Abby SS, Cury J, Guglielmini J, Néron B, Touchon M, Rocha EPC. Identification of protein secretion systems in bacterial genomes. Sci Rep. 2016;6:23080.
Article
CAS
PubMed
PubMed Central
Google Scholar
Abe F. Dynamic structural changes in microbial membranes in response to high hydrostatic pressure analyzed using time-resolved fluorescence anisotropy measurement. Biophys Chem. 2013;183:3–8.
Article
CAS
PubMed
Google Scholar
Allen EA, Facciotti D, Bartlett DH. Monosaturated but not polyunsaturated fatty acids are required for growth of the deep-sea bacterium Photobacterium profundum SS9 at high pressure and low temperature. Appl Environ Microbiol. 1999;65:1710–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Article
CAS
PubMed
Google Scholar
Anderson RE, Brazelton WJ, Baross JA. Is the genetic landscape of the deep subsurface biosphere affected by viruses? Front Microbiol. 2011;2:219.
Article
PubMed
PubMed Central
Google Scholar
Aono E, Baba T, Ara T, Nishi T, Nakamichi T, Inamoto E, Toyonaga H, Hasegawa M, Takai Y, Okumura Y, Baba M, Tomita M, Kato C, Oshima T, Nakasone K, Mori H. Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep sea floor sediments. Mol BioSyst. 2010;6:1216–26.
Article
CAS
PubMed
Google Scholar
Arrieta JM, Mayol E, Hansman RL, Herndl GJ, Dittmar T, Duarte CM. Dilution limits dissolved organic carbon utilization in the deep ocean. Science. 2015;348:331–3.
Article
CAS
PubMed
Google Scholar
Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Grosdidier EGA, Hernandez C, Ioannidis V, Kuznetsov D, Liechti R, Moretti S, Mostaguir K, Redaschi N, Rossier G, Xenarios I, Stockinger H. ExPASy: SIB bioinformatics resource portal. Nucl Acid Res. 2012;40:W597–603.
Article
CAS
Google Scholar
Baker LJ, Freed LL, Easson CG, Lopez JV, Fenolio D, Sutton TT, Nyholm SV, Hendry TA. Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment. eLife. 2019;8:e47606.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler T, Alekseyev MA, Pevzner PA. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bartlett D, Chi E. Genetic characterization of ompH mutants in the deep-sea bacterium Photobacterium sp. strain SS9. Arch. Microbiol. 1994;162:323–8.
CAS
Google Scholar
Bartlett D, Wright M, Yayanos AA, Silverman M. Isolation of a gene regulated by hydrostatic pressure in a deep-sea bacterium. Nature. 1989;342:572–4.
Article
CAS
PubMed
Google Scholar
Bertelli C, Laird MR, Williams KP, Simon Fraser University Research Computing Group, Lau BY, Hoad G, Winsor GL, Brinkman FSL. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucl Acid Res. 2017;45:W30-W35.
Beszteri B, Temperton B, Frickenhaus S, Giovannoni SJ. Average genome size: a potential source of bias in comparative metagenomics. ISME J. 2010;4:1075–7.
Article
PubMed
Google Scholar
Boeuf D, Edwards BR, Eppley JM, Hu SK, Poff KE, Romano AE, Caron DA, Karl DM, DeLong EF. Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean. Proc Natl Acad Sci. 2019;201903080.
Bowman JP. The family Colwelliaceae. Prokaryotes. 2014:179–95.
Cabello-Yeves PJ, Rodriguez-Valera F. Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome. Microbiome. 2019;7:117.
Article
PubMed
PubMed Central
Google Scholar
Campanaro S, Vezzi A, Vitulo N, Lauro FM, D’Angelo M, Simonato F, Cestaro A, Malacrida G, Bertoloni G, Valle G, Bartlett DH. Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains. BMC Genomics. 2005;6:122.
Article
PubMed
PubMed Central
CAS
Google Scholar
Campanaro S, De Pascale F, Telatin A, Schiavon R, Bartlett DH, Valle G. The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain. BMC Genomics. 2012;13:567.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen SC, Sun GX, Rosen BP, Zhang SY, Deng Y, Zhu BK, Rensing C, Zhu YG. Recurrent horizontal transfer of arsenite methyltransferase genes facilitated adaptation of life to arsenic. Sci Rep. 2017;7:7741.
Article
PubMed
PubMed Central
CAS
Google Scholar
Chi E, Bartlett DH. An rpoE-like locus controls outer membrane protein synthesis and growth at cold temperatures and high pressures in the deep-sea bacterium Photobacterium sp. strain SS9. Mol Microbiol. 1995;17:713–26.
