Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics

Cooper, Zachary S.; Rapp, Josephine Z.; Shoemaker, Anna M. D.; Anderson, Rika E.; Zhong, Zhi-Ping; Deming, Jody W.

doi:10.3389/fmicb.2022.879116

Title: Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics

Journal Article · Mon Jun 06 00:00:00 EDT 2022 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2022.879116· OSTI ID:1871225

Cooper, Zachary S.; Rapp, Josephine Z.; Shoemaker, Anna M. D.; Anderson, Rika E.; Zhong, Zhi-Ping; Deming, Jody W.

Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner–Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited. Assessing these new extremophile genomes in a pangenomic context has provided a unique view into the ecological and evolutionary history of the genus Marinobacter , particularly with regard to its remarkable diversity and its opportunism in extremely cold and saline environments.

View Journal Article

Cite

Export

Save

Research Organization:: USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); Gordon and Betty Moore Foundation

Grant/Contract Number:: AC02-772 05CH11231; AC02-05CH11231; 5488

OSTI ID:: 1871225

Alternate ID(s):: OSTI ID: 1904090

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 13; ISSN 1664-302X

Publisher:: Frontiers Media SACopyright Statement

Country of Publication:: Switzerland

Language:: English

References (100)

Intra‐ice and intra‐sediment cryopeg brine occurrence in permafrost near Utqiaġvik (Barrow) Iwahana, Go; Cooper, Zachary S.; Carpenter, Shelly D. Permafrost and Periglacial Processes, Vol. 32, Issue 3 https://doi.org/10.1002/ppp.2101	journal	March 2021
Genome Sequence of Deep-Sea Manganese-Oxidizing Bacterium Marinobacter manganoxydans MnI7-9 Wang, Haifang; Li, Hang; Shao, Zongze Journal of Bacteriology, Vol. 194, Issue 4 https://doi.org/10.1128/JB.06551-11	journal	February 2012
Marinobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from the Arctic Zhang, D. -C.; Li, H. -R.; Xin, Y. -H. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 6 https://doi.org/10.1099/ijs.0.65690-0	journal	June 2008
Anvi’o: an advanced analysis and visualization platform for ‘omics data Eren, A. Murat; Esen, Özcan C.; Quince, Christopher PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1319	journal	January 2015
Microbial ecology of the cryosphere: sea ice and glacial habitats Boetius, Antje; Anesio, Alexandre M.; Deming, Jody W. Nature Reviews Microbiology, Vol. 13, Issue 11 https://doi.org/10.1038/nrmicro3522	journal	September 2015
Brine Assemblages of Ultrasmall Microbial Cells within the Ice Cover of Lake Vida, Antarctica Kuhn, Emanuele; Ichimura, Andrew S.; Peng, Vivian Applied and Environmental Microbiology, Vol. 80, Issue 12 https://doi.org/10.1128/AEM.00276-14	journal	April 2014
The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights Bosi, Emanuele; Fondi, Marco; Orlandini, Valerio BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-016-3382-y	journal	January 2017
The enzymatic conversion of phosphonates to phosphate by bacteria Kamat, Siddhesh S.; Raushel, Frank M. Current Opinion in Chemical Biology, Vol. 17, Issue 4 https://doi.org/10.1016/j.cbpa.2013.06.006	journal	August 2013
ATP-binding-cassette (ABC) transport systems: Functional and structural aspects of the ATP-hydrolyzing subunits/domains Schneider, Erwin; Hunke, Sabine FEMS Microbiology Reviews, Vol. 22, Issue 1 https://doi.org/10.1111/j.1574-6976.1998.tb00358.x	journal	April 1998
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes Kim, M.; Oh, H. -S.; Park, S. -C. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 2 https://doi.org/10.1099/ijs.0.059774-0	journal	February 2014
