References on BIODEEP-related aspects

a) Microbiology and biotechnology

Acinas, S.G., J. Anton, and F. Rodriguez-Valera - 1999  - Diversity of free-living and attached bacteria in offshore western Mediteranean waters as depicted by analysis of genes encoding 16S rRNA.  Applied and Environmental Microbiology, 2: 512-522.

Aguilar, A. - 1996 - Extremophile research in the European Union: from Fundamental aspect to industrial expectation.  FEMS Microbiology Review: 89-92.

Aguilar, A.,  T. Ingemansson, E. Magnien - 1998 - Extremophile microorganisms as cell factories: support from the European Union.  Extremophiles, :367-373.

Allen, E.E., D. Facciotti, and D.H. Bartlett - 1999 -  Monounsaturated but not polyunsaturated fatty acids are required for growth of the deep-sea bacterium Photobacterium profondum SS9 at high pressure.  Applied and Environmental Microbiology, 4: 1710-1720.

Amann, R.I., L. Krumholz, and D.A. Stahl - 1990 -  Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology.  Journal of Bacteriology, 2: 762-770 .

Amann, R.I., W. Ludwig, and K.-H. Schleifer -1995 -  Phylogenetic identification and in situ detection of individual microbial cell without cultivation.  Microbiological Review, 1: 143-169.

Anton, J., R.Rossel-Mora, F. Rodriguez-Valera, and R.Amann -2000 -  Extremely halophilic bacteria in crystallizer ponds from solar salterns.  Applied and Environmental Microbiology, 7: 3052-3057.

Atlas, R.M..   Biodegradation of petroleum hydrocarbons: an environmental prospective - 1981 -  Microbiological Review,  : 180-209.

Bale, S.J., K. Goodman, P.A. Rochelle, J.R. Marchesi, J.C. Fry, A.J. Weightman, and R. J. Parkes - 1997 - Desulfovibrio profondus, sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea.  Nat. J. Sys. Bacteriol., 2: 515-521.

Bianchi, M., C. Fosset, P. Conan - 1999 -  Nitrification rates in the NW Mediterranean sea.  Aquat. Microb. Ecol., : 267-278.

Boivin-Jahns, V., R. Ruimy, A. Bianchi, S. Daumas, and R. Christien - 1996 -   Bacterial diversity in a deep-subsurface clay environment.  Applied and Environmental Microbiology, 9: 3405-3412.

Brandt, K.K., B.K.C. Patel, and K. Ingvorsen - 1999 -  Desulfocella halophila gen.nov., sp. Nov., a halophilic, fatty-acid-oxidizing, sulfate-reducing bacterium isolated from sediments of the Grat Salt Lake.  Int.l J. of Syst. Bact., : 193-200.

Brinkhoff, T., and G. Muyzer - 1997 - Increased Species diversity and extended habitat range of sulfur-oxidizing Thiomicrospira spp..  Applied and Environmental Microbiology, 10: 3789-3796.

Britschgi, T.B., and S.J. Giovannoni - 1991 -  Phylogenetic Analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing.  Applied and Environmental Microbiology, 6: 1707-1713 .

Brusa, T., E. Del Puppo, A. Ferrari, G. Rodondi, C. Andreis, S. Pellegrini - 1997 -  Microbes in  deep-sea anoxic basins.  Microbiological Research,  : 45-56.

Button, C.C., D.K. , F. Schut ,P. Quang, R. Martin, and B.R. Robertson - 1993 -  Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results.  Applied and Environmental Microbiology, 3: 881-891.

Canovas, D., C. Vargas, Laszlo N. Csonka, A. Ventosa, and J.J. Niento - 1998 -  Synthesis of glycine betaine from exogenous choline in the moderately holphilic bacterium Halomonas elongata.  Applied and Environmental Microbiology, 10: 4095-4097 .

Cayol, J.L., S. Ducerf, B.K.C. Patel, Garcia J.L., P. Thomas, and B.Ollivier - 2000 -  Thermohaloanaerobacter berrensis gen. Nov., sp. Nov., a thermophilic, strictly halophilic bacterium from a solar saltern.  Int.l J. of Syst. Bact., : 559-564.

Cerniglia, C.E. - 1992 -  Biodegradation of polycyclic aromatic hydrocarbons.  Biodegradation, : 351-368.

