tesi integrale

Document Sample
tesi integrale Powered By Docstoc

Acinas S.G., Anton J. and Rodrigues F. (1999) “Diversity of Free-Living

and Attached Bacteria in Offshore Western Mediterranean Waters as

Despicted by Analysis of Genes Encoding 16S rRNA”. Appl. Environ.

Microb, 65 (2) 514–522 ,

Alberelli G., A. Covazzi-Harriague, R. Danovaro, M. Fabiano, S.

Fraschetti, A. Pusceddu. (1999) “Differential responses of bacteria,

meiofauna and macrofauna in a shelf area (Ligurian Sea, NW

Mediterranean): role of food availability” Journal of Sea Research 42


Amann R.I., Ludwig W. and Schleifer K.H. (1995) “Phylogenetic

Identification and In Situ Detection of    Individual Microbial Cells

without Cultivation” Microbiological Review, 59 (1) p. 143–169

Anderson R.F., G.T. Rowe, P.F. Kemp, S. Trumboes and P.E. Biscaye,

(1994) “Carbon budget for the mid-slope depocenter of the middle

Atlantic Bight”. Deep Sea Research II 41: 669-703.

Azam F, Fenchel T, Field JG, Gray JS, Meyer-Reil LA, Thingstad F

(1983) “he ecological role of water-column microbes in the sea” Marine

Ecology Progress Series 10: 257-26

Balzer W., Helder W., Epping E., Lohse L., Otto S. (1998). “Benthic

denitrification and nitrogen cycling at the slope and rise of the NW

European    Continental    Margin     (Goban   Spur)”.    Progress    in

Oceanography. 42: 111-126.

Bernè S. and Loubrieu B (2005) “Les canyons sous-marins

languedociens et pyrénéens en quatre dimensions”. Recherches Marines

Boccaletti M., Cello G., Tortoric L. (1987) “Transtensional tectonics in

the Sicily Channel”. Journal Structural Geology, 9 pp. 869-876

Boetius A, S. Scheibe, A. Tselepidess, H. Thiel (1996) “Microbial

biomass and activities in deep-sea sediments of the Eastern

Mediterranean: trenches are benthic hotspots”. Deep-Sea Research I, 43

(9), pp. 1439-1460

Bohannan Brendan JM and Jennifer Hughesy.(2003) “New approaches

to analyzing microbial biodiversity data”. Current Opinion in

Microbiology 6: 282–287

Bouillon, F. Pagès, J.-M. Gili, A. Palanques, P. Puig and S. Heussner

(2000).   ”Deep-water     Hydromedusae     from    the   Lacaze-Duthiers

submarine    canyon     (Banyuls,   northwestern   Mediterranean)   and

description of two new genera, Guillea and Parateclaia”. Sci. Mar., 64


Boucher Y, Doolittle WF (2002) “Biodiversity: Something new under

the sea”. Nature 41 (7): 27-28

Bratbak G. (1985). “Bacterial biovolume and biomass estimations”. Appl

Environ Microbiol 49: 1488-1493.

Bruni Saija V.”La microbiologia marina nel sistema delle misure

oceanografiche”. Incontro italo-spagnolo “Oceanografia e risorse del

mare”- ed. Selecon SL- Madrid

Canals M., Casamor J.L., Lastras G., Monaco A., Acosta J., Berné S.,

Loubrieu B.,Weaver P.P.E., Grehan A. and Dennielou B. (2004). "The

role of canyons in strata formation". Oceanography, Volume 17,

Number 4

Canfield DE, Jorgensen BB, Fossing H, Glud R, Gundersen J, Ramsing

NB, Thamdrup B, Hansen JW, Nielsen LP, Hall PO (1993) “Pathways of

organic carbon oxidation in three continental margin sediments”. Mar

Geol. 113:27-40.

