Budwill, Karen; Kublanov, Ilya V. & Haverkamp, Thomas Hendricus Augustus [Show all 7 contributors for this article] (2019). Genomic analysis of the mesophilic Thermotogae genus Mesotoga reveals phylogeographic structure and genomic determinants of its distinct metabolism. Environmental Microbiology. ISSN 1462-2912. 21(1), p. 456–470. doi: 10.1111/1462-2920.14477. Full text in Research Archive Show summary

  The genus Mesotoga , the only described mesophilic Thermotogae lineage, is common in mesothermic anaerobic hydrocarbon‐rich environments. Besides mesophily, Mesotoga displays lineage‐specific phenotypes, such as no or little H2 production and dependence on sulfur‐compound reduction, which may influence its ecological role. We used comparative genomics of 18 Mesotoga strains (pairwise 16S rRNA identity >99%) and a transcriptome of M. prima to investigate how life at moderate temperatures affects phylogeography and to interrogate the genomic features of its lineage‐specific metabolism. We propose that Mesotoga accomplish H2 oxidation and thiosulfate reduction using a sulfide dehydrogenase and a hydrogenase‐complex and that a pyruvate:ferredoxin oxidoreductase acquired from Clostridia is responsible for oxidizing acetate. Phylogenetic analysis revealed three distinct Mesotoga lineages (89.6%–99.9% average nucleotide identity [ANI] within lineages, 79.3%–87.6% ANI between lineages) having different geographic distribution patterns and high levels of intra‐lineage recombination but little geneflow between lineages. Including data from metagenomes, phylogeographic patterns suggest that geographical separation historically has been more important for Mesotoga than hyperthermophilic Thermotoga and we hypothesize that distribution of Mesotoga is constrained by their anaerobic lifestyle. Our data also suggest that recent anthropogenic activities and environments (e.g., wastewater treatment, oil exploration) have expanded Mesotoga habitats and dispersal capabilities.

• Haverkamp, Thomas Hendricus Augustus; Geslin, Claire; Lossouarn, Julien; Podosokorskaya, Olga A.; Kublanov, Ilya V. & Nesbø, Camilla Lothe (2018). Thermosipho spp. Immune System Differences Affect Variation in Genome Size and Geographical Distributions. Genome Biology and Evolution (GBE). 10(11), p. 2853–2866. doi: 10.1093/gbe/evy202. Full text in Research Archive Show summary

  Thermosipho species inhabit thermal environments such as marine hydrothermal vents, petroleum reservoirs, and terrestrial hot springs. A 16S rRNA phylogeny of available Thermosipho spp. sequences suggested habitat specialists adapted to living in hydrothermal vents only, and habitat generalists inhabiting oil reservoirs, hydrothermal vents, and hotsprings. Comparative genomics of 15 Thermosipho genomes separated them into three distinct species with different habitat distributions: The widely distributed T. africanus and the more specialized, T. melanesiensis and T. affectus. Moreover, the species can be differentiated on the basis of genome size (GS), genome content, and immune system composition. For instance, the T. africanus genomes are largest and contained the most carbohydrate metabolism genes, which could explain why these isolates were obtained from ecologically more divergent habitats. Nonetheless, all the Thermosipho genomes, like other Thermotogae genomes, show evidence of genome streamlining. GS differences between the species could further be correlated to differences in defense capacities against foreign DNA, which influence recombination via HGT. The smallest genomes are found in T. affectus that contain both CRISPR-cas Type I and III systems, but no RM system genes. We suggest that this has caused these genomes to be almost devoid of mobile elements, contrasting the two other species genomes that contain a higher abundance of mobile elements combined with different immune system configurations. Taken together, the comparative genomic analyses of Thermosipho spp. revealed genetic variation allowing habitat differentiation within the genus as well as differentiation with respect to invading mobile DNA.