Colwell, R.R., I.T. Knight, C. Somerville, S. Shults, and C.W. Kaspar -  Viable but non-colturable phenomenon in relationship to starvation/survival, "injury", and strategies for survival of bacteria in the environment.

Csonka, L. N., A. D. Hanson - 1991 - Prokaryotic osmoregulation: Genetics and Physiology.  Ann. Rev. Microbiology, 45: 569-606.

Cummings, S.P., G.W. Black - 1999 -  Polymer Hydrolysis in a cold climate.  Extremophiles, : 81-87.

Deming, J.W..  Current opinion in biotechnology - 1998 -  Deep Ocean Environmental Biotechnology, 3: 283-287.

Fabiano, M. R. Danovaro - 1998 -  Enzimatic activity, bacterial distribution, and organic matterv composition in sediments of the ross sea (Antartica).  Applied and Environmental Microbiology, 10: 3838-3845.

Feller, G., E. Narinx, J.L. Arpigny, M. Aittaleb, E.Baise, S. Genicot, C. Gerday - 1996 -  Enzymes from psychrophilic organisms. FEMS Microbiology Review, : 189-203.

Foord, R.L., and R.J. Leatherbarrow - 1998 - Effect of osmolytes on the exchange rates of backbone amide protons in proteins.  Biochemistry,  : 2969-2978.

Fry, N.K., J.K. Fredrickson, S. Fishbain, M. Wagner, and D.A. Stahl - 1997 -  Population structure of microbial communities associated with two deep, anaerobic, alkaline aquifers.  Applied and Environmental Microbiology, 4: 1498-1504.

Fuchs, B.M., F.O. Glockner, J. Wulf, and R. Amann - 2000 -  Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of Fluorescent labeled oligonucleotide probes.  Applied and Environmental Microbiology, 8: 3603-3607.

Fuhrman, J.A.,  D.E. Comeau, A. Hangstrom, and A.M. Chan - 1988 -  Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies.  Applied and Environmental Microbiology, 6: 1426-1429.

Fuhrman, J.A., K. McCallum and A.A. Davis - 1993 -  Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific oceans.  Applied and Environmental Microbiology, : 1294-1302.

Galinski, E.A. - 1993 - Compatible solutes of halophilic eubacteria: molecular principles, water-solute interaction, stress protection.  Experentia,: 487.

Gauthier, M.J., B. Lafay, R. Christen, L. Fernandez, M. Acquaviva, P. Bonin, and J.-C. Bertrand - 1992 - Marinobacterium hydrocarbonoclasticus gen. Nov., sp. Nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium.  Int.l J. of Syst. Bact., 4: 568-576.

Glockner, F.O., R. Amann, A. Alfreider, J. Pernthaler, R. Psenner, K. Trebesius, and K.-H. Schleifer - 1996 -  An in situ hybridization protocol for detection and identification of planktonic bacteria.  System. Appl. Microbiol., : 403-406.

Gonzalez, J.M., W.B. Whitman, R.E. Hodson, and M.A. Moran - 1996 - Identifying numerically abundant culturable bacteria from complex community: an example from lignin enrichment culture.  Applied and Environmental Microbiology, 12: 4433-4440 .

Gordon, D.A., and S.J. Giovannoni - 1996 - Detection of stratified microbial population related to chlorobium and fibrobacter species in the Atlantic and Pacific oceans.  Applied and Environmental Microbiology, 4: 1171-1177.

Greenblatt, C.L., A. Davis, B.G. Clement, C.L. Kitts, T. Cox, R.J. Cano - 1999 -  Diversity of microorganisms isolated from amber.  Microbial Ecology.

Haller, C.M., S.Rolleke, D. Vybrial, A. Witte, B. Velimirov - 1999 -  Investigation of 0.2 um filterable bacteria frome the Western Mediterranean Sea using a molecular approach: dominance of potential starvation forms.  FEMS Microbiology Ecology, : 153-161.

Harold, F.M. - 1990 - To shape a cell: an inquiry into the causes of morphogenesis of microorganisms.  Microbiological Review, 4: 381-431 .

Hattori, T. - 1983 - Further Analysis of plate count data of bacteria.  J. Gen. Appl. Microbiol., : 9-16.

