Deep water samples ( ca. 4,200 m) were taken from two hydrologically-similar sites around the Crozet islands with highly contrasting surface water productivities. Site M5 was characteristic of high productivity waters (high chlorophyll) whilst site M6 was subject to a low productivity regime (low chlorophyll) in the overlying waters. Samples were incubated for three weeks at 4 °C at in-situ and surface pressures, with and without added nutrients. Prokaryotic abundance increased by at least two-fold for all nutrient-supplemented incubations of water from M5 with little difference in abundance between incubations carried out at atmospheric and in-situ pressures. Abundance only increased for incubations of M6 waters (1.6-fold) when they were carried out at in-situ pressures and with added nutrients. Changes in community structure as a result of incubation and enrichment (as measured by DGGE banding profiles and phylogenetic analysis) showed that diversity increased for incubations of M5 waters but decreased for those with M6 waters. Moritella spp. came to dominate incubations carried out under in-situ pressure whilst the Archaeal community was dominated by Crenarchaea in all incubations. Comparisons between atmospheric and in situ pressure incubations demonstrated that community composition was significantly altered and community structure changes in unsuspplemented incubations at in situ pressure was indicative of the loss of functional taxa as a result of depressurisation during sampling. The use of enrichment incubations under in-situ conditions has contributed to understanding the different roles played by microorganisms in deep sea ecosystems in regions of low and high productivity.
References
[1]
Yokokawa, T.; Nagata, T. Linking bacterial community structure to carbon fluxes in MARINE environments. J. Oceanogr. 2010, 66, 1–12, doi:10.1007/s10872-010-0001-4.
[2]
Pedros-Alio, C. Ecology: Dipping into the rare biosphere. Science 2007, 315, 192–193, doi:10.1126/science.1135933.
[3]
Dumestre, J.F.; Casamayor, E.O.; Massana, R.; Pedros-Alio, C. Changes in bacterial and archaeal assemblages in an equatorial river induced by the water eutrophication of Petit Saut dam reservoir (French Guiana). Aquat. Microb. Ecol. 2002, 26, 209–221, doi:10.3354/ame026209.
[4]
Lebaron, P.; Servais, P.; Troussellier, M.; Courties, C.; Vives-Rego, J.; Muyzer, G.; Bernard, L.; Guindulain, T.; Schafer, H.; Stackebrandt, E. Changes in bacterial community structure in seawater mesocosms differing in their nutrient status. Aquat. Microb. Ecol. 1999, 19, 255–267, doi:10.3354/ame019255.
[5]
Leflaive, J.; Danger, M.; Lacroix, G.; Lyautey, E.; Oumarou, C.; Ten-Hage, L. Nutrient effects on the genetic and functional diversity of aquatic bacterial communities. FEMS Microbiol. Ecol. 2008, 66, 379–390, doi:10.1111/j.1574-6941.2008.00593.x.
[6]
Riemann, L.; Steward, G.F.; Azam, F. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl. Environ. Microbiol. 2000, 66, 578–587, doi:10.1128/AEM.66.2.578-587.2000.
[7]
Egan, S.T.; McCarthy, D.M.; Patching, J.W.; Fleming, G.T.A. An investigation of the physiology and potential role of components of the deep ocean bacterial community (of the NE Atlantic) by enrichments carried out under minimal environmental change. Deep Sea Res. Part I Oceanogr. Res. Pap. 2012, 61, 11–20, doi:10.1016/j.dsr.2011.11.005.
[8]
Jorgensen, B.B.; Boetius, A. Feast and famine: Microbial life in the deep-sea bed. Nat. Rev. Microbiol. 2007, 5, 770–781, doi:10.1038/nrmicro1745.
[9]
Tamburini, C.; Boutrif, M.; Garel, M.; Colwell, R.R.; Deming, J.W. Prokaryotic responses to hydrostatic pressure in the ocean—A review. Environ. Microbiol. 2013, 15, 1262–1274, doi:10.1111/1462-2920.12084.
[10]
Pollard, R.T.; Venables, H.J.; Read, J.F.; Allen, J.T. Large-scale circulation around the Crozet Plateau controls an annual phytoplankton bloom in the Crozet Basin. DeepSea Res. Part II Top. Stud. Oceanogr. 2007, 54, 1915–1929, doi:10.1016/j.dsr2.2007.06.012.
[11]
Pollard, R.; Sanders, R.; Lucas, M.; Statham, P. The Crozet natural Iron Bloom and Export Experiment (CROZEX). DeepSea Res. Part II Top. Stud. Oceanogr. 2007, 54, 1905–1914, doi:10.1016/j.dsr2.2007.07.023.
[12]
Treguer, P.; Jacques, G. Dynamics of nutrients and phytoplankton, and fluxes of carbon, nitrogen and silicon in the Antarctic Ocean. Polar Biol. 1992, 12, 149–162.
[13]
Pitchford, J.; Brindley, J. Iron limitation, grazing pressure and oceanic High Nutrient-Low Chlorophyll (HNLC) regions. J. Plankton Res. 1999, 21, 525–547, doi:10.1093/plankt/21.3.525.
[14]
Planquette, H.; Statham, P.J.; Fones, G.R.; Charette, M.A.; Moore, C.M.; Salter, I.; Nedelec, F.H.; Taylor, S.L.; French, M.; Baker, A.R.; et al. Dissolved iron in the vicinity of the Crozet Islands, Southern Ocean. DeepSea Res. Part II Top. Stud. Oceanogr. 2007, 54, 1999–2019, doi:10.1016/j.dsr2.2007.06.019.
[15]
Pollard, R.; Read, J. Circulation pathways and transports of the Southern Ocean in the vicinity of the Southwest Indian Ridge. J. Geophys. Res. 2001, 106, 2881–2898, doi:10.1029/2000JC900090.
[16]
Young-Hyang, P.; Gamberoni, L.; Charriaud, E. Frontal structure, water masses, and circulation in the Crozet Basin. J. Geophys. Res. 1993, 98, 361–385.
[17]
Pollard, R.T.; Lucas, M.I.; Read, J.F. Physical controls on biogeochemical zonation in the Southern Ocean. DeepSea Res. Part II Top. Stud. Oceanogr. 2002, 49, 3289–3305, doi:10.1016/S0967-0645(02)00084-X.
[18]
Hughes, J.A.; Smith, T.; Chaillan, F.; Bett, B.J.; Billett, D.S.M.; Boorman, B.; Fischer, E.H.; Frenz, M.; Wolff, G.A. Two abyssal sites in the Southern Ocean influenced by different organic matter inputs: Environmental characterisation and preliminary observations on the benthic foraminifera. DeepSea Res. Part II Top. Stud. Oceanogr. 2007, 54, 2275–2290, doi:10.1016/j.dsr2.2007.06.006.
[19]
Martin, J.H.; Knauer, G.A.; Karl, D.M.; Broenkow, W.W. VERTEX: Carbon cycling in the northeast Pacific. DeepSea Res. Part I Oceanogr. Res. Pap. 1987, 34, 267–285, doi:10.1016/0198-0149(87)90086-0.
[20]
Sanders, R.; Morris, P.J.; Stinchcombe, M.; Seeyave, S.; Venables, H.; Lucas, M