• Pollo, Stephen M.J.; Adebusuyi, Abigail; Straub, Timothy J.; Foght, Julia M.; Zhaxybayeva, Olga & Nesbø, Camilla Lothe (2017). Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20 to 79 °C. Extremophiles. ISSN 1431-0651. 21(6), p. 963–979. doi: 10.1007/s00792-017-0956-9. Full text in Research Archive
• Mercier, C.; Lossouarn, J.; Nesbø, Camilla Lothe; Haverkamp, Thomas Hendricus Augustus; Baudoux, A. C. & Jebbar, M. [Show all 10 contributors for this article] (2017). Two new viruses, MCV1 and MCV2, which infect Marinitoga bacteria isolated from deep-sea hydrothermal vents: Functional and genomic analysis. Environmental Microbiology. ISSN 1462-2912. 20(2), p. 577–587. doi: 10.1111/1462-2920.13967. Full text in Research Archive
• Valseth, Karoline; Nesbø, Camilla Lothe; Easterday, William Ryan; Turner, Wendy Christine; Olsen, Jaran Strand & Stenseth, Nils Christian [Show all 7 contributors for this article] (2017). Temporal dynamics in microbial soil communities at anthrax carcass sites. BMC Microbiology. doi: 10.1186/s12866-017-1111-6. Full text in Research Archive Show summary

  BackgroundAnthrax is a globally distributed disease affecting primarily herbivorous mammals. It is caused by the soil-dwelling and spore-forming bacterium Bacillus anthracis. The dormant B. anthracis spores become vegetative after ingestion by grazing mammals. After killing the host, B. anthracis cells return to the soil where they sporulate, completing the lifecycle of the bacterium. Here we present the first study describing temporal microbial soil community changes in Etosha National Park, Namibia, after decomposition of two plains zebra (Equus quagga) anthrax carcasses. To circumvent state-associated-challenges (i.e. vegetative cells/spores) we monitored B. anthracis throughout the period using cultivation, qPCR and shotgun metagenomic sequencing. ResultsThe combined results suggest that abundance estimation of spore-forming bacteria in their natural habitat by DNA-based approaches alone is insufficient due to poor recovery of DNA from spores. However, our combined approached allowed us to follow B. anthracis population dynamics (vegetative cells and spores) in the soil, along with closely related organisms from the B. cereus group, despite their high sequence similarity. Vegetative B. anthracis abundance peaked early in the time-series and then dropped when cells either sporulated or died. The time-series revealed that after carcass deposition, the typical semi-arid soil community (e.g. Frankiales and Rhizobiales species) becomes temporarily dominated by the orders Bacillales and Pseudomonadales, known to contain plant growth-promoting species. ConclusionOur work indicates that complementing DNA based approaches with cultivation may give a more complete picture of the ecology of spore forming pathogens. Furthermore, the results suggests that the increased vegetation biomass production found at carcass sites is due to both added nutrients and the proliferation of microbial taxa that can be beneficial for plant growth. Thus, future B. anthracis transmission events at carcass sites may be indirectly facilitated by the recruitment of plant-beneficial bacteria.