Casamayor E.O., Schafer H., Banéras L., Pedrò-Aliò C and Muyzer G

(2000) “Identification of and Spatio-Temporal Differences between

Microbial Assemblages from Two Neighboring Sulfurous Lakes:

Comparison     by   Microscopy     and    Denaturing    Gradient   Gel

Electrophoresis”. Appl. Environ. Microb., 66 (2) p. 499–508

Danovaro R., Fabiano M., Boyer M., (1994).” Seasonal changes of

benthic bacteria in a seagrass bed (Posidonia oceanica) of the Ligurian

Sea in relation to origin, composition and fate of the sediment organic

matter”. Marine Biology, Vol. 119 n°4 pp. 489-500

Danovaro R., Dinet A., Duineveld G., Tselepides A. (1999 a) “Benthic

response to particulate fluxes in different trophic environments: a

comparison   between    the   Gulf   of   Lions-Catalan   sea   (western

Mediterranean) and the Cretan Sea (eastern Mediterranean)”. Progress in

Oceanography 44 p: 287-312

Danovaro R., D. Marrale, N. Della Croce b, P. Parodi b, M. Fabiano

(1999 b) “Biochemical composition of sedimentary organic matter and


distribution in the Aegean Sea: trophic state and pelagic–benthic

coupling”. Journal of Sea Research 42 117–129

Danovaro R. and Serresi M. (2000) “Viral density and virus-to-

bacterium ratio in deep-sea sediments of the Eastern Mediterranean”.

Appl. Environ. Microb.. 66 p. 1857-1861

Danovaro R, Marrale D, Dell'Anno A, Della Croce N, Tselepides A,

Fabiano M. (2000) “Bacterial response to seasonal changes in labile

organic matter composition on the continental shelf and bathyal

sediments of the Cretan Sea”.Progress In Oceanography 46: 345-366

Danovaro R., Manini E. and Dell’anno A. (2002) “Higher abundance of

bacteria than viruses in deep Mediterranean sediments”. Appl. Environ.

Microb. 68 p. 1468-1472

Danovaro R., C. Corinaldesi, A. Dell’Anno, M. Fabiano and C. Corselli.

(2005) “Viruses, prokaryotes and DNA in the sediments of a deep-

hypersaline anoxic basin (DHAB) of the Mediterranean Sea”.

Environmental Microbiology 7 (4), 586–592

Delille D., Guidi L.D., & Cahet G. (1990). “ Temporal variations of

benthic bacterial microflora on the North Western Mediterranean

continental shelf and slope”. Marine Ecology, 11, 105-115

Delong E.F. (1992) “Archaea in coastal marine environments”. Proc.

Natl. Acad. Sci. USA Vol. 89, pp. 5685-5689

De Mesel I., Derycke S., Moens T., Van der Gucht K., Vincx M. and

Swing J.(2004) “Top-down impact of bacterivorous nematodes on the

bacterial   community     structure:     a   microcosm   study”.   Environ.

Microbiology 6(7), 733-744

Durrier de Madron X, Abassi A, Serge Heussner, Andre´ Monaco, Jean

Claude Aloisi, Olivier Radakovitch, Pierre Giresse, Roselyne Buscail,

Philippe Kerherve Oceanologia Acta 23 (6) 717–730.

Durrier de Madron X., L. Denis, F. Diaz, N. Garcia, C. Guieu, C. Grenz,

M.D. Loÿe -Pilot, W. Ludwig, T. Moutin and P. Raimbault and Ridame

C. (2003). “Nutrients and carbon budget for the Gulf of Lions during

MOOGLI cruises”. Oceanologia Acta. 26 421–433

Eder W., Wolfgang Ludwig, Robert Huber (1999) “Novel 16S rRNA

gene sequences retrieved from highly saline brine sediments of Kebrit

Deep, Red Sea” Arch Microbiol 172 :213–218

Fabres J., S. Miserocchi, S. Heussner, A.M. Calafat, D. Zúñiga, M.

Canals, T. Tesi, P. Puig, A. Palanques, X. Durrieu de Madron. (2005).

“The Impact of the December 2003 Catastrophic Storm on Near Bottom

Particle Fluxes at Canyon Heads in the Gulf of Lions”. Geophysical

research abstract, Vol. 7, 09225

Fuhrmann J.A. and M. Schwalbach (2003). “Viral Influence on Aquatic

Bacterial Communities”. Biol. Bull. 204: 192–195.