Article
CAS
PubMed
Google Scholar
Chikuma S, Kasahara R, Kato C, Tamegai H. Bacterial adaptation to high pressure: a respiratory system in the deep-sea bacterium Shewanella violacea DSS12. FEMS Microbiol Lett. 2007;267:108–12.
Article
CAS
PubMed
Google Scholar
Colangelo-Lillis JR, Deming JW. Genomic analysis of cold-active Colwelliaphage 9A and psychrophilic phage-host interactions. Extremophiles. 2013;17:99–114.
Article
CAS
PubMed
Google Scholar
Collins RE, Deming JW. An inter-order horizontal gene transfer event enables the catabolism of compatible solutes by Colwellia psychrerythraea 34H. Extremophiles. 2013;17:601–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dalmasso C, Oger P, Selva G, Courtine D, L'Haridon S, Garlaschelli A, Roussel E, Miyazaki J, Reveillaud J, Jebbar M, Takai K, Maignien L, Alain K. Thermococcus piezophilus sp. nov., a novel hyperthermophilic and piezophilic archaeon with a broad pressure range for growth, isolated from a deepest hydrothermal vent at the mid-Cayman rise. Syst Appl Microbiol. 2016;39:440–4.
Article
CAS
PubMed
Google Scholar
Paul S, Bag SK, Das S, Harvill ET, Dutta C. Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes. Genome Biol. 2008;9:R70.
Article
PubMed
PubMed Central
CAS
Google Scholar
De Brito DM, Maracaja-Coutinho V, de Farias ST, Batista LV, do Rêgo TG. A novel method to predict genomic islands based on mean shift clustering algorithm. PLoS One. 2016;11:e0146352.
Article
PubMed
PubMed Central
Google Scholar
DeLong E, Franks DG, Yayanos AA. Evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria. Appl Environ Microbiol. 1997;63:2105–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
DeLong EF, Yayanos AA. Adaptation of the membrane lipids of a deep-sea bacterium to changes in hydrostatic pressure. Science. 1985;228:1101–3.
Article
CAS
PubMed
Google Scholar
DeLong EF, Yayanos AA. Biochemical function and ecological significance of novel bacterial lipids in deep-sea procaryotes. Appl Environ Microbiol. 1986;51:730–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard N, Martinez A, Sullivan MB, Edwards R, Rodriguez Brito B, Chisholm SW, Karl DM. Community genomics among stratified microbial assemblages in the ocean’s interior. Science. 2006;311:496–503.
Article
CAS
PubMed
Google Scholar
Deming JW, Somers LK, Straube WL, Swartz DG, Macdonell MT. Isolation of an obligately barophilic bacterium and description of a new genus, Colwellia gen. Nov. Systemic and Applied Microbiology. 1988;10:152–60.
Article
Google Scholar
Di Giulio M. A comparison of proteins from Pyrococcus furiosus and Pyrococcus abyssi: barophily in the physicochemical properties of amino acids and in the genetic code. Gene. 2005;346:1–6.
Article
PubMed
CAS
Google Scholar
Dombrowski N, Teske AP, Baker BJ. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat Commun. 2018;9:4999.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dyksma S, Bischof K, Fuchs BM, Hoffmann K, Meier D, Meyerdierks A, Pjevac P, Probandt D, Richter M, Stepanauskas R, Mußmann M. Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. ISME J. 2016;10:1939–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
El-Hajj ZW, Tryfona T, Allcock DJ, Hasan F, Lauro FM, Sawyer L, Bartlett DH, Ferguson GP. Importance of proteins controlling initiation of DNA replication in the growth of the high-pressure-loving bacterium Photobacterium profundum SS9. J Bacteriol. 2009;191:6383–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucl Acid Res. 2002;30:1575–84.
Article
CAS
Google Scholar
Eloe EA, Lauro FM, Vogel RF, Bartlett DH. The deep-sea bacterium Photobacterium profundum SS9 utilizes separate flagellar systems for swimming and swarming under high-pressure conditions. Appl Environ Microbiol. 2008;74:6298–305.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eloe EA, Fadrosh DW, Novotny M, Allen LZ, Kim M, Lombardo MJ, Yee-Greenbaum J, Yooseph S, Allen EE, Lasken R, Williamson SJ, Bartlett DH. Going deeper: metagenome of a hadopelagic microbial community. PLoS One. 2011;6:e20388.
Article
CAS
PubMed
PubMed Central
Google Scholar
Faruque SM, Mekalanos JJ. Pathogenicity islands and phages in Vibrio cholerae evolution. Trends Microbiol. 2013;11:505–10.