• Aguilar, Maria; Richardson, Elisabeth; Tan, BoonFei; Walker, Giselle; Dunfield, Peter F. & Bass, David [Show all 9 contributors for this article] (2016). Next-Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water. Journal of Eukaryotic Microbiology. ISSN 1066-5234. 63(6), p. 732–743. doi: 10.1111/jeu.12320. Full text in Research Archive
• Pollo, Stephen M.J.; Charchuk, Rhianna & Nesbø, Camilla Lothe (2016). Draft genome sequences of Kosmotoga sp. strain DU53 and Kosmotoga arenicorallina S304. Microbiology Resource Announcements (MRA). 4(3). doi: 10.1128/genomeA.00570-16. Full text in Research Archive
• Mercier, Coraline; Lossouarn, Julien; Haverkamp, Thomas Hendricus Augustus; Bienvenu, Nadege; Godfroy, Anne & Cueff-Gauchard, Valerie [Show all 8 contributors for this article] (2016). Draft genome sequences of two Marinitoga camini isolates producing bacterioviruses. Microbiology Resource Announcements (MRA). 4(6). doi: 10.1128/genomeA.01261-16. Full text in Research Archive
• Valseth, Karoline; Nesbø, Camilla Lothe; Easterday, William Ryan; Turner, Wendy Christine; Olsen, Jaran Strand & Stenseth, Nils Christian [Show all 7 contributors for this article] (2016). Draft Genome Sequences of Two Bacillus anthracis Strains from Etosha National Park, Namibia. Microbiology Resource Announcements (MRA). 4(4). doi: 10.1128/genomeA.00861-16. Full text in Research Archive
• Lossouarn, Julien; Nesbø, Camilla Lothe; Mercier, Coraline; Zhaxybayeva, Olga; Johnson, Milo S & Charchuck, Rhianna [Show all 12 contributors for this article] (2015). 'Ménage à trois': A selfish genetic element uses a virus to propagate within Thermotogales. Environmental Microbiology. ISSN 1462-2912. 17(9), p. 3278–3288. doi: 10.1111/1462-2920.12783. Full text in Research Archive
• Nesbø, Camilla Lothe; Swithers, Kirsten S.; Dahle, Håkon; Haverkamp, Thomas Hendricus Augustus; Birkeland, Nils-Kåre & Sokolova, Tatiana [Show all 8 contributors for this article] (2015). Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments. The ISME Journal. ISSN 1751-7362. 9(7), p. 1532–1542. doi: 10.1038/ismej.2014.238. Full text in Research Archive
• Pollo, Stephen M.J.; Zhaxybayeva, Olga & Nesbø, Camilla Lothe (2015). Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae. Canadian Journal of Microbiology (print). ISSN 0008-4166. 61(9), p. 655–670. doi: 10.1139/cjm-2015-0073. Full text in Research Archive Show summary

  Thermophiles are extremophiles that grow optimally at temperatures >45 °C. To survive and maintain function of their biological molecules, they have a suite of characteristics not found in organisms that grow at moderate temperature (mesophiles). At the cellular level, thermophiles have mechanisms for maintaining their membranes, nucleic acids, and other cellular structures. At the protein level, each of their proteins remains stable and retains activity at temperatures that would denature their mesophilic homologs. Conversely, cellular structures and proteins from thermophiles may not function optimally at moderate temperatures. These differences between thermophiles and mesophiles presumably present a barrier for evolutionary transitioning between the 2 lifestyles. Therefore, studying closely related thermophiles and mesophiles can help us determine how such lifestyle transitions may happen. The bacterial phylum Thermotogae contains hyperthermophiles, thermophiles, mesophiles, and organisms with temperature ranges wide enough to span both thermophilic and mesophilic temperatures. Genomic, proteomic, and physiological differences noted between other bacterial thermophiles and mesophiles are evident within the Thermotogae. We argue that the Thermotogae is an ideal group of organisms for understanding of the response to fluctuating temperature and of long-term evolutionary adaptation to a different growth temperature range.