Gage J.D. and Tyler P.A. (1992). “A natural history of organism at the

deep sea floor”. In Deep-Sea Biology Cambrige University Press. New


Gili J.M., F. Page`, J. Bouillon, A. Palanques, P. Puig, S. Heussner, A.

Calafat, M. Canals, A. Monaco (2000).” A multidisciplinary approach to

the    understanding   of    hydromedusan      populations    inhabiting

Mediterranean submarine canyons” Deep-Sea Research I 47: 1513-1533

Handel B. and Marxsen J. (1997). “ Indicators of low level extracellular

enzymatic activity natural waters using fluorigenic model substrates”

Acta hydochim. Hydrobiol, 25: 253-258

Harnett H.E., R.G. Keil, J. Hedges and A.H. Devol, (1998). “Influence

of oxygen exposure time on organic carbon preservation in continental

margin sediments”. Nature 391: 572-575

Herndl G. J., T. Reinthaler, E. Teira, H. van Aken, C. Veth, A.

Pernthaler and J. Pernthaler (2004) “Contribution of Archaea to Total

Prokaryotic Production in the Deep Atlantic Ocean” Appl. Environ.

Microb 71 (5): 2303–2309

Hobbie J.E., R.J. Daley and S. Jasper. (1997) “Use of Nucleopore filters

for counting bacteria by fluorescence microscopy”. Appl. Environ.

Microb. 33: 1225-1228

IUCN- (2004) “The Mediterranean deep-sea ecosystems. An overview of

their diversity structure, functioning and anthropogenic impacts, whit a

proposal for their conservation”.

Ishii K., Marc Mußmann, Barbara J. MacGregor, Rudolf Amann (2004).

“An improved fluorescence in situ hybridization protocol for the

identification of bacteria and archaea in marine sediments”. FEMS

Microbiology Ecology 50: 203-212

Jahnke R.A. (1996) “The global ocean flux of particulate organic carbon

Areal distribution and magnitude”. Global Biogeochem. Cycles, 10 (1) p.


Jahnke R.A, Deborah B. Jahnke (2000) “Rates of C, N, P and Si

recycling and denitrification at the US Mid-Atlantic continental slope

depocenter”. Deep-Sea Research I 47: 1405-1428

Jørgensen B.B. (1982) “Mineralization of organic matter in the sea bed

the role of sulphate reduction”. Nature 296, 643 - 645

Jurgens G., Lindstrom K., Saano A.(1997) “Novel Group within the

Kingdom Crenarchaeota from Boreal Forest Soil” Appl. Environ.

Microb., 63, (2) p. 803–805

Karner M.B., Delong E.F. Karl D.M. (2001). “Archaeal dominance in

the mesopelagic zone of the Pacific Ocean”. Nature Vol 409 507-509

Kato,C., Li,L., Tamaoka,J., Horikoshi,K. (1997). “Molecular analyses of

the sediment of the 11,000-m deep Mariana Trench”. Extremophiles 1:


Kepner R.L. jr, Pratt J.R. (1994) “Use of Fluorochromes for Direct

Enumeration of Total Bacteria in Environmental Samples: Past and

Present”. Microbiological Review, p. 603-615 Vol. 58, No. 4

Krijgsman, W., Hilgen, F. J., Raffi, I., Sierro, F. J. and Wilson, D. S.,

(1999). “Chronology, causes and progression of the Messinian salinity

crisis”. Nature, 400: 652-655.

Lebaron P.,Servais P., Agogué H., Couties C. and Joux F. (2001) “Does

the High Nucleic Acid Content of Individual Bacterial Cells Allow Us

To Discriminate between Active Cells and Inactive Cells in Aquatic

Systems? Appl. Environ Microb. 67, 4 p. 1775–1782

Leveau M, B. Coste (1987). “Impact des apports rhodaniens sue le

milieu pélegique du Golfe du Lion ». Bullettin d’Ecologie 18: 114-122

Levinton, J.S., G.R. Lopez, H.H. Lassen, and U. Rahn. (1977).

“Feedback and structure in feeding marine benthic communities”. 11th

Europ. Mar. Biol. Symp., pp. 409-416. Oxford: Pergamon Press.