Feng Z, Caceres NE, Sarath G, Barletta RG. Mycobacterium smegmatis L-alanine dehydrogenase (Ald) is required for proficient utilization of alanine as a sole nitrogen source and sustained anaerobic growth. J Bacteriol. 2002;184:5001–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Feng S, Powell SM, Wilson R, Bowman JP. Extensive gene acquisition in the extremely psychrophilic bacterial species Psychroflexus torquis and the link to sea-ice ecosystem specialism. Genome Biol Evol. 2014;6:133–48.
Article
PubMed
PubMed Central
Google Scholar
Fontanez KM, Eppley JM, Samo TJ, Karl DM, DeLong EF. Microbial community structure and function on sinking particles in the North Pacific subtropical gyre. Front Microbiol. 2015;6:469.
Article
PubMed
PubMed Central
Google Scholar
Gallegos MT, Schleif R, Bairoch A, Hofmann K, Ramos JL. Arac/XylS family of transcriptional regulators. Microbiol Mol Biol Rev. 1997;61:393–410.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ganesh S, Parris DJ, DeLong EF, Stewart FJ. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. ISME J. 2014;8:187–211.
Article
CAS
PubMed
Google Scholar
Guy L, Kultima JR, Andersson SGE. genoPlotR: comparative gene and genome visualization in R. Bioinformatics. 2010;26:2334–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guelorget A, Roovers M, Guérineau V, Barbey C, Li X, Golinelli-Pimpaneau B. Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase. Nucl Acid Res. 2010;38:6206–18.
Article
CAS
Google Scholar
Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM, Harris SR. Phandango: an interactive viewer for bacterial population genomics. Bioinformatics. 2018;34:292–3.
Article
CAS
PubMed
Google Scholar
Hoffmann K, Hassenrück C, Salman-Carvalho V, Holtappels M, Bienhold C. Response of bacterial communities to different detritus compositions in Arctic deep-sea sediments. Front Microbiol. 2017;8:226.
Google Scholar
Holtwick R, Meinhardt F, Keweloh H. cis-trans isomerization of unsaturated fatty acids: Cloning and sequencing of the cti gene from Pseudomonas putida P8. Appl Environ Microbiol. 1997;63:4292–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hu P, Dubinsky EA, Probst AJ, Wang J, Sieber CMK, Tom LM, et al. Simulation of oil plume reveals substrate specialization within a complex community of hydrocarbon degraders. Proc Natl Acad Sci. 2017;114(28):7432–7437.
Hummer G, Garde S, Garcia AE, Paulaitis ME, Pratt LR. The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins. Proc Natl Acad Sci. 1998;95:1552–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huston AL, Krieger-Brockett BB, Deming JW. Remarkably low temperature optima for extracellular enzyme activity from Arctic bacteria and sea ice. Environ Microbiol. 2000;2:383–8.
Article
CAS
PubMed
Google Scholar
Hutter B, Dick T. Incrased alanine dehydrogenase activity during dormancy in Mycobacterium spegmatis. FEMS Microbiol Lett. 1998;167:7–11.
Article
CAS
PubMed
Google Scholar
Ivars-Martinez E, Martin-Cuadrado AB, D’Auria G, Mira A, Ferriera S, Johnson J, Friedman R, Rodriguez-Valera F. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME J. 2008;2:1194–212.
Article
CAS
PubMed
Google Scholar
Jebbar M, Franzetti B, Girard E, Oger P. Microbial diversity and adaptation to high hydrostatic pressure in deep-sea hydrothermal vents prokaryotes. Extremophiles. 2015;19:721–40.
Article
CAS
PubMed
Google Scholar
Jeong JA, Oh JI. Alanine dehydrogenases in mycobacteria. J Microbiol. 2019;57:81–92.
Article
CAS
PubMed
Google Scholar
Jun X, Lupeng L, Minjuan X, Oger P, Fengping W, Jebbar M, Xiang X. Complete genome sequence of the obligate piezophilic hyperthermophilic archaeon Pyrococcus yayanosii CH1. J Bacteriol. 2011;193:4297–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kiraga J, Mackiewicz P, Mackiewicz D, Kowalczuk M, Biecek P, Polak N, Smolarczyk K, Dudek MR, Cebrat S. The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms. BMC Genomics. 2007;8:163.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kleindienst S, Seidel M, Ziervogel K, Grim S, Loftis K, Harrison S, Malkin SY, Perkins MJ, Field J, Sogin ML, Dittmar T, Passow U, Medeiros PM, Joye SB. Chemical dispersants can suppress the activity of natural oil-degrading microoganisms. Proc Natl Acad Sci. 2015;112:14900–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Konstantinidis KT, Braff J, Karl DM, DeLong EF. Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre. Appl Environ Microbiol. 2009;75:5345–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kusube M, Kyaw TS, Tanikawa K, Chastain RA, Hardy KM, Cameron J, Bartlett DH. Colwellia marinimaniae sp. nov., a hyperpiezophilic species isolated from an amphipod within the challenger deep, Mariana trench. Int J Sys Evol Microbiol. 2017;67:824–31.