Haygood, M.G., E.W. Schmidt, S.K. Davidson, and D.J. Faulkner - 1999 -   Microbial symbionts of marine invertebrates,: opportunities for microbial biotechnology.  J. Mol. Microbiol. Biotechnol., 1: 33-43.

Hodson, R.E., W.A. Dustman, R.P. Garg, and M.A. Moran - 1995 -  In situ PCR for visualization of microscale distribution of specific genes and gene products in prokaryotic communities.  Applied and Environmental Microbiology, 11: 4074-4082 .

Hofle, M.G. - 1992 -  Bacterioplankton community structure and dynamics after large-scale release of nonindigenous bacteria as revealed by low-molecular-weight-RNA analysis.  Applied and Environmental Microbiology, 10: 3387-3394.

Huber, R., W. Eder, S. Heldwein, G. Wanner, H. Huber, R. Rachel, and K.O. Stetter - 1998 -  Thermocrinis ruber gen. Nov., sp. Nov., a pink-filament-hyperthermophilic bacterium isolated from Yellowstone National Park.  Applied and Environmental Microbiology, 10: 3576-3583.

Hugenholtz, P.,  B.M. Goebel and N.R. Pace - 1998 - Impact of colture-indipendent studies on the emerging phylogenetic view of bacterial diversity.  Journal of Bacteriology, 18: 4765-4774.

Hugenholtz, P., N.R. Pace - 1996 - Identifying microbial diversity in the natural environment: a molecular phylogenetic approach.  Trends Biotechnol, 6: 190-197        .

Kuypers, M.M.M., P. Blokker, L. Erbacher, H. Kinkel, R.D. Pancost, S. Schouten, J.S.S. Damstè - 2001 - Massive expansion of marine archaea during a mid-cretaceous oceanic anoxic event.  Science, : 92-94.

Lee, S.H., and J.A. Fuhrman - 1991 - Spatial and temporal variation of natural bacterioplankton assemblages studies by total genomic DNA cross-hybridization.  Limnology and Oceanography, 7: 1277-1287 .

Leff, L.G., J.R. Dana, J.V. McArthur, and L.J. Shimkets - 1995 - Comparision of methods of DNA extraction from stream sediments.  Applied and Environmental Microbiology, 3: 1141-1143 .

Lopez-Garcia, P., D. Moreira, A. Lopez-Lopez, and F. Rodriguez Valera - 2001 - A novel Haloarchaeal-realted lineage is widely distributed in deep oceanic regions.  Environmental Microbiology, 3(1): 72-79.

Madera, D., C. Ebel, , G. Zaccai - 2000 - Halophilic adaptation of enzymes.  Extremophiles, : 91-98.

Madigan, M.T.,  A. Oren - 1999 - Thermophilic and halophlic extremophiles.  Current Opinion in Microbiology, 3: 265-269.

Magot, M., G. Ravot, X. Campaignolle, B. Olliver, B.K.C. Patel, M.-L. Fardeau, P. Thomas, J.-L. Crolet, and J.-L. Garcia - 1997 - Dethiosulfovibrio peptidovorans gen. Nov., sp. Nov., a new anaerobic slightly halophilic, thiosulfate-reducing bacterium from corroding offshore oil wells.  Int.l J. of Syst. Bact., 3: 818-824.

Manz, W.,  R. Amann, W. Ludwid, M. Wagner, and K.-H. Schleifer - 1992 - Phylogenetic oligodeoxynucleotide probes for the major subclass of proteobacteria: problems and solutions.  System. Appl. Microbiol., : 593-600.

Martin, D.D., R.A. Ciulla, and M.F. Roberts - 1995 - Osmoadaptation in archaea.  J. Antimicrob. Chemoter., 5: 1815-1825 .

Minz, D., S. Fishbain, S.J. Green, G. Muyzer, Y. Cohen, B.E. Rittmann, and D.A. Stahl - 1999 - Unexpected population distribution in a microbial mat community: sulfate-reducing bacteria localized to the highly oxic chemocline in contrast to a eukariotic prefernece for anoxia.  Applied and Environmental Microbiology, 10:

Olliver, B., P. Caumette, J.-L. Garcia, R.A. Mah - 1994 - Anaerobic bacteria from hypersaline environments.  Microbiological Review Mar, : 27-38.