Using MCL to Extract Clusters from Networks van Dongen, Stijn; Abreu-Goodger, Cei Bacterial Molecular Networks https://doi.org/10.1007/978-1-61779-361-5_15	book	October 2011
Role of Glyoxylate Shunt in Oxidative Stress Response Ahn, Sungeun; Jung, Jaejoon; Jang, In-Ae Journal of Biological Chemistry, Vol. 291, Issue 22 https://doi.org/10.1074/jbc.M115.708149	journal	April 2016
Ecology and evolution of bacterial microdiversity: Table 1 Schloter, Michael; Lebuhn, Michael; Heulin, Thierry FEMS Microbiology Reviews, Vol. 24, Issue 5 https://doi.org/10.1111/j.1574-6976.2000.tb00564.x	journal	December 2000
Permafrost evidence for severe winter cooling during the Younger Dryas in northern Alaska: YOUNGER DRYAS CLIMATE FROM PERMAFROST Meyer, Hanno; Schirrmeister, Lutz; Yoshikawa, Kenji Geophysical Research Letters, Vol. 37, Issue 3 https://doi.org/10.1029/2009GL041013	journal	February 2010
Bacterial Diversity Associated with Blood Falls, a Subglacial Outflow from the Taylor Glacier, Antarctica Mikucki, Jill A.; Priscu, John C. Applied and Environmental Microbiology, Vol. 73, Issue 12 https://doi.org/10.1128/AEM.01396-06	journal	June 2007
GToTree: a user-friendly workflow for phylogenomics Lee, Michael D. Bioinformatics, Vol. 35, Issue 20 https://doi.org/10.1093/bioinformatics/btz188	journal	March 2019
Assembly of long, error-prone reads using repeat graphs Kolmogorov, Mikhail; Yuan, Jeffrey; Lin, Yu Nature Biotechnology, Vol. 37, Issue 5 https://doi.org/10.1038/s41587-019-0072-8	journal	April 2019
Surface Area to Volume Ratio: A Natural Variable for Bacterial Morphogenesis Harris, Leigh K.; Theriot, Julie A. Trends in Microbiology, Vol. 26, Issue 10 https://doi.org/10.1016/j.tim.2018.04.008	journal	October 2018
Diversity and Structure of Bacterial Communities in Arctic versus Antarctic Pack Ice Brinkmeyer, R.; Knittel, K.; Jurgens, J. Applied and Environmental Microbiology, Vol. 69, Issue 11 https://doi.org/10.1128/AEM.69.11.6610-6619.2003	journal	November 2003
Prochlorococcus: the structure and function of collective diversity Biller, Steven J.; Berube, Paul M.; Lindell, Debbie Nature Reviews Microbiology, Vol. 13, Issue 1 https://doi.org/10.1038/nrmicro3378	journal	December 2014
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
The Ecology and Evolution of Pangenomes Brockhurst, Michael A.; Harrison, Ellie; Hall, James P. J. Current Biology, Vol. 29, Issue 20 https://doi.org/10.1016/j.cub.2019.08.012	journal	October 2019
Marinobacter shengliensis sp. nov., a moderately halophilic bacterium isolated from oil-contaminated saline soil Luo, Yi-Jing; Xie, Bai-Sheng; Lv, Xiang-Lin Antonie van Leeuwenhoek, Vol. 107, Issue 4 https://doi.org/10.1007/s10482-015-0401-y	journal	February 2015
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses Methe, B. A.; Nelson, K. E.; Deming, J. W. Proceedings of the National Academy of Sciences, Vol. 102, Issue 31 https://doi.org/10.1073/pnas.0504766102	journal	July 2005
Marinobacter alkaliphilus sp. nov., a novel alkaliphilic bacterium isolated from subseafloor alkaline serpentine mud from Ocean Drilling Program Site 1200�at South Chamorro Seamount, Mariana Forearc Takai, Ken; Moyer, Craig L.; Miyazaki, Masayuki Extremophiles, Vol. 9, Issue 1 https://doi.org/10.1007/s00792-004-0416-1	journal	August 2004
Modelled and measured dynamics of viruses in Arctic winter sea-ice brines Wells, Llyd E.; Deming, Jody W. Environmental Microbiology, Vol. 8, Issue 6 https://doi.org/10.1111/j.1462-2920.2006.00984.x	journal	June 2006