Llobet-Brossa E., Rossello-Mora R., and Amann R. (1998). “ Microbial

community composition of Wadden Sea sediments as revealed by

fluorescence in situ hybridization” Appl. Environ. Microb. 64 (7) p.


Locat, J., and Lee, H., 2002. “Submarine landslides: advances and

challenges”. Canadian Geotechnical Journal, 39: 193-212

Lofi J. (2002). La crise de salinité messinienne: conséquences directes et

différées sur l’évolution sédimentaire de la marge du Golfe du Lion.

Thèse de doctorat - Université des Sciences et Techniques Lille 1 , p 260

Loreau    M    (2000)    “Microbial      diversity,   producer-decomposer

interactions and ecosystem processes: a theoretical model”. Proceeding

of the Royal Society of London 268 : 303-309

Luna G.M., E. Manini, and R. Danovaro (2002). ”Large Fraction of

Dead and Inactive Bacteria in Coastal Marine Sediments: Comparison of

Protocols for Determination and Ecological Significance”. Appl,.

Environ. Microb., 68, (7) p. 3509–3513

Luna G.M. and Danovaro R. (2003): “Active, dormant and dead

bacterial fractions in aquatic environments”. Res. Devel. Microbiology, 7


Luna G.M., Dell'Anno A., Giuliano L. and Danovaro R. (2004) “

Bacterial diversity in deep Mediterranean sediments: relationship with

the active bacterial fraction and substrate availability”. Environmental

Microbiology 6(7), 745-753

Manini E., C. Fiordelmondo, C. Gambi, A. Pusceddu, R. Danovaro.

(2003) “Benthic microbial loop functioning in coastal lagoons: a

comparative approach”. Oceanologica Acta 26 27–38

Manini E., Luna G.M., Danovaro R. (2005) “Benthic bacterial response

to variable estuarine water inputs”. FEMS Microbiology Ecology 50 (3):


Massana R., Murray A.E., Preston C.M. and Delong E.F. (1997)

“Vertical Distribution and Phylogenetic Characterization of Marine

Planktonic Archaea in the Santa Barbara Channel” Appl. Environ.

Microb., 63, (1) p.50–56

McInerney J.O., Wilkinson M., Patching J.W., Embley T.M. and Powell

R. (1995) “Recovery and Phylogenetic Analysis of Novel Archaeal

rRNA Sequences from a Deep-Sea Deposit Feeder” Appl. Environ.

Microb., 61, (4) p. 1646–1648

Meyer-Reil L.A. (1983). “Benthic response to sedimentation events

during autumn to spring at a shallow water station in the Western Kiel

Bight. II Analysis of benthic bacterial populations”. Marine Biology 77:


Mienert, J., J. Posewang, and M. Baumann. (1998). “Gas hydrates along

the northeastern Atlantic Margin: Possible hydrate-bound margin

instabilities and possible release of methane”. Pp. 275-291 in Gas

Hydrates; Relevance to World Margin Stability and Climate Change, J.-

P. Henriet, and J. Mienert, eds. Special Publication 137. Geological

Society of London, United Kingdom

Millot C. 1990 “The Gulf of Lion’s Hydrodynamics”. Continental shelf

research, 10, (9-11) pp 885-894

Molcard A., Gervasio L., Griffa A., Gasparini G.P., Mortier L.,

Ozgokmen T.M. (2002); ”Numerical investigation of the Sicily Channel

dynamics density currents and water mass advection”. Journal of Marine

Systems 36: 219-238

Montagna P.A. (1982). “Sampling Design and Enumeration Statistics for

Bacteria Extracted from Marine Sediments” Appl. Environ. Microb. 43,

(6) p. 1366-1372

Montagna P.A. (1984). “In situ measurement of meiobenthic grazing

rateson sediment bacteria and edaphic diatoms”. Mar. Ecol. Prog. Ser.