Article
CAS
Google Scholar
Kyrpides NC, Woyke T, Eisen JA, Garrity G, Lilburn TG, Beck BJ, Whitman WB, Hugenholtz P, Klenk HP. Genomic encyclopedia of type strains, phase I: the one thousand microbial genomes (KMG-I) project. Stand Genomic Sci. 2014;9:9031278.
Google Scholar
Landry Z, Swan BK, Herndl GJ, Stepanauskas R, Giovannoni SJ. SAR202 genomes from the dark ocean predict pathways for the oxidation of recalcitrant dissolved organic matter. mBio. 2017;8:e00413–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lauro FM, Chastain RA, Blankenship LE, Yayanos AA, Bartlett DH. The unique 16S rRNA genes of piezophiles reflect both phylogeny and adaptation. Appl Environ Microbiol. 2007a;73:838–45.
Article
CAS
PubMed
Google Scholar
Lauro FM, Tran K, Vezzi A, Vitulo N, Valle G, Bartlett DH. Large-scale transposon mutagenesis of Photobacterium profundum SS9 reveals new genetic loci important for growth at low temperature and high pressure. J Bacteriol. 2007b;190:1699–709.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lauro FM, Bartlett DH. Prokaryotic lifestyles in deep sea habitats. Extremophiles. 2008;12:15–25.
Article
PubMed
Google Scholar
Lauro FM, Chastain RA, Ferriera S, Johnson J, Yayanos AA, Bartlett DH. Draft genome sequence of the deep-sea bacterium Shewanella benthica strain KT99. Genome Announc. 2013a;1:e00210–3.
PubMed
PubMed Central
Google Scholar
Lauro FM, Stratton TK, Chastain RA, Ferriera S, Johnson J, Goldberg SMD, Yayanos AA, Bartlett DH. Complete genome sequence of the deep-sea bacterium Psychromonas strain CNPT3. Genome Announc. 2013b;1:e00304–13.
PubMed
PubMed Central
Google Scholar
Lauro FM, Eloe-Fadrosh EA, Richter TKS, Vitulo N, Ferriera S, Johnson JH, Bartlett DH. Ecotype diversity and conversion in Photobacterium profundum strains. PLoS One. 2014;9:e96953.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lee I, Kim YO, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Sys Evol Microbiol. 2016;66:1100–3.
Article
CAS
Google Scholar
Leon-Zayas R, Novotny M, Podell S, Shepard CM, Berkenpas E, Nikolenko S, Pevzner P, Lasken RS, Bartlett DH. Single cells within the Puerto Rico trench suggest hadal adaptation of microbial lineages. Appl Environ Microbiol. 2015;81:8265–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucl Acid Res. 2016;44:W242–5.
Article
CAS
Google Scholar
Li Z, Li X, Xiao X, Xu J. An integrative genomic island affects the adaptations of the piezophilic hyperthermophilic archaeon Pyrococcus yayanosii to high temperature and high hydrostatic pressure. Front Microbiol. 2016;7:1927.
PubMed
PubMed Central
Google Scholar
Li Z, Song Q, Wang Y, Xiao X, Xu J. Identification of a functional toxin-antitoxin system located in the genomic island PYG1 of piezophilic hyperthermophilic archaeon Pyrococcus yayanosii. Extremophiles. 2018;22:347–57.
Article
CAS
PubMed
Google Scholar
Loffeld B, Keweloh H. cis/trans isomerization of unsaturated fatty acids as possible control mechanism of membrane fluidity in Pseudomonas putida P8. Lipids. 1996;31:811–5.
Article
CAS
PubMed
Google Scholar
Lossouarn J, Dupont S, Gorlas A, Mercier C, Bienvenu N, Marguet E, Forterre P, Geslin C. An abyssal mobilome: viruses, plasmids, and vesicles from deep-sea hydrothermal vents. Res Microbiol. 2015;166:742–52.
