Antunes A, Alam I, Bajic VB, Stingl U (2011) Genome sequence of salinisphaera shabanensis, a gammaproteobacterium from the harsh, variable environment of the brine-seawater interface of the shaban deep in the red sea. J Bacteriol 193:4555–4556. https://doi.org/10.1128/JB.05459-11
Article
CAS
PubMed
PubMed Central
Google Scholar
Barbato M, Mapelli F, Magagnini M, Chouaia B, Armeni M, Marasco R, Crotti E, Daffonchio D, Borin S (2016a) Hydrocarbon pollutants shape bacterial community assembly of harbor sediments. Mar Pollut Bull 104:211–220
Article
CAS
PubMed
Google Scholar
Barbato M, Scoma A (2020) Mild hydrostatic-pressure (15 MPa) affects the assembly, but not the growth, of oil-degrading coastal microbial communities tested under limiting conditions (5°C, no added nutrients). FEMS Microbiol Ecol 96:1–12. https://doi.org/10.1093/femsec/fiaa160
Article
CAS
Google Scholar
Barbato M, Scoma A, Mapelli F, De Smet R, Banat IM, Daffonchio D, Boon N, Borin S (2016b) Hydrocarbonoclastic Alcanivorax isolates exhibit different physiological and expression responses to n-dodecane. Front Microbiol 7:1–14. https://doi.org/10.3389/fmicb.2016.02056
Article
Google Scholar
Bargiela R, Mapelli F, Rojo D, Chouaia B, Tornés J, Borin S, Richter M, Del Pozo MV, Cappello S, Gertler C, Genovese M, Denaro R, Martínez-Martínez M, Fodelianakis S, Amer RA, Bigazzi D, Han X, Chen J, Chernikova TN, Golyshina OV, Mahjoubi M, Jaouanil A, Benzha F, Magagnini M, Hussein E, Al-Horani F, Cherif A, Blaghen M, Abdel-Fattah YR, Kalogerakis N, Barbas C, Malkawi HI, Golyshin PN, Yakimov MM, Daffonchio D, Ferrer M (2015) Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature. Sci Rep 5:11651. https://doi.org/10.1038/srep11651
Article
CAS
PubMed
PubMed Central
Google Scholar
Borin S, Brusetti L, Mapelli F, D’Auria G, Brusa T, Marzorati M, Rizzi A, Yakimov M, Marty D, De Lange GJ, Van Der Wielen P, Bolhuis H, McGenity TJ, Polymenakou PN, Malinverno E, Giuliano L, Corselli C, Daffonchio D (2009) Sulfur cycling and methanogenesis primarily drive microbial colonization of the highly sulfidic Urania deep hypersaline basin. Proc Natl Acad Sci U S A 106. https://doi.org/10.1073/pnas.0811984106
Borin S, Mapelli F, Rolli E, Song B, Tobias C, Schmid MC, De Lange GJ, Reichart GJ, Schouten S, Jetten M, Daffonchio D (2013) Anammox bacterial populations in deep marine hypersaline gradient systems. Extremophiles 17:289–299
Article
CAS
PubMed
Google Scholar
Brusa T, Borin S, Ferrari F, Sorlini C, Corselli C, Daffonchio D (2001) Aromatic hydrocarbon degradation patterns and catechol 2,3-dioxygenase genes. Microbiol Res 156:49–57
Article
CAS
PubMed
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336. https://doi.org/10.1038/nmeth.f.303.
De Lange GJ, Middelburg JJ, Van Der Weijden CH, Catalano G, Luther GW III, Hydes DJ, Woittiez JRW, Klinkhammer GP (1990) Composition of anoxic hypersaline brines in the Tyro and Bannock Basins, eastern Mediterranean. Mar Chem 31:63–88
Daffonchio D, Borin S, Brusa T, Brusetti L, Van Der Wielen PWJJ, Bolhuis H, Yakimov MM, D’Auria G, Giuliano L, Marty D, Tamburini C, McGenity TJ, Hallsworth JE, Sass AM, Timmis KN, Tselepides A, De Lange GJ, Hübner A, Thomson J, Varnavas SP, Gasparoni F, Gerber HW, Malinverno E, Corselli C, Garcin J, McKew B, Golyshin PN, Lampadariou N, Polymenakou P, Calore D, Cenedese S, Zanon F, Hoog S (2006) Stratified prokaryote network in the oxic-anoxic transition of a deep-sea halocline. Nature 440:203–207. https://doi.org/10.1038/nature04418
Article
CAS
PubMed
Google Scholar
Edgar RC (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461. https://doi.org/10.1093/bioinformatics/btq461.