18: 119-130

Mountin T. & Raimbault P. (2002).” Primary production, carbon export

and nutrients availability in western and eastern Mediterranean Sea in

early summer 1996 (MINOS cruise)” Journal of Marine Systems 33-34:


Murray A.E, Preston C.M., Massana R., Taylor L.T., Blakis A., Wu K.

and Delong E.F. (1998) “Seasonal and Spatial Variability of Bacterial

and Archaeal Assemblages in the Coastal Waters near Anvers Island,

Antarctica” Appl. Environ. Microb., 64, (7) p. 2585–2595

Mussi, B. & Miragliuolo A. (2003).”I cetacei della costa nord

occidentale dell’isola d’Ischia”. pp. 213-232. In: Ambiente marino e

costiero e territorio delle isole Flegree (Ischia, Procida e Vivara - Golfo

di Napoli). Risultati di uno studio multidisciplinare. Editori M. C.

Gambi, M. De Lauro e F. Jannuzzi. Memorie dell'Accademia di Scienze

Fisiche e Matematiche, Società Italiana di Scienze, Lettere e Arti in

Napoli. Liguori Editore. Pp 425

Norem, H., Locat, J., and Schieldrop, B., (1990). “An approach to the

physics   and the modelling of submarine landslides”. Marine

Geotechnology, 9: 93-111

Normark, W.R., and Piper, D.J.W., (1991). “Initiation processes and

flow evolution of turbidity currents: implications for the depositional

record”. In: From Shoreline to Abyssal, SEPM Special Publication 46,

pp.: 20-230

Ovreas L (2000) “Population and community level approaches for

analysing microbial diversity in natural environments”. Ecology Letters

3: 236–251

Pernthaler A., Jakob Pernthaler and Rudolf Amann. (2002 a)

“Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition

for the Identification of Marine Bacteria”. Appl. Environ. Microb.,, 68

(6) p. 3094–3101

Pernthaler, A, Preston, CM, Pernthaler, J, DeLong, EF, Amann, R (2002

b)   Comparison    of   fluorescently   labeled   oligonucleotide   and

polynucleotide probes for the detection of pelagic marine Bacteria and

Archaea. Appl Environ Microbiol 68: 661-667

Puig P., A.S. Ogston, B.L.Mullenbach, C.A. Nittrouer and R.W.

Sternberg (2003). “Shelf-to-canyon sediment-transport processes on the

Eel continental margin (northern California)”. Mar. Geol. 193:129-149.

Purvis A, Hector A (2000) “Getting the measure of biodiversity”. Nature

405: 212-219

Quéric N., T. Soltwedel, W.E. Arntz (2004). “Application of a rapid

direct viable count method to deep-sea sediment bacteria” Journal of

Microbiological Methods 57 351-367

Ravenschag K., Sahm K., Knoblauch C. (2000) ”Community Structure,

Cellular rRNA Content, and Activity of Sulfate-Reducing Bacteria in

Marine Arctic Sediments” Appl. Environ. Microb., 66 (8) p. 3592–3602

Ryan W. B. F., (1976). “Quantitative evaluation of the depth of the

Mediterranean before, during and after the Late Miocene salinity crisis”.

Sedimentology, 23 (6): 791-813.

Reyss D., (1971). Les canyons sous-marins de la mer Catalane: le rech

du Cap et le rech Lacaze-Duthiers. III. Les peuplements de la

macrofaune benthique". Vie Milieu, 22: 529-613

Rex M.A., C. T. Stuart, G. Coyne (2000) “Latitudinal gradients of

species richness in the deep-sea benthos of the North Atlantic”. PNAS

97 (8): 4082-4085

Sanders B.C. and Kalff J. (1993) “Factor controlling bacterial production

in marine and freshwater sediments”. Microb. Ecol. 26:79-99

Sardà F., Calafat A., Mar Flexas M.,Tselepides A., Canals M., Espino

M. and Tursi A.(2004) “An Introduction to Mediterranean deep-sea

biology.” SCI. MAR 68 (suppl. 3): 7-38

Signorini S.R., Munchow A., Heidvogel D. (1997). “ Flow dynamics of

a wide Arctic canyon”. J. Geoph. Res. Vol. 102 n°8 p.18,661-18,680

Simon M, Azam F (1989) “Protein content and protein synthesis rates of

planktonic marine bacteria”. Marine Ecology Progress Series 51: 201-


Stanley D.L.- (1977). “Post Miocene depositional patterns and structural

displacement in the Mediterranean”. In: A.E.M. Nairn, W.H. Kanes and

F.G. Stheli (eds.), The oceans basins and margins: the Eastern

Mediterranean, pp. 77-128. Plenum Press, New York.