Article
PubMed
Google Scholar
Lucas S, Han J, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Peters L, Mikhailova N, Teshima H, Detter JC, Han C, Tapia R, Land M, Hauser L, Kyrpides NC, Ivanova N, Pagani I, Vannier P, Oger P, Bartlett DH, Noll KM, Woyke T, Jebbar M. Complete genome sequence of the thermophilic, piezophilic, heterotrophic bacterium Marinitoga piezophila KA3. J Bacteriol. 2012;194:5974–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Luo H, Tolar BB, Swan BK, Zhang CL, Stepanauskas R, Moran MA, Hollibaugh JT. Single-cell genomics shedding light on marine Thaumarchaeota diversification. ISME J. 2014;8:732–6.
Article
CAS
PubMed
Google Scholar
Maddocks SE, Oyston PCF. Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology. 2008;154:3609–23.
Article
CAS
PubMed
Google Scholar
Martin D, Bartlett DH, Roberts MF. Solute accumulation in the deep-sea bacterium Photobacterium profundum. Extremophiles. 2002;6:507–14.
Article
CAS
PubMed
Google Scholar
Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008;9:286–98.
Article
CAS
PubMed
Google Scholar
Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27:2957–63.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mao D, Grogan DW. How a genetically stable extremophile evolves: modes of genome diversification in the Archaeon Sulfolobus acidocaldarius. J Bacteriol. 2017;199:e00177–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Anderson MHI, Billis K, Varghese N, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucl Acid Res. 2014;42:D560–7.
Article
CAS
Google Scholar
Martin-Cuadrado AB, Lopez-Garcia P, Alba JC, Moreira D, Monticelli L, Strittmatter A, Gottschalk G, Rodriguez-Valera F. Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS One. 2007;9:e914.
Article
CAS
Google Scholar
Marx JG, Carpenter SD, Deming JW. Production of cryoprotectant extracellular polysaccharide substances (EPS) by the marine psychrophilic bacterium Colwellia psychrerythraea strain 34H under extreme conditions. Can J Microbiol. 2009;55:63–72.
Article
CAS
PubMed
Google Scholar
Mason OU, Han J, Woyke T, Jansson JK. Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater horizon oil spill. Front Microbiol. 2014;5:332.
Article
PubMed
PubMed Central
Google Scholar
McCutcheon JP, Moran NA. Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol. 2012;10:13–26.
Article
CAS
Google Scholar
McDonald JH, Grasso AM, Rejto LK. Patterns of temperature adaptation in proteins from Methanococcus and bacillus. Mol Biol Evol. 1999;16:1785–90.
Article
CAS
PubMed
Google Scholar
Methé BA, Nelson KE, Deming JW, Momen B, Melamud E, Zhang X, Moult J, Madupu R, Nelson WC, Dodson RJ, Brinkac LM, Daugherty SC, Durkin AS, DeBoy RT, Kolonay JF, Sullivan SA, Zhou L, Davidsen TM, Wu M, Huston AL, Lewis M, Weaver B, Weidman JF, Khouri H, Utterback TR, Feldblyum TV, Fraser CM. The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses. Proc Natl Acad Sci. 2005;102:10913–8.
Article
PubMed
CAS
PubMed Central
Google Scholar
Michoud G, Jebbar M. High hydrostatic pressure adaptive strategies in an obligate piezophile Pyrococcus yayanosii. Sci Rep. 2016;6:27289.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In 2010 Gateway Computing Environments Workshop (GCE). 2010;1–8.
Mußmann M, Pjevac P, Krüger K, Dyksma S. Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments. ISME J. 2017;11:1276–81.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nakayama A, Saito R, Matsuzaki M, Yano Y, Yoshida K. Phylogenetic analysis based on 16S rRNA gene sequences of deep-sea bacteria isolated from intestinal contents of deep-sea fishes retrieved from the abyssal zone. J Gen Appl Microbiol. 2005;51:385–94.
Article
CAS
PubMed
Google Scholar
Navarro CA, von Bernath D, Jerez CA. Heavy metal resistance strategies of acidophilic bacteria and their acquisition: importance for biomining and bioremediation. Biol Res. 2013;46:363–71.
Article
PubMed
Google Scholar
Nogi Y, Hosoya S, Kato C, Horikoshi K. Colwellia piezophila sp. nov., a novel piezophilic species from deep-sea sediments of the Japan trench. Int J Sys Evol Microbiol. 2004;54:1627–31.
Article
CAS
Google Scholar
Nogi Y. Microbial life in the deep sea: Psychropiezophiles. In: Margesin R, editor. Psychrophiles: from biodiversity to biotechnology. Cham: Springer; 2017. p. 133–52.