Ferrer M, Werner J, Chernikova TN, Bargiela R, Fernández L, La Cono V, Waldmann J, Teeling H, Golyshina OV, Glöckner FO, Yakimov MM, Golyshin PN (2012) Unveiling microbial life in the new deep-sea hypersaline Lake Thetis. Part II: A metagenomic study. Environ Microbiol 14:268–281. https://doi.org/10.1111/j.1462-2920.2011.02634.x
Article
CAS
PubMed
Google Scholar
Filker S, Stock A, Breiner HW, Edgcomb V, Orsi W, Yakimov MM, Stoeck T (2013) Environmental selection of protistan plankton communities in hypersaline anoxic deep-sea basins, Eastern Mediterranean Sea. Microbiologyopen 2:54–63. https://doi.org/10.1002/mbo3.56
Article
CAS
PubMed
Google Scholar
Fisher LA, Pontefract A, Som M, Carr S, Klempay CE, Schmidt BE, Bowman JS, Bartlett DH (2021) Current state of athalassohaline deep-sea hypersaline anoxic basin research—recommendations for future work and relevance to astrobiology. Environ Microbiol 23:3360–3369. https://doi.org/10.1111/1462-2920.15414
Article
PubMed
Google Scholar
Gobet A, Boetius A, Ramette A (2014) Ecological coherence of diversity patterns derived from classical fingerprinting and Next Generation Sequencing techniques. Environ Microbiol 16:2672–2681. https://doi.org/10.1111/1462-2920.12308
Article
CAS
PubMed
Google Scholar
L’Haridon S, Haroun H, Corre E, Roussel E, Chalopin M, Pignet P, Balière C, la Cono V, Jebbar M, Yakimov M, Toffin L (2020) Methanohalophilus profundi sp. nov., a methylotrophic halophilic piezophilic methanogen isolated from a deep hypersaline anoxic basin. Syst Appl Microbiol 43:126107. https://doi.org/10.1016/j.syapm.2020.126107
Article
CAS
PubMed
Google Scholar
La Cono V, Bortoluzzi G, Messina E, La Spada G, Smedile F, Giuliano L, Borghini M, Stumpp C, Schmitt-Kopplin P, Harir M, O’Neill WK, Hallsworth JE, Yakimov M (2019) The discovery of Lake Hephaestus, the youngest athalassohaline deep-sea formation on Earth. Sci Rep 9:1–11. https://doi.org/10.1038/s41598-018-38444-z
Article
CAS
Google Scholar
La Cono V, Smedile F, Bortoluzzi G, Arcadi E, Maimone G, Messina E, Borghini M, Oliveri E, Mazzola S, L’Haridon S, Toffin L, Genovese L, Ferrer M, Giuliano L, Golyshin PN, Yakimov MM (2011) Unveiling microbial life in new deep-sea hypersaline Lake Thetis. Part I: Prokaryotes and environmental settings. Environ Microbiol 13:2250–2268. https://doi.org/10.1111/j.1462-2920.2011.02478.x
Article
PubMed
Google Scholar
Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814–821. https://doi.org/10.1038/nbt.2676
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu J, Zheng Y, Lin H, Wang X, Li M, Liu Y, Yu M, Zhao M, Pedentchouk N, Lea-Smith DJ, Todd JD, Magill CR, Zhang WJ, Zhou S, Song D, Zhong H, Xin Y, Yu M, Tian J, Zhang XH (2019) Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench. Microbiome 7:1–13. https://doi.org/10.1186/s40168-019-0652-3
Article
Google Scholar
Mapelli F, Barozzi A, Michoud G, Merlino G, Crotti E, Borin S, Daffonchio D (2017a) An updated view of the microbial diversity in deep hypersaline anoxic basins, Adaption of Microbial Life to Environmental Extremes: Novel Research Results and Application, 2nd edn. https://doi.org/10.1007/978-3-319-48327-6_2
Book
Google Scholar
Mapelli F, Varela MM, Barbato M, Alvariño R, Fusi M, Álvarez M, Merlino G, Daffonchio D, Borin S (2013b) Biogeography of planktonic bacterial communities across the whole Mediterranean Sea. Ocean Sci 9:585–595. https://doi.org/10.5194/os-9-585-2013
Article
Google Scholar
Mapelli F, Marasco R, Rolli E, Barbato M, Cherif H, Guesmi A, Ouzari I, Daffonchio D, Borin S (2013a) Potential for plant growth promotion of rhizobacteria associated with Salicornia growing in Tunisian hypersaline soils. Biomed Res Int. 2013, 248078. https://doi.org/10.1155/2013/248078.