Stetter K.O (1999).” Extremophiles and their adaptation to hot

environments”. FEBS Letters 452 22-25

Takai K., and Koki Horikoshi (1999) “Genetic Diversity of Archaea in

Deep-Sea Hydrothermal Vent Environments”. Genetics 152: 1285–1297

Tankéré S.P.C., D. G. Bourne, F. L. L. Muller and V. Torsvik (2002)

“Microenvironments and microbial community structure in sediments”

Environmental Microbiology 4(2): 97–105

Tappin D.R., Watts P., McMurty G.M., Lafoy Y.,and Matsumoto T.

(2001). “ The Sissano, Papua New Guinea tsunami of July, 1998-

offshore evidence on the source mechanism”. Marine Geology, 175: 1-


Tesson Michel, Caroline Labaune, Bernard Gensous. (2005) “Small

rivers contribution to the Quaternary evolution of a Mediterranean

littoral system: The western gulf of Lion, France”. Marine Geology 222–

223 313– 334

Thomsen L. and van Weeting T.C., (1998). “Spatial and temporal

variability of particulate matter in the benthic boundary layer at the

North East Atlantic Continental Margin”. Progr. Oceanogr. 42: 61-76.

Thomsen L., van Weering T., Gust G. (2002) Processes in the benthic

boundary layer at the Iberian continental margin and their implication for

carbon mineralization. Progr. Oceanogr. 52: 315-329.

Turley C (2000) “Bacteria in the cold deep-sea benthic boundary layer


sediment-water interface of the NE Atlantic”. FEMS Microbiology

Ecology 33: 89-99

Van Den Broeck N. & Moutin T. (2002). “Phosphate in the sediments of

the Gulf of Lions (NW Mediterranean Sea), relationship with input by

the river Rhone”. Hydrobiologia 472: 85–94,

Vetriani C., H. W. Jannasch, B. J. MacGregor, D. A. StahlL, A.

Reysenbach     (1999)    “Population     Structure   and    Phylogenetic

Characterization of Marine Benthic Archaea in Deep-Sea Sediments”

Appl. Environ. Microb, 65 (10) p. 4375–4384.

Vetter E.W. (1998). “Population dynamics of a dense assemblage of

marine detritivors”. Journal of experimental Marine Biology and

Ecology. 226 131-161

Vrba J., Nedoma J., Simek K., Seda J. (1992) “Microbial decomposition

of polymer organic matter related to plankton development in a

reservoir: activity of α-, ß-glucosidase, and ß-N-acetylglocosammidase

and uptake of N-acetylglucosamine”. Arch. Hydrobiol. 126, 193-211

Wagner M., M. Horn, H. Daims (2003)“Fluorescence in situ

hybridisation for the identification and characterisation of prokaryotes”

Curr. Opinion Microbiol. 6: 302-309.

Weinbauer M.G., F. Rassoulzadegan. (2004) “Are viruses driving

microbial diversification and diversity?” Environmental Microbiology

6(1), 1–11

Winter C., Arjan Smit, Gerhard J. Herndl, and Markus G. Weinbauer.

(2005) “Linking bacterial richness with viral abundance and prokaryotic

activity”. Limnol. Oceanogr., 50(3), , 968–977

Wobus A., C. Bleul, S. Maassen, C. Scheerer, M. Schuppler, E. Jacobs,

I. Roske. (2003) ”Microbial diversity and functional characterization of

sediments   from   reservoirs   of    different   trophic   state”.   FEMS

Microbiology Ecology 46 331-347

Woese CR, Kandler O, Wheelis ML (1990) “Towards a natural system

of organisms: proposal for the domains Archaea, Bacteria, and Eucarya”.

PNAS 87: 4576-4579

Zweifel U.L. and Hagstrom A. (1995). “Total Counts of Marine Bacteria

Include a Large Fraction of Non-Nucleoid-Containing Bacteria

(Ghosts)”. Appl. Environ. Microb., 61, (6) p. 2180–2185.