Chapter
Google Scholar
Nunn BL, Slattery KV, Cameron KA, Timmins-Schiffman E, Junge K. Proteomics of Colwellia psychrerythraea at subzero temperatures – a life with limited movement, flexible membranes and vital DNA repair. Environ Microbiol. 2015;17:2319–35.
Article
CAS
PubMed
Google Scholar
Oger PM, Jebbar M. The many ways of coping with pressure. Res Microbiol. 2010;161:799–809.
Article
PubMed
Google Scholar
Orellana LH, Jerez CA. A genomic island provides Acidithiobacillus ferrooxidans ATCC 53993 additional copper resistance: a possible competitive advantage. Appl Microbiol Biotech. 2011;92:761.
Article
CAS
Google Scholar
Pachiadaki MG, Sintes E, Bergauer K, Brown JM, Record NR, Swan BK, Mathyer ME, Hallam SJ, Lopez-Garcia P, Takaki Y, Nunoura T, Woyke T, Herndl GJ, Stepanauskas R. Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Science. 2017;358:1046–51.
Article
CAS
PubMed
Google Scholar
Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, Fookes M, Falush D, Keane JA, Parkhill J. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31:3691–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pante E, Simon-Bouhet B. marmap: A package for importing, plotting, and analyizng bathymetric and topographic data in R. PLoS One. 2013;8:e73051.
Article
CAS
PubMed
PubMed Central
Google Scholar
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peoples LM, Bartlett DH. Ecogenomics of deep-ocean microbial bathytypes. In: Chénard C, Lauro FM, editors. Microbial ecology of extreme environments. Springer: Cham; 2017. p. 7–50.
Chapter
Google Scholar
Peoples LM, Donaldson S, Osuntokun O, Xia Q, Nelson A, Blanton J, Allen EE, Church MJ, Bartlett DH. Vertically distinct microbial communities in the Mariana and Kermadec trenches. PLoS One. 2018;13:e0195102.
Article
PubMed
PubMed Central
CAS
Google Scholar
Peoples LM. Composition and Functional Potential of Hadal Microbial Communities. eScholarship, University of California; 2018.
Peoples LM, Grammatopoulou E, Pombrol M, Xu X, Osuntokun O, Blanton J, Allen EE, Nunnally CC, Drazen JC, Mayor DJ, Bartlett DH. Microbial community diversity within sediments from two geographically separated hadal trenches. Front Microbiol. 2019a;10:347.
Article
PubMed
PubMed Central
Google Scholar
Peoples LM, Norenberg M, Price D, McGoldrick M, Novotny M, Bochdansky A, Bartlett DH. A full-ocean depth rated modular lander and pressure-retaining sampler capable of collecting hadal-endemic microbes under in situ conditions. Deep Sea Res Pt 1. 2019b;143:50–57.
Pinchuk EG, Hill EA, Geydebrekht OV, De Ingeniis J, Zhang X, Osterman A, Scott JH, Reed SB, Romine MF, Konopka AE, Beliaev AS, Fredrickson JK, Reed JL. Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation. PLoS One. 2010;6:e1000822.
Google Scholar
Planet PJ, Kachlany SC, Fine DH, DeSalle R, Figurski DH. The widespread colonization island of Actinobacillus actinomycetemcomitans. Nat Genet. 2003;34:193–8.
Article
CAS
PubMed
Google Scholar
Pradel N, Ji B, Gimenez G, Talla E, Lenoble P, Garel M, Tamburini C, Fourquet P, Lebrun R, Bertin P, Denis Y, Pophillat M, Barbe V, Ollivier B, Dolla A. The first genomic and proteomic characterization of a deep-sea sulfate reducer: insights into the piezophilic lifestyle of Desulfovibrio piezophilus. PLoS One. 2013;8:e55130.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 2012;28:1823–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pu M, Duriez P, Arazi M, Rowe-Magnus DA. A conserved tad pilus promotes Vibrio vulnificus oyster colonization. Environ Microbiol. 2018;20:828–41.
Article
CAS
PubMed
Google Scholar
Qin QL, Li Y, Zhang YJ, Zhou ZM, Zhang WX, Chen XL, Zhang XY, Zhou BC, Wang L, Zhang YZ. Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913. ISME J. 2011;5:274.
Article
PubMed
Google Scholar
Redmond MC, Valentine DL. Natural gas and temperature structured a microbial community response to the Deepwater horizon oil spill. Proc Nat Acad Sci. 2012;109:20292–7.