Mapelli F, Scoma A, Michoud G, Aulenta F, Boon N, Borin S, Kalogerakis N, Daffonchio D (2017b) Biotechnologies for marine oil spill cleanup: indissoluble ties with microorganisms. Trends Biotechnol. https://doi.org/10.1016/j.tibtech.2017.04.003
Marasco R, Rolli E, Ettoumi B, Vigani G, Mapelli F, et al. (2012) A Drought Resistance-Promoting Microbiome Is Selected by Root System under Desert Farming. PLoS ONE 7(10): e48479. https://doi.org/10.1371/journal.pone.0048479.
Merlino G, Barozzi A, Michoud G, Ngugi DK, Daffonchio D (2018) Microbial ecology of deep-sea hypersaline anoxic basins. FEMS Microbiol Ecol 94:1–15. https://doi.org/10.1093/femsec/fiy085
Article
CAS
Google Scholar
Michoud G, Ngugi DK, Barozzi A, Merlino G, Calleja ML, Delgado-Huertas A, Morán XAG, Daffonchio D (2021) Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline. ISME J 15:2351–2365. https://doi.org/10.1038/s41396-021-00931-z
Article
CAS
PubMed
PubMed Central
Google Scholar
Muyzer G, Dewa al E, Uitterlinden A (1993). Profiling of complex microbialpopulations by denaturing gradient gelelectrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16S ribosomal-RNA. Appl Environ Microbiol. 59, 695–700.
Ngugi DK, Blom J, Alam I, Rashid M, Ba-Alawi W, Zhang G, Hikmawan T, Guan Y, Antunes A, Siam R, El Dorry H, Bajic V, Stingl U (2015) Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea. ISME J 9:396–411. https://doi.org/10.1038/ismej.2014.137
Article
CAS
Google Scholar
Parinos C, Gogou A, Bouloubassi I, Pedrosa-Pàmies R, Hatzianestis I, Sanchez-Vidal A, Rousakis G, Velaoras D, Krokos G, Lykousis V (2013) Occurrence, sources and transport pathways of natural and anthropogenic hydrocarbons in deep-sea sediments of the eastern Mediterranean Sea. Biogeosciences 10:6069–6089. https://doi.org/10.5194/bg-10-6069-2013
Article
CAS
Google Scholar
Parks DH, Beiko RG (2010) Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26:715–721. https://doi.org/10.1093/bioinformatics/btq041
Article
CAS
PubMed
Google Scholar
Parks DH, Tyson GW, Hugenholtz P, Beiko RG (2014) STAMP: Statistical analysis of taxonomic and functional profiles. Bioinformatics 30:3123–3124. https://doi.org/10.1093/bioinformatics/btu494
Article
CAS
PubMed
PubMed Central
Google Scholar
Sankaranarayanan K, Timofeeff MN, Spathis R, Lowenstein TK, Lum JK (2011) Ancient microbes from halite fluid inclusions: optimized surface sterilization and DNA extraction. PLoS One 6(6):e20683. https://doi.org/10.1371/journal.pone.0020683
Article
CAS
PubMed
PubMed Central
Google Scholar
Sass AM, Sass H, Coolen MJL, Cypionka H, Overmann J (2001) Microbial communities in the chemocline of a hypersaline deep-sea basin (Urania Basin, Mediterranean Sea). Appl Environ Microbiol 67:5392–5402. https://doi.org/10.1128/AEM.67.12.5392-5402.2001
Article
CAS
PubMed
PubMed Central
Google Scholar
Scoma A, Yakimov MM, Boon N (2016) Challenging oil bioremediation at deep-sea hydrostatic pressure. Front Microbiol 7:1203. https://doi.org/10.3389/fmicb.2016.01203
Article
PubMed
PubMed Central
Google Scholar
Steinle L, Knittel K, Felber N, Casalino C, De Lange G, Tessarolo C, Stadnitskaia A, Sinninghe Damsté JS, Zopfi J, Lehmann MF, Treude T, Niemann H (2018) Life on the edge: active microbial communities in the Kryos MgCl2-brine basin at very low water activity. ISME J 12:1414–1426. https://doi.org/10.1038/s41396-018-0107-z
Article
CAS
PubMed
PubMed Central
Google Scholar
Stock A, Edgcomb V, Orsi W, Filker S, Breiner HW, Yakimov MM, Stoeck T (2013) Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection. BMC Microbiol 13:1. https://doi.org/10.1186/1471-2180-13-150
Article
CAS
Google Scholar