Oren, A. - 1988 - Anaerobic degradation of organic compounds at high salt concentration.  Antonie Van Leeuwenhoek, : 267-277.

Oren, A. - 1999 -  Bioenergetic aspect of halophilism.  Mic. and Mol. Biol. Rev.,  2: 334-348.

Oren, A., C.D. Litchfield - 1999 - A procedure for the enrichment and isolation of Halobacterium.  FEMS Microbiology Letters, : 353-358.

Orphan, V.J., K.-U. Hinrichs, W.Ussler III, C.K. Paull, L.T. Taylor, S.P. Sylvia, J.M. Hayes, and E.F. Delong - 2001 - Comparative analysis of methane-oxidizing Archea and sulfate-reducing bacteria in anoxic marine sediments. Applied and Environmental Microbiology, 4: 1922-1934.

Ouverney, and J. A. Fuhrman - 1997 - Increase in fluorescent intensity of 16S rRNA in situ hybridization in natural samples treated with cloramphenicol.  Applied and Environmental Microbiology, 7: 2735-2740.

Pace, N.R., D.A. Stahl, D.J. Lane, and G.J. Olsen -  The analysis of natural microbial population by ribosomal RNA.

Pancost, R.D., J.S. Sinninghe Damstè, S. de Lint, M.J.E. vand der Maarel, J.C. Gottschal, and The Medinaut Shipboard Scientific Party -  Biomarker evidence for widespread anaerobic methane oxidation in Mediterranean sediments by a consortium of methanogenic arche and bacteria.  Applied and Environmental

Raskin,L., L.K. Poulsen, D.R. Noguera, B.E. Rittmann, and D.A. Stahl - 1994 -  Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization.  Applied and Environmental Microbiology, 4: 1241-1248.

Rosemberg, E., R. Legmann, A. Kushmaro, R. Taube, E. Adler, and E.Z. Ron - 1992 - Petroleum bioremediation - a multiphase problem.  Biodegradation, : 337-350 .

Roszak, D.B., and R.R. Colwell - 1987 -  Survival Strategies of bacteria in the natural environment.  Microbiological Review,  3: 365-379 .

Schut, F. E., J. De Vries, J.C. Gottshal, B.R. Robertson, W. Harder, R.A. Prins, and D.K. Button - 1993 - Isolation of typical marine bacteria by dilution culture: growth, maintenance, and characteristics of isolates under laboratory conditions.  Applied and Environmental Microbiology, 7: 2150-2106.

Shedl, M., T. Behr, W. Ludwig, K.H. Schleifer, R. Niesser, and D. Knopp - 2000 - Optimization of reverse Hybridization in microplates coated with rRNA targeted oligonucleotide probes.  System. Appl. Microbiol. : 573-581.

Steffan, R.J.,  R.M. Atlas - 1991 - Polymerase chain reaction: Application in environmental microbiology.  Ann. Rev. Microbiology, : 137-61.

Stoffels, M., R. Amann, W. Ludwig, D. Hekmat, and K.-H. Schleifer - 1998 -  Bacterial community dynamics during start-up of trickle-bed bioreactor degrading aromatic compounds.  Applied and Environmental Microbiology, 3: 930-939        .

Takay, K., and K. Horikoshi - 1999 - Molecular phylogenetic analysis of archeal intron-containing genes coding for rRNA obtained from a deep-subsurface geothermail water pool.  Applied and Environmental Microbiology, 12: 5586-5589.

Tholosan, O., F. Lamy, J. Garcin, T. Polychronaki, and A. Bianchi - 1999 - Biphasic extracellular proteolytic enzyme activity in benthic water and sediment in the Northwestern Mediterranean sea.  Applied and Environmental Microbiology, 4: 1619-1626.

Tholosan, O., J. Garcin, A. Bianchi - 1999 - Effects of idrostatic pressure on microbial activity through a 2000 m deep water column in the NW Mediterranean Sea.  Mar. Ecol. Prog. Ser., : 49-57.

Thomsen, T.R., Finster K., and N.B. Ramsing - 2001 - Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine sediment.  Applied and Environmental Microbiology, 4: 1646-1656.