• Tan, Boon Fei; Silva, Renata de Araújo; Rozycki, Trent; Nesbø, Camilla Lothe & Foght, Julia (2014). Draft genome sequences of three Smithella spp. obtained from a methanogenic alkane-degrading culture and oil field produced water. Microbiology Resource Announcements (MRA). 2(5). doi: 10.1128/genomeA.01085-14. Full text in Research Archive
• Tan, BoonFei; Charchuk, Rhianna; Li, Carmen; Nesbø, Camilla Lothe; Laban, Nidal Abu & Foght, Julia (2014). Draft genome sequence of uncultivated Firmicutes (Peptococcaceae SCADC) single cells sorted from methanogenic alkane-degrading cultures. Microbiology Resource Announcements (MRA). 2(5). doi: 10.1128/genomeA.00909-14. Full text in Research Archive
• An, Dongshan; Caffrey, Sean M.; Soh, Jung; Agrawal, Akhil; Brown, Damon & Budwill, Karen [Show all 33 contributors for this article] (2013). Metagenomics of Hydrocarbon Resource Environments Indicates Aerobic Taxa and Genes to be Unexpectedly Common. Environmental Science and Technology. ISSN 0013-936X. 47(18), p. 10708–10717. doi: 10.1021/es4020184. Full text in Research Archive
• Siddique, Tariq; Penner, Tara; Klassen, Jonathan; Nesbø, Camilla Lothe & Foght, Julia M. (2012). Microbial Communities Involved in Methane Production from Hydrocarbons in Oil Sands Tailings. Environmental Science and Technology. ISSN 0013-936X. 46(17), p. 9802–9810. doi: 10.1021/es302202c. Full text in Research Archive
• Zhaxybayeva, Olga; Swithers, Kristen S.; Foght, Julia; Green, A.G.; Bruce, David C. & Detter, Christopher [Show all 19 contributors for this article] (2012). Genome Sequence of the Mesophilic Thermotogales Bacterium Mesotoga prima MesG1.Ag.4.2 Reveals the Largest Thermotogales Genome To Date. Genome Biology and Evolution (GBE). 4(8), p. 812–820. doi: 10.1093/gbe/evs059. Full text in Research Archive
• Swithers, Kristen S.; Petrus, Amanda K.; Secinaro, Michael A; Nesbø, Camilla Lothe; Gogarten, J. Peter & Noll, Kenneth M. [Show all 7 contributors for this article] (2012). Vitamin B12 Synthesis and Salvage PathwaysWere Acquired by Horizontal Gene Transfer to the Thermotogales. Genome Biology and Evolution (GBE). 4(8), p. 842–851. doi: 10.1093/gbe/evs057. Full text in Research Archive
• Arndt, David; Xia, Jianguo; Liu, Yifeng; Zhou, You; Guo, An Chi & Cruz, Joseph A. [Show all 10 contributors for this article] (2012). METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Research (NAR). ISSN 0305-1048. 40(W1), p. W88–W95. doi: 10.1093/nar/gks497. Full text in Research Archive
• Nesbø, Camilla Lothe; Bradnan, Danielle M.; Adebusuyi, Abigail; Dlutek, Marlena; Petrus, Amanda K. & Foght, Julia [Show all 8 contributors for this article] (2012). Mesotoga prima gen. nov., sp nov., the first described mesophilic species of the Thermotogales. Extremophiles. ISSN 1431-0651. 16(3), p. 387–393. doi: 10.1007/s00792-012-0437-0. Full text in Research Archive
• Swithers, Kristen S.; DiPippo, Jonathan L.; Bruce, David C.; Detter, Christopher; Tapia, Roxanne & Han, Shunsheng [Show all 17 contributors for this article] (2011). Genome Sequence of Kosmotoga olearia Strain TBF 19.5.1, a Thermophilic Bacterium with a Wide Growth Temperature Range, Isolated from the Troll B Oil Platform in the North Sea. Journal of Bacteriology. ISSN 0021-9193. 193(19), p. 5566–5567. doi: 10.1128/JB.05828-11. Full text in Research Archive
• Nesbø, Camilla Lothe; Kumaraswamy, Rajkumari; Dlutek, Marlena; Doolittle, WF & Foght, Julia (2010). Searching for Mesophilic Thermotogales Bacteria: "Mesotogas" in the Wild. Applied and Environmental Microbiology. ISSN 0099-2240. 76(14), p. 4896–4900. doi: 10.1128/AEM.02846-09. Full text in Research Archive
• Nesbø, Camilla Lothe; Bapteste, Eric; Curtis, Bruce; Dahle, Håkon; Lopez, Philippe & Macleod, Dave [Show all 11 contributors for this article] (2009). The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. Journal of Bacteriology. ISSN 0021-9193. p. 1974–1978. doi: 10.1128/JB.01448-08. Full text in Research Archive
• Zhaxybayeva, O; Swithers, KS; Lapierre, P; Fournier, GP; Bickhart, DM & Deboy, RT [Show all 11 contributors for this article] (2009). On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 106(14), p. 5865–5870. doi: 10.1073/pnas.0901260106. Full text in Research Archive
• Koenig, Jeremy; Boucher, Yan; Charlebois, Robert; Nesbø, Camilla Lothe; Zhaxybayeva, Olga & Bapteste, Eric [Show all 10 contributors for this article] (2008). Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments. Environmental Microbiology. ISSN 1462-2912. 10, p. 1024–1024. Full text in Research Archive
• Zhaxybayeva, Olga; Nesbø, Camilla Lothe & Doolittle, Ford (2007). Systematic overestimation of gene gain through false diagnosis of gene absence. Genome Biology. ISSN 1465-6906. 8, p. 402–402. Full text in Research Archive