Low‐temperature chemotaxis, halotaxis and chemohalotaxis by the psychrophilic marine bacterium Colwellia psychrerythraea 34H Showalter, G. M.; Deming, J. W. Environmental Microbiology Reports, Vol. 10, Issue 1 https://doi.org/10.1111/1758-2229.12610	journal	December 2017
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life Parks, Donovan H.; Chuvochina, Maria; Waite, David W. Nature Biotechnology, Vol. 36, Issue 10 https://doi.org/10.1038/nbt.4229	journal	August 2018
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
Bacterial growth at −15 °C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1 Mykytczuk, Nadia C. S.; Foote, Simon J.; Omelon, Chris R. The ISME Journal, Vol. 7, Issue 6 https://doi.org/10.1038/ismej.2013.8	journal	February 2013
Halophilic microbial communities and their environments Oren, Aharon Current Opinion in Biotechnology, Vol. 33 https://doi.org/10.1016/j.copbio.2015.02.005	journal	June 2015
Microbial genome analysis: the COG approach Galperin, Michael Y.; Kristensen, David M.; Makarova, Kira S. Briefings in Bioinformatics, Vol. 20, Issue 4 https://doi.org/10.1093/bib/bbx117	journal	September 2017
Fast and sensitive protein alignment using DIAMOND Buchfink, Benjamin; Xie, Chao; Huson, Daniel H. Nature Methods, Vol. 12, Issue 1 https://doi.org/10.1038/nmeth.3176	journal	November 2014
Equations for Determining the Gas and Brine Volumes in Sea-Ice Samples Cox, G. F. N.; Weeks, W. F. Journal of Glaciology, Vol. 29, Issue 102 https://doi.org/10.3189/s0022143000008364	journal	January 1983
Cycloclasticus pugetii gen. nov., sp. nov., an Aromatic Hydrocarbon-Degrading Bacterium from Marine Sediments Dyksterhouse, S. E.; Gray, J. P.; Herwig, R. P. International Journal of Systematic Bacteriology, Vol. 45, Issue 1 https://doi.org/10.1099/00207713-45-1-116	journal	January 1995
seaborn: statistical data visualization Waskom, Michael Journal of Open Source Software, Vol. 6, Issue 60 https://doi.org/10.21105/joss.03021	journal	April 2021
Marinobacter confluentis sp. nov., a lipolytic bacterium isolated from a junction between the ocean and a freshwater lake Park, Sooyeon; Kim, Sona; Kang, Chul-Hyung International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue Pt_12 https://doi.org/10.1099/ijsem.0.000659	journal	December 2015
Marinobacter guineae sp. nov., a novel moderately halophilic bacterium from an Antarctic environment Montes, M. J.; Bozal, N.; Mercade, E. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 6 https://doi.org/10.1099/ijs.0.65298-0	journal	June 2008
The Entner-Doudoroff pathway: history, physiology and molecular biology Conway, Tyrrell FEMS Microbiology Letters, Vol. 103, Issue 1 https://doi.org/10.1111/j.1574-6968.1992.tb05822.x	journal	September 1992
Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a New, Extremely Halotolerant, Hydrocarbon-Degrading Marine Bacterium Gauthier, M. J.; Lafay, B.; Christen, R. International Journal of Systematic Bacteriology, Vol. 42, Issue 4 https://doi.org/10.1099/00207713-42-4-568	journal	October 1992
An inter-order horizontal gene transfer event enables the catabolism of compatible solutes by Colwellia psychrerythraea 34H Collins, R. Eric; Deming, Jody W. Extremophiles, Vol. 17, Issue 4 https://doi.org/10.1007/s00792-013-0543-7	journal	May 2013
Marinobacter nitratireducens sp. nov., a halophilic and lipolytic bacterium isolated from coastal surface sea water Vaidya, Bhumika; Kumar, Ravinder; Korpole, Suresh International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue Pt_7 https://doi.org/10.1099/ijs.0.000218	journal	July 2015