Sun QL, Sun YL, Sun YY, Luan ZD, Lian C (2020) Marinobacter fonticola sp. Nov., isolated from deep sea cold seep sediment. Int J Syst Evol Microbiol 70:1172–1177. https://doi.org/10.1099/ijsem.0.003895
Article
CAS
PubMed
Google Scholar
Van Der Wielen PWJJ, Bolhuis H, Borin S, Daffonchio D, Corselli C, Giuliano L, D’Auria G, De Lange GJ, Huebner A, Varnavas SP, Thomson J, Tamburini C, Marty D, McGenity TJ, Timmis KN (2005) The enigma of prokaryotic life in deep hypersaline anoxic basins. Science (80- ) 307:121–123. https://doi.org/10.1126/science.1103569
Article
CAS
Google Scholar
Van Der Wielen PWJJ, Heijs SK (2007) Sulfate-reducing prokaryotic communities in two deep hypersaline anoxic basins in the Eastern Mediterranean deep sea: brief report. Environ Microbiol 9:1335–1340. https://doi.org/10.1111/j.1462-2920.2006.01210.x
Article
CAS
PubMed
Google Scholar
van Dorst J, Bissett A, Palmer AS, Brown M, Snape I, Stark JS, Raymond B, McKinlay J, Ji M, Winsley T, Ferrari BC (2014) Community fingerprinting in a sequencing world. FEMS Microbiol Ecol 89:316–330. https://doi.org/10.1111/1574-6941.12308
Article
CAS
PubMed
Google Scholar
Varrella S, Tangherlini M, Corinaldesi C (2020) Deep hypersaline anoxic basins as untapped reservoir of polyextremophilic prokaryotes of biotechnological interest. Mar Drugs 18:1–32. https://doi.org/10.3390/md18020091
Article
CAS
Google Scholar
Wang W, Cai B, Shao Z (2014) Oil degradation and biosurfactant production by the deep sea bacterium Dietzia maris As-13-3. Front Microbiol 5:1–11. https://doi.org/10.3389/fmicb.2014.00711
Article
Google Scholar
Werner J, Ferrer M, Michel G, Mann AJ, Huang S, Juarez S, Ciordia S, Albar JP, Alcaide M, La Cono V, Yakimov MM, Antunes A, Taborda M, da Costa MS, Hai T, Glöckner FO, Golyshina OV, Golyshin PN, Teeling H (2014) Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader. Environ Microbiol 16:2525–2537. https://doi.org/10.1111/1462-2920.12393
Article
CAS
PubMed
PubMed Central
Google Scholar
Yakimov MM, La Cono V, Denaro R, D’Auria G, Decembrini F, Timmis KN, Golyshin PN, Giuliano L (2007) Primary producing prokaryotic communities of brine, interface and seawater above the halocline of deep anoxic lake L’Atalante, Eastern Mediterranean Sea. ISME J 1:743–755. https://doi.org/10.1038/ismej.2007.83
Article
CAS
PubMed
Google Scholar
Yakimov MM, La Cono V, Slepak VZ, La Spada G, Arcadi E, Messina E, Borghini M, Monticelli LS, Rojo D, Barbas C, Golyshina OV, Ferrer M, Golyshin PN, Giuliano L (2013) Microbial life in the Lake Medee, the largest deep-sea salt-saturated formation. Sci Rep 3:1–9. https://doi.org/10.1038/srep03554
Article
Google Scholar
Yakimov MM, La Cono V, Spada GL, Bortoluzzi G, Messina E, Smedile F, Arcadi E, Borghini M, Ferrer M, Schmitt-Kopplin P, Hertkorn N, Cray JA, Hallsworth JE, Golyshin PN, Giuliano L (2015) Microbial community of the deep-sea brine Lake Kryos seawater-brine interface is active below the chaotropicity limit of life as revealed by recovery of mRNA. Environ Microbiol 17:364–382. https://doi.org/10.1111/1462-2920.12587
Article
CAS
PubMed
Google Scholar
Zeaiter Z, Marasco R, Booth JM, Prosdocimi EM, Mapelli F, Callegari M, Fusi M, Michoud G, Molinari F, Daffonchio D, Borin S, Crotti E (2019) Phenomics and genomics reveal adaptation of Virgibacillus dokdonensis strain 21D to its origin of isolation, the seawater-brine interface of the mediterranean sea deep hypersaline anoxic basin discovery. Front Microbiol 10. https://doi.org/10.3389/fmicb.2019.01304
Zhou M, Dong B, Shao Z (2020) Complete genome sequence of Marinobacter sp. LQ44, a haloalkaliphilic phenol-degrading bacterium isolated from a deep-sea hydrothermal vent. Mar Genomics 50:100697. https://doi.org/10.1016/j.margen.2019.100697
Article
Google Scholar