Tourova, T.P. , E.S. Boulygina, T.N. Zhilina, R.S. Hanson, and G.A. Zavarzin - 1995 - Phylogenetic study of halobacteria by 16S ribosomial RNA sequences analysis.  System. Appl. Microbiol., 18: 189-195.

Tsai, C.R., J.L. Garcia, B.K.C. Patel, J.L. Cayol, L. Baresi, and R.A. Mah - 1995 - Haloanaerobum alcaliphilum sp. Nov., an anaerobic moderate halophile from the sediments of Great Salt Lake, Utah.  Int.l J. of Syst. Bact., 2: 301-307.

Vetriani, V., H.W. Jannasch, B.J. MacGregor, D.A. Stahl, and A.L. Reysenbach - 1999 - Population structure and phylogenetic characterization of marine benthic archea in deep-sea sediments.  Applied and Environmental Microbiology, 10: 4375-4384.

Watanabe. K, Y. Kodama, S. Harayama - 2001 - Design of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting.  Journal of Microbiological Methods, : 253-262.

Whiteley, A.S., and M.J. Bailey - 2000 - Bacterial community structure and physiological state within an industrial phenol bioremediation system.  Applied and Environmental Microbiology, 6: 2400-2407.

Wirsen, C.O., and S.J.Molyneauxc - 1999 - A study of deep-sea natural microbial populations and barophilic pure cultures using high-pressure chemostat.  Applied and Environmental Microbiology, 12: 5314-5321.

Woese, C.R., R.Gutell, R. Gupta, and H.F. Noller - 1983 - Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids.  Microbiological Review, 4: 621-669        .

Wolfe, R.S. - 1999 - Anaerobic life - a centennial view.  Journal of Bacteriology, 11: 3317-3320.

Yayanos, A.A. - 1995 -  Microbiology to 10,500 meters in the deep sea.  Ann. Rev. Microbiology, : 777-805.

Zhilina, T.N., G.A. Zavarzin - 1994 - Alkaliphilic anaerobic community at pH10.  Current Microbiology, : 109-112.

b) Geology

in progress.....

c) Chemistry

in progress...

Bregant, D., G. Catalano, G. Civitarese, and A. Luchetta - 1990 -  Some chemical characteristics of the brines in Bannock and Tyro basins: salinity, sulphur compounds, Ca2+, F-, pH, At, PO43-, SiO2, NH3.  Marine Chemistry,  : 35-62.

De Lange, G.J., J.J. Middelburg, C.H. Van der Weijden, G. Catalano, G.W. Luther, III, D.J. Hydes, J.R.W. Woittiez, and G.P. Klinkammer - 1990 -  Compostion of anoxic hypersaline brines in the Tyro and Bannok basins, eastern Mediterranean.  Marine Chemistry,  : 63-88.

Haven, H.L.T., M. Baas, J.W. De Leeuw, J.M. Maassen and P.A. Schenk - 1987 - Organic geochemical characteristics of sediments from the anoxic brine-filled Tyro basin (eastern Mediterranean).  Org. Geochem., 6: 605-611.

d) Technology

in progress...

Bianchi, A., J. Garcin, O. Tholosan - 1999 -  A high-pressure serial sampler to measure microbial activity in the deep sea.  Deep-Sea Research, 46 (12): 2129-2142. (PDF File, 771 KB)

Beranzoli et al. - 2000 - European Seafloor Observatory Offers New Possibilities for Deep-Sea Study. EOS, 81 (5)

Gasparoni F., et al. - 2000 - Results and perspectives from the first mission of the European Abyssal Observatory GEOSTAR. Proc. Oceanology International Conference, March 2000, Brighton, UK.

Gerber H.W., Schulze D. - 1998 - GEOSTAR - Development and test of a deployment and recovery system for deep-sea benthic observatories. Proceedings Oceans '98 Conference, Nice (France) 28 September-1 October 1998.

Gerber H., Schultze D., Gasparoni F. - 1999 - GEOSTAR: first mission results and future perspectives for intervention with heavy deep-sea long-term laboratories. Proceedings OMAE 1999 Conference, July 99, St.John's, Canada.

Gerber H., Clauss G. - 2001 - Development and operational optimisation of Modus, the Geostar subsea docking system. Proceedings OMAE 2001 Conference, June 2001, Rio de Janeiro, Brazil.