Marinobacter halophilus sp. nov., a halophilic bacterium isolated from a salt lake Zhong, Zhi-Ping; Liu, Ying; Liu, Hong-Can International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue Pt_9 https://doi.org/10.1099/ijs.0.000338	journal	September 2015
Linking pangenomes and metagenomes: the Prochlorococcus metapangenome Delmont, Tom O.; Eren, A. Murat PeerJ, Vol. 6 https://doi.org/10.7717/peerj.4320	journal	January 2018
Binning metagenomic contigs by coverage and composition Alneberg, Johannes; Bjarnason, Brynjar Smári; de Bruijn, Ino Nature Methods, Vol. 11, Issue 11 https://doi.org/10.1038/nmeth.3103	journal	September 2014
Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice Zhong, Zhi-Ping; Rapp, Josephine Z.; Wainaina, James M. mSystems, Vol. 5, Issue 3 https://doi.org/10.1128/msystems.00246-20	journal	June 2020
Completing bacterial genome assemblies with multiplex MinION sequencing Wick, Ryan R.; Judd, Louise M.; Gorrie, Claire L. Microbial Genomics, Vol. 3, Issue 10 https://doi.org/10.1099/mgen.0.000132	journal	October 2017
Bacteriorhodopsin Lanyi, Janos K. Annual Review of Physiology, Vol. 66, Issue 1 https://doi.org/10.1146/annurev.physiol.66.032102.150049	journal	March 2004
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
Bacterial use of choline to tolerate salinity shifts in sea-ice brines Firth, E.; Carpenter, S. D.; Sørensen, H. L. Elementa: Science of the Anthropocene, Vol. 4 https://doi.org/10.12952/journal.elementa.000120	journal	August 2016
Potential for primary productivity in a globally-distributed bacterial phototroph Graham, E. D.; Heidelberg, J. F.; Tully, B. J. The ISME Journal, Vol. 12, Issue 7 https://doi.org/10.1038/s41396-018-0091-3	journal	March 2018
Marinobacter piscensis sp. nov., a Moderately Halophilic Bacterium Isolated from Salty Food in Tunisia Hedi, Abdeljabbar; Cayol, Jean Luc; Sadfi, Najla Current Microbiology, Vol. 70, Issue 4 https://doi.org/10.1007/s00284-014-0754-x	journal	December 2014
Distinctive microbial communities in subzero hypersaline brines from Arctic coastal sea ice and rarely sampled cryopegs Cooper, Zachary S.; Rapp, Josephine Z.; Carpenter, Shelly D. FEMS Microbiology Ecology, Vol. 95, Issue 12 https://doi.org/10.1093/femsec/fiz166	journal	October 2019
KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold Aramaki, Takuya; Blanc-Mathieu, Romain; Endo, Hisashi Bioinformatics, Vol. 36, Issue 7 https://doi.org/10.1093/bioinformatics/btz859	journal	November 2019
Biogeochemical implications of the ubiquitous colonization of marine habitats and redox gradients by Marinobacter species Handley, Kim M.; Lloyd, Jonathan R. Frontiers in Microbiology, Vol. 4 https://doi.org/10.3389/fmicb.2013.00136	journal	January 2013
A Genomic Perspective on Protein Families Tatusov, R. L. Science, Vol. 278, Issue 5338 https://doi.org/10.1126/science.278.5338.631	journal	October 1997
Marinobacter vinifirmus sp. nov., a moderately halophilic bacterium isolated from a wine-barrel-decalcification wastewater Liebgott, Pierre-Pol; Casalot, Laurence; Paillard, Sebastien International Journal of Systematic and Evolutionary Microbiology, Vol. 56, Issue 11 https://doi.org/10.1099/ijs.0.64368-0	journal	November 2006
Marinobacter fonticola sp. nov., isolated from deep sea cold seep sediment Sun, Qing-lei; Sun, Yan-ling; Sun, Yuan-yuan International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 2 https://doi.org/10.1099/ijsem.0.003895	journal	February 2020
Marinobacter santoriniensis sp. nov., an arsenate-respiring and arsenite-oxidizing bacterium isolated from hydrothermal sediment Handley, K. M.; Hery, M.; Lloyd, J. R. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 4 https://doi.org/10.1099/ijs.0.003145-0	journal	April 2009
