UWB Crest

Marine Metagenomics for New Biotechnological Applications


 

 

 

 

 

 


Publications 2013-2014

  • Yakimov MM, La Cono V, La Spada G, 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. 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 2014 (in press) DOI: 10.1111/1462-2920.12587
  • Yakimov M M., La Cono V, Smedile F, Crisafi F, Arcadi E, Leonardi M, Decembrini F, Catalfamo M, Bargiela R, Ferrer M, Golyshin P, Giuliano L. Heterotrophic bicarbonate assimilation is the main process of de novo organic carbon synthesis in hadal zone of the Hellenic Trench, the deepest part of Mediterranean Sea. (in press) Environ Microbiol Reports). 2014. DOI: 10.1111/1758-2229.12192.

  • Tchigvintsev A, Tran H, Popovic A, Kovacic F, Brown G, Flick R, Hajighasemi M, Egorova O, Somody JC, Tchigvintsev D, Khusnutdinova A, Chernikova TN, Golyshina OV, Yakimov MM, Savchenko A, Golyshin PN, Jaeger KE, Yakunin AF. The environment shapes microbial enzymes: five cold-active and salt-resistant carboxylesterases from marine metagenomes. Appl Microbiol Biotechnol. 2014 [Epub ahead of print] PubMed PMID: 25194841.

  • Pachiadaki MG, Yakimov MM, LaCono V, Leadbetter E, Edgcomb V. Unveiling microbial activities along the halocline of Thetis, a deep-sea hypersaline anoxic basin. ISME J. 2014 Jun 20. doi: 10.1038/ismej.2014.100. PubMed PMID: 24950109.

  • Smedile F, Messina E, La Cono V, Yakimov MM. Comparative analysis of deep-sea bacterioplankton OMICS revealed the occurrence of habitat-specific genomic attributes. Mar Genomics. 2014 Jun 14. pii: S1874-7787(14)00072-5

  • 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; The MAMBA Consortium. 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. 2014 16(8):2525-37

  • 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. Microbial life in the Lake Medee, the largest deep-sea salt-saturated formation. Sci Rep. 2013 3:3554.

  • Kube M, Chernikova TN, Al-Ramahi Y, Beloqui A, Lopez-Cortez N, Guazzaroni ME, Heipieper HJ, Klages S, Kotsyurbenko OR, Langer I, Nechitaylo TY, Lünsdorf H, Fernández M, Juárez S, Ciordia S, Singer A, Kagan O, Egorova O, Petit PA, Stogios P, Kim Y, Tchigvintsev A, Flick R, Denaro R, Genovese M, Albar JP, Reva ON, Martínez-Gomariz M, Tran H, Ferrer M, Savchenko A, Yakunin AF, Yakimov MM, Golyshina OV, Reinhardt R, Golyshin PN. Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica. Nature Communications. 2013;4:2156.

  • Jan C, Petersen JM, Werner J, Teeling H, Huang S, Glöckner FO, Golyshina OV, Dubilier N, Golyshin PN, Jebbar M, Cambon-Bonavita MA. The gill chamber epibiosis of deep-sea shrimp Rimicaris exoculata: an in-depth metagenomic investigation and discovery of Zetaproteobacteria. Environ Microbiol. 2014 16(9):2723-38