Article
CAS
PubMed
Google Scholar
Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome. 2017;5:69.
Article
PubMed
PubMed Central
Google Scholar
Roux S, Enault F, Hurwitz BL, Sullivan MB. VirSorter: mining viral signal from microbial genomic data. PeerJ. 2015;3:e985.
Article
PubMed
PubMed Central
CAS
Google Scholar
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.
Article
CAS
PubMed
Google Scholar
Showalter GM, Deming JW. Low-temperature chemotaxis, halotaxis and chemohalotaxis by the psychrophilic marine bacterium Colwellia psychrerythraea 34H. Environ Microbiol Rep. 2018;10:92–101.
Article
CAS
PubMed
Google Scholar
Simonato F, Campanaro S, Lauro FM, Vezzi A, D’Angelo M, Vitulo N, Valle G, Bartlett DH. Piezophilic adaptation: a genomic point of view. J Biotechnol. 2006;126:11–25.
Article
CAS
PubMed
Google Scholar
Simpson RK, Gilmour A. The effect of high hydrostatic pressure on the activity of intraceullar enzyems of Listeria monocytogenes. Lett Appl Microbiol. 1997;25:48–53.
Article
CAS
PubMed
Google Scholar
Smedile F, Messina E, La Cono V, Tsoy O, Monticelli LS, Borghini M, Giuliano L, Golyshin PN, Mushegian A, Yakimov MM. Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of the Mediterranean Sea, Matapan-Vavilov Deep. Environ Microbiol. 2013;15:167–82.
Article
PubMed
Google Scholar
Somero GN. Protein adaptations to temperature and pressure: complementary roles of adaptive changes in amino acid sequence and internal milieu. Comp Biochem Physiol B: Biochem Mol Biol. 2003;136:577–91.
Article
CAS
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sutton GG, White O, Adams MD, Kerlavage AR. TIGR assembler: a new tool for assembling large shotgun sequencing projects. Genome Sci Technol. 1995;1:9–19.
Article
CAS
Google Scholar
Somero GN. Adaptations to high hydrostatic pressure. Annu Rev Physiol. 1992;1:557–77.
Article
Google Scholar
Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D, Reinthaler T, Poulton NJ, Masland EDP, Gomez ML, Sieracki ME, DeLong EF, Herndl GJ, Stepanauskas R. Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science. 2011;333:1296–300.
Article
CAS
PubMed
Google Scholar
Swan BK, Chaffin MD, Martinez-Garcia M, Morrison HG, Field EK, Poulton NJ, Masland EDP, Harris CC, Sczyrba A, Chain PSG, Koren S, Woyke T, Stepanauskas R. Genomic and metabolic diversity of marine group I Thaumarchaeota in the mesopelagic of two subtropical gyres. PLoS One. 2014;9:e95380.
Article
PubMed
PubMed Central
Google Scholar
Tabor PS, Deming JW, Ohwada K, Colwell RR. Activity and growth of microbial populations in pressurized deep-sea sediment and animal gut samples. Appl Environ Microbiol. 1982;44:413–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tamegai H, Nishikawa S, Haga M, Bartlett DH. The respiratory system of the piezophile Photobacterium profundum SS9 grown under various pressures. Biosci Biotechnol Biochem. 2012;76:1506–10.
Article
CAS
PubMed
Google Scholar
Tarn J, Peoples LM, Hardy K, Cameron J, Bartlett DH. Identification of free-living and particle-associated microbial communities present in hadal regions of the Mariana trench. Front Microbiol. 2016;7:665.
Article
PubMed
PubMed Central
Google Scholar
Techtmann SM, Fitzgerald KS, Stelling SC, Joyner DC, Uttukar SM, Harris AP, Alshibli NK, Brown SD. Hazen TC. Front Environ Sci. 2016;4:33.
Article
Google Scholar
Thrash JC, Temperton B, Swan BK, Landry ZC, Woyke T, DeLong EF, Stepanauskas R, Giovannoni SJ. Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. ISME J. 2014;8:1440–51.
Article
PubMed
CAS
Google Scholar
Tomich M, Planet PJ, Figurski DH. The tad locus: postcards from the widespread colonization island. Nat Rev Microbiol. 2007;5:363–75.
Article
CAS
PubMed
Google Scholar
Tully BJ, Wheat CG, Glazer BT, Huber JA. A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. ISME J. 2018;12:1–16.
Article
CAS
PubMed
Google Scholar
Usui K, Hiraki T, Kawamoto J, Kurihara T, Nogi Y, Kato C, Abe F. Eicosapentaenoic acid plays a role in stabilizing dynamic membrane structure in the deep-sea piezophile Shewanella violacea: a study employing high-pressure time-resolved fluorescence anisotropy measurement. Biochim Biophys Acta. 2012;1818:574–83.