The limits for life under multiple extremes Harrison, Jesse P.; Gheeraert, Nicolas; Tsigelnitskiy, Dmitry Trends in Microbiology, Vol. 21, Issue 4 https://doi.org/10.1016/j.tim.2013.01.006	journal	April 2013
Supercooled Water Brines Within Permafrost—An Unknown Ecological Niche for Microorganisms: A Model for Astrobiology Gilichinsky, D.; Rivkina, E.; Shcherbakova, V. Astrobiology, Vol. 3, Issue 2 https://doi.org/10.1089/153110703769016424	journal	June 2003
Marinobacter maritimus sp. nov., a psychrotolerant strain isolated from sea water off the subantarctic Kerguelen islands Shivaji, S.; Gupta, Pratima; Chaturvedi, Preeti International Journal of Systematic and Evolutionary Microbiology, Vol. 55, Issue 4 https://doi.org/10.1099/ijs.0.63478-0	journal	July 2005
Marinobacter gudaonensis sp. nov., isolated from an oil-polluted saline soil in a Chinese oilfield Gu, Jun; Cai, Hua; Yu, Su-Lin International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 2 https://doi.org/10.1099/ijs.0.64522-0	journal	February 2007
Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H Czajka, Jeffrey J.; Abernathy, Mary H.; Benites, Veronica T. Proceedings of the National Academy of Sciences, Vol. 115, Issue 49 https://doi.org/10.1073/pnas.1807804115	journal	November 2018
Microbial communities evolve faster in extreme environments Li, Sheng-Jin; Hua, Zheng-Shuang; Huang, Li-Nan Scientific Reports, Vol. 4, Issue 1 https://doi.org/10.1038/srep06205	journal	August 2014
Marinobacter salexigens sp. nov., isolated from marine sediment Han, Ji-Ru; Ling, Si-Kai; Yu, Wen-Nan International Journal of Systematic and Evolutionary Microbiology, Vol. 67, Issue 11 https://doi.org/10.1099/ijsem.0.002337	journal	November 2017
The bacterial translation stress response Starosta, Agata L.; Lassak, Jürgen; Jung, Kirsten FEMS Microbiology Reviews, Vol. 38, Issue 6 https://doi.org/10.1111/1574-6976.12083	journal	November 2014
The Ubiquity of Small Species: Patterns of Local and Global Diversity Fenchel, Tom; Finlay, Bland J. BioScience, Vol. 54, Issue 8 https://doi.org/10.1641/0006-3568(2004)054[0777:TUOSSP]2.0.CO;2	journal	January 2004
Explaining microbial genomic diversity in light of evolutionary ecology Cordero, Otto X.; Polz, Martin F. Nature Reviews Microbiology, Vol. 12, Issue 4 https://doi.org/10.1038/nrmicro3218	journal	March 2014
Differences in Applied Redox Potential on Cathodes Enrich for Diverse Electrochemically Active Microbial Isolates From a Marine Sediment Lam, Bonita R.; Barr, Casey R.; Rowe, Annette R. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01979	journal	August 2019
A family of cold shock proteins in Bacillus subtilis is essential for cellular growth and for efficient protein synthesis at optimal and low temperatures Graumann, Peter; Wendrich, Thomas M.; Weber, Michael H. W. Molecular Microbiology, Vol. 25, Issue 4 https://doi.org/10.1046/j.1365-2958.1997.5121878.x	journal	August 1997
Biodiversity of cryopegs in permafrost Gilichinsky, David; Rivkina, Elizaveta; Bakermans, Corien FEMS Microbiology Ecology, Vol. 53, Issue 1 https://doi.org/10.1016/j.femsec.2005.02.003	journal	June 2005
Genome sequence analysis of Pseudomonas extremaustralis provides new insights into environmental adaptability and extreme conditions resistance Raiger Iustman, Laura J.; Tribelli, Paula M.; Ibarra, José G. Extremophiles, Vol. 19, Issue 1 https://doi.org/10.1007/s00792-014-0700-7	journal	October 2014
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads Wick, Ryan R.; Judd, Louise M.; Gorrie, Claire L. PLOS Computational Biology, Vol. 13, Issue 6 https://doi.org/10.1371/journal.pcbi.1005595	journal	June 2017