  • Matallana-Surget S, Cavicchioli R, Fauconnier C, Wattiez R, Leroy B, Joux F, Raftery MJ, Lebaron P. Shotgun redox proteomics: identification and quantitation of carbonylated proteins in the UVB-resistant marine bacterium, Photobacterium angustum S14. PLoS One. 2013 Jul 9;8(7):e68112. doi: 10.1371/journal.pone.0068112. Print 2013. PubMed PMID: 23874515; PubMed Central PMCID: PMC3706606.
  • Smedile F, Messina E, La Cono V, Tsoy O, Monticelli LS, Borghini M, Giuliano L, Golyshin PN, Mushegian A, Yakimov MM. 2013. Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of Mediterranean Sea, Matapan-Vavilov Deep. Environ Microbiol 15(1):167-182.
  • Golyshin P.N., Werner J., Chernikova T.N., Tran H., Ferrer M., Yakimov M.M., Teeling H., Golyshina O.V., MAMBA SCIENTIFIC CONSORTIUM. 2013. Genome Sequence of Thalassolituus oleivorans MIL-1 (DSM 14913T). Genome Announcements 1(2):e0014113.
  • Alcaide M, Tornes J, Stogios PJ, Xu X, Gertler C, Di Leo R, Bargiela R., Lafraya A, Guazzaroni ME, Lopez-Cortes N, Chernikova TN, Golyshina OV, Nechitaylo TY, Plumeier I, Pieper DH, Yakimov MM, Savchenko A, Golyshin PN, Ferrer M. 2013. Single residues dictate the co-evolution of dual esterases - MCP hydrolases from the α/β hydrolase family. Biochem J. 2013 Jun 10.
  • La Cono V, La Spada G, Arcadi E, Placenti F, Smedile F, Ruggeri G, Michaud L, Raffa C, De Domenico E, Sprovieri M, Mazzola S, Genovese L, Giuliano L, Slepak VZ, Yakimov MM. 2013. Partaking of Archaea to biogeochemical cycling in oxygen-deficient zones of meromictic saline Lake Faro (Messina, Italy). Environ Microbiol 15(6):1717-1733.

  • Giovannelli D, Grosche A, Starovoytov V, Yakimov M, Manini E, Vetriani C. 2012.Galenea microaerophila gen. nov., sp. nov., a mesophilic, microaerophilic,chemosynthetic, thiosulfate-oxidizing bacterium isolated from a shallow-water
    hydrothermal vent. Int J Syst Evol Microbiol 62(Pt 12):3060-3066.
  • Smedile F, Messina E, La Cono V, Tsoy O, Monticelli LS, Borghini M, Giuliano L, Golyshin PN, Mushegian A, Yakimov MM. 2013. Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of Mediterranean Sea, Matapan-Vavilov Deep. Environ Microbiol 15(1):167-182.
  • Golyshin P.N., Werner J., Chernikova T.N., Tran H., Ferrer M., Yakimov M.M., Teeling H., Golyshina O.V., MAMBA SCIENTIFIC CONSORTIUM. 2013. Genome Sequence of Thalassolituus oleivorans MIL-1 (DSM 14913T). Genome Announcements 1(2):e0014113.
  • Alcaide M, Tornes J, Stogios PJ, Xu X, Gertler C, Di Leo R, Bargiela R., Lafraya A, Guazzaroni ME, Lopez-Cortes N, Chernikova TN, Golyshina OV, Nechitaylo TY, Plumeier I, Pieper DH, Yakimov MM, Savchenko A, Golyshin PN, Ferrer M. 2013.
  • Single residues dictate the co-evolution of dual esterases - MCP hydrolases from the α/β hydrolase family. Biochem J. 2013 Jun 10.

  • La Cono V, La Spada G, Arcadi E, Placenti F, Smedile F, Ruggeri G, Michaud L, Raffa C, De Domenico E, Sprovieri M, Mazzola S, Genovese L, Giuliano L, Slepak VZ, Yakimov MM. 2013. Partaking of Archaea to biogeochemical cycling in oxygen-deficient zones of meromictic saline Lake Faro (Messina, Italy). Environ Microbiol 15(6):1717-1733.
  • Kube M., Chernikova T.N, Al-Ramahi, Y, Beloqui, A, Lopez-Cortez, N , María-Eugenia Guazzaroni M-E, Heipieper H.J, Klages, S., Kotsyurbenko O.R, Langer, I, Nechitaylo T.Y., Lünsdorf, H, Fernández, M, Juárez, S, Ciordia, S., Singer, A, Kagan, O., Egorova, O., Petit, P.A., Stogios, P., Kim, Y., Tchigvintsev, A., Flick, R., Denaro, R., Genovese, M., Albar, J.P., Reva, O.N., Martínez-Gomariz, M., Tran, H., Ferrer, M., Savchenko, A., Yakunin, A.F., Yakimov, M.M., Golyshina O.V., Reinhardt, R., and Golyshin P.N. 2013. Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica. Nature Communications 4:2156.
  • Matallana-Surget S, Cavicchioli R, Fauconnier C, Wattiez R, Leroy B, et al. 2013. Shotgun Redox Proteomics: Identification and Quantitation of Carbonylated Proteins in the UVB-Resistant Marine Bacterium, Photobacterium angustum S14. PLoS ONE 8(7): e68112.