Article
CAS
PubMed
Google Scholar
Vannier P, Marteinsson VT, Fridjonsson OH, Oger P, Jebbar M. Complete genome sequence of the hyperthermophilic, pezophilic, heterotrophic, and carboxydotrophic archaeon Thermococcus barophilus MP. J Bacteriol. 2011;193:1481–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vannier P, Michoud G, Oger P, Marteinsson V, Jebbar M. Genome expression of Thermococcus barophilus and Thermococcus kodakarensis in response to different hydrostatic pressure conditions. Res Microbiol. 2015;166:717–25.
Article
CAS
PubMed
Google Scholar
Vezzi A, Campanaro S, D’angelo M, Simonato F, Vitulo N, Lauro FM, Cestaro A, Malacrida G, Simionati B, Cannata N, Romualdi C, Bartlett DH, Valle G. Life at depth: Photobacterium profundum genome sequence and expression analysis. Science. 2005;307:1459–61.
Article
CAS
PubMed
Google Scholar
Wang F, Wang J, Jian H, Zhang B, Li S, Wang F, Zeng X, Gao L, Bartlett DH, Yu J, Hu S, Xiao X. Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3. PLoS One. 2008;3:e1937.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wintersinger JA, Wasmuth JD. Kablammo: an interactive, web-based BLAST results visualizer. Bioinformatics. 2015;31:1305–6.
Article
PubMed
Google Scholar
Xiong L, Jian H, Zhang Y, Xiao X. The two sets of DMSO respiratory systems of Shewanella piezotolerans WP3 are involved in deep sea environmental adaptation. Front Microbiol. 2016;7:1418.
PubMed
PubMed Central
Google Scholar
Yamada M, Nakasone K, Tamegai H, Kato C, Usami R, Horikoshi K. Pressure regulation of soluble cytochromes c in a deep-sea piezophilic bacterium, Shewanella violacea. J Bacteriol. 2000;182:2945.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yancey PH. Organic osmolytes as compatible, metabolic and counteracting cryoprotectants in high osmolarity and other stresses. J Experiment Biol. 2005;208:2819–30.
Article
CAS
Google Scholar
Yancey PH, Fyfe-Johnson AL, Kelly RH, Walker VP, Auñón MT. Trimethylamine oxide counteracts effects of hydrostatic pressure on proteins of deep-sea teleosts. J Experimental Zoology. 2001;289:172–6.
Article
CAS
Google Scholar
Yancey PH, Gerringer ME, Drazen JC, Rowden AA, Jamieson A. Marine fish may be biochemically constrained from inhabiting the deepest ocean depths. Proc Natl Acad Sci. 2014;111:4461–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yano Y, Nakayama A, Ishihara K, Saito H. Adaptive changes in membrane lipids of barophilic bacteria in response to changes in growth pressure. Appl Environ Microbiol. 1998;64:479–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yayanos AA. Evolutional and ecological implications of the properties of deep-sea barophilic bacteria. Proc Natl Acad Sci. 1986;83:9542–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yayanos AA, Dietz AS, Van Boxtel R. Obligately barophilic bacterium from the Mariana trench. Proc Natl Acad Sci. 1981;78:5212–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucl Acids Res. 2012;40:W445–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang W, Tian RM, Sun J, Bougouffa S, Ding W, Cai L, Lan Y, Tong H, Li Y, Jamieson AJ, Bajic VB, Drazen JC, Bartlett D, Qian PY. Genome reduction in Psychromonas species within the gut of an amphipod from the ocean’s deepest point. mSystems. 2018;3:e00009–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang W, Watanabe HK, Ding W, Lan Y, Tian RM, Sun J, Chen C, Cai L, Li Y, Oguri K, Toyofuku T, Kitazato H, Drazen JC, Bartlett D, Qian PY. Gut microbial divergence between two populations of the hadal amphipod Hirondellea gigas. Appl Environ Microbiol. 2019a;85:e02032–18.
CAS
PubMed
Google Scholar
Zhang WJ, Cui XH, Chen LH, Yang J, Li XG, Zhang C, Barbe V, Mangenot S, Fouteau S, Guerin T, Kato C, Wu LF. Complete genome sequence of Shewanella benthica DB21MT-2, an obligate piezophilic bacterium isolated from the deepest Mariana trench sediment. Mar Gen. 2019b;44:52–6.
Article
CAS
Google Scholar