Marinobacter antarcticus sp. nov., a halotolerant bacterium isolated from Antarctic intertidal sandy sediment Liu, Chang; Chen, Chun-Xiao; Zhang, Xi-Ying International Journal of Systematic and Evolutionary Microbiology, Vol. 62, Issue Pt_8 https://doi.org/10.1099/ijs.0.035774-0	journal	August 2012
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets Wu, Yu-Wei; Simmons, Blake A.; Singer, Steven W. Bioinformatics, Vol. 32, Issue 4 https://doi.org/10.1093/bioinformatics/btv638	journal	October 2015
Microbial life at -13 C in the brine of an ice-sealed Antarctic lake Murray, A. E.; Kenig, F.; Fritsen, C. H. Proceedings of the National Academy of Sciences, Vol. 109, Issue 50 https://doi.org/10.1073/pnas.1208607109	journal	November 2012
Marinobacter salsuginis sp. nov., isolated from the brine–seawater interface of the Shaban Deep, Red Sea Antunes, André; França, Luis; Rainey, Fred A. International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 5 https://doi.org/10.1099/ijs.0.64862-0	journal	May 2007
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy Sieber, Christian M. K.; Probst, Alexander J.; Sharrar, Allison Nature Microbiology, Vol. 3, Issue 7 https://doi.org/10.1038/s41564-018-0171-1	journal	May 2018
Halomonas and Marinobacter ecotypes from hydrothermal vent, subseafloor and deep-sea environments: Halomonas and Marinobacter from hydrothermal vent habitats Kaye, Jonathan Z.; Sylvan, Jason B.; Edwards, Katrina J. FEMS Microbiology Ecology, Vol. 75, Issue 1 https://doi.org/10.1111/j.1574-6941.2010.00984.x	journal	November 2010
Microbial characterization of a subzero, hypersaline methane seep in the Canadian High Arctic Niederberger, Thomas D.; Perreault, Nancy N.; Tille, Stephanie The ISME Journal, Vol. 4, Issue 10 https://doi.org/10.1038/ismej.2010.57	journal	May 2010
Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines Rapp, Josephine Z.; Sullivan, Matthew B.; Deming, Jody W. Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.701186	journal	July 2021
Genomic and physiological characterization and description of Marinobacter gelidimuriae sp. nov., a psychrophilic, moderate halophile from Blood Falls, an antarctic subglacial brine Chua, Michelle J.; Campen, Richard L.; Wahl, Lindsay FEMS Microbiology Ecology, Vol. 94, Issue 3 https://doi.org/10.1093/femsec/fiy021	journal	February 2018
Marinobacter algicola sp. nov., isolated from laboratory cultures of paralytic shellfish toxin-producing dinoflagellates Green, D. H. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 3 https://doi.org/10.1099/ijs.0.63447-0	journal	March 2006
Accelerated Profile HMM Searches Eddy, Sean R. PLoS Computational Biology, Vol. 7, Issue 10 https://doi.org/10.1371/journal.pcbi.1002195	journal	October 2011
VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature Zablocki, Olivier; Michelsen, Michelle; Burris, Marie PeerJ, Vol. 9 https://doi.org/10.7717/peerj.11088	journal	January 2021
Genome-scale models of bacterial metabolism: reconstruction and applications Durot, Maxime; Bourguignon, Pierre-Yves; Schachter, Vincent FEMS Microbiology Reviews, Vol. 33, Issue 1 https://doi.org/10.1111/j.1574-6976.2008.00146.x	journal	January 2009
Metagenomic Identification of a Novel Salt Tolerance Gene from the Human Gut Microbiome Which Encodes a Membrane Protein with Homology to a brp/blh-Family β-Carotene 15,15′-Monooxygenase Culligan, Eamonn P.; Sleator, Roy D.; Marchesi, Julian R. PLoS ONE, Vol. 9, Issue 7 https://doi.org/10.1371/JOURNAL.PONE.0103318	journal	July 2014