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• Nayfach, S; Roux, S; Seshadri, R; Udwary, D; Varghese, Neha & Schulz, F [Show all 263 contributors for this article] (2021). Publisher Correction: A genomic catalog of Earth’s microbiomes (Nature Biotechnology, (2021), 39, 4, (499-509), 10.1038/s41587-020-0718-6). Nature Biotechnology. ISSN 1087-0156. 39(4), p. 520–520. doi: 10.1038/s41587-020-00769-4. Full text in Research Archive
• Haverkamp, Thomas Hendricus Augustus; Zhaxybayeva, Olga; Geslin, Claire; Lossouarn, Julien; Kublanov, Ilya V. & Nesbø, Camilla Lothe (2015). Pangenomic analysis of Thermosipho reveals limited gene flow between species but high within-species similarity. Full text in Research Archive
• Haverkamp, Thomas Hendricus Augustus & Nesbø, Camilla Lothe (2014). Comparative analysis of genome methylation in Thermotogae isolates from deep-sea hydrothermal vents. Full text in Research Archive Show summary

  Recent advances in single-molecule, real-time (SMRT) sequecing has made it possible to detected methylated bases in bacterial genomes. This method detects different types of DNA methylation while simulatously identify putative recognition sequences fro the methyltranserase proteins. Common prokaryotic base modifications are N4-methylcytosine (m4C), 5-meth- ylcytosine (m5c) and N6-methyladenine (m6A). Here we use SMRT sequencing to compare the m4C and m6A genomic methylation pattern of four Thermotogae isolates from deep-sea hydrothermal vents; Thermosipho melanesiensis 431, Marinitoga sp. strain 1137 and Thermosipho sp. strains 1063 and 1070. The members of the bacterial phylum Thermotogae can be found in ecosystems with hyperthermic to mesothermic conditions such as oilfields and hydrothermal vents.

• Nesbø, Camilla Lothe; Haverkamp, Thomas Hendricus Augustus; Foght, Julia; Birkeland, Kåre; Kublanov, Ilya & Zhaxybayeva, Olga (2014). There is a lot going on underground. Full text in Research Archive
• Pollo, Stephen & Nesbø, Camilla Lothe (2013). Temperature adaptation in the Thermotogales Bacterium Kosmotoga olearia. Full text in Research Archive
• Nesbø, Camilla Lothe (2012). Discovery and Characterization of the First Prophage in Thermotogales: a Tailed Bacteriophage Predicted to Infect Thermosipho and Thermotoga. Full text in Research Archive
• Nesbø, Camilla Lothe (2012). Mesotoga lineages: important bacterial constituents of the ‘rare biosphere’ in polluted environments. Full text in Research Archive

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