Marinobacter subterrani, a genetically tractable neutrophilic Fe(II)-oxidizing strain isolated from the Soudan Iron Mine Bonis, Benjamin M.; Gralnick, Jeffrey A. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00719	journal	July 2015
Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus Sulfurovum in Geographically Distinct Deep-Sea Hydrothermal Vents Moulana, Alief; Anderson, Rika E.; Fortunato, Caroline S. mSystems, Vol. 5, Issue 2 https://doi.org/10.1128/mSystems.00673-19	journal	April 2020
HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers Zhu, Qiyun; Kosoy, Michael; Dittmar, Katharina BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-717	journal	January 2014
Temperature dependence of metabolic rates for microbial growth, maintenance, and survival Price, P. B.; Sowers, T. Proceedings of the National Academy of Sciences, Vol. 101, Issue 13 https://doi.org/10.1073/pnas.0400522101	journal	March 2004
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies Kang, Dongwan D.; Li, Feng; Kirton, Edward PeerJ, Vol. 7 https://doi.org/10.7717/peerj.7359	journal	January 2019
Marinobacter persicus sp. nov., a moderately halophilic bacterium from a saline lake in Iran Bagheri, Maryam; Amoozegar, Mohammad Ali; Didari, Maryam Antonie van Leeuwenhoek, Vol. 104, Issue 1 https://doi.org/10.1007/s10482-013-9923-3	journal	April 2013
Extensive Gene Acquisition in the Extremely Psychrophilic Bacterial Species Psychroflexus torquis and the Link to Sea-Ice Ecosystem Specialism Feng, Shi; Powell, Shane M.; Wilson, Richard Genome Biology and Evolution, Vol. 6, Issue 1 https://doi.org/10.1093/gbe/evt209	journal	January 2014
Carbon-Phosphorus Lyase—the State of the Art Stosiek, Natalia; Talma, Michał; Klimek-Ochab, Magdalena Applied Biochemistry and Biotechnology, Vol. 190, Issue 4 https://doi.org/10.1007/s12010-019-03161-4	journal	December 2019
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement Walker, Bruce J.; Abeel, Thomas; Shea, Terrance PLoS ONE, Vol. 9, Issue 11 https://doi.org/10.1371/journal.pone.0112963	journal	November 2014
Abundant dissolved genetic material in Arctic sea ice Part II: Viral dynamics during autumn freeze-up Collins, R. Eric; Deming, Jody W. Polar Biology, Vol. 34, Issue 12 https://doi.org/10.1007/s00300-011-1008-z	journal	June 2011
Lateglacial and Holocene isotopic and environmental history of northern coastal Alaska – Results from a buried ice-wedge system at Barrow Meyer, Hanno; Schirrmeister, Lutz; Andreev, Andrei Quaternary Science Reviews, Vol. 29, Issue 27-28 https://doi.org/10.1016/j.quascirev.2010.08.005	journal	December 2010

Similar Records

Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice

Journal Article · Tue Jun 30 00:00:00 EDT 2020 · mSystems · OSTI ID:1871225

Zhong, Zhi-Ping; Rapp, Josephine Z.; Wainaina, James M.; +10 more

Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources

Journal Article · Fri Aug 24 00:00:00 EDT 2012 · BMC Genomics · OSTI ID:1871225

Siddaramappa, Shivakumara; Challacombe, Jean F.; Petersen, Jeannine M.; +2 more

Comparative genomics reveals complex natural product biosynthesis capacities and carbon metabolism across host‐associated and free‐living Aquimarina ( Bacteroidetes, Flavobacteriaceae ) species

Journal Article · Mon Aug 05 00:00:00 EDT 2019 · Environmental Microbiology · OSTI ID:1871225

Silva, Sandra G.; Blom, Jochen; Keller‐Costa, Tina; +1 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
cryopeg
extremophile bacteria
evolution
ecology
pangenomics
oceanography
astrobiology

Title: Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics

Citation Formats

References (100)

Similar Records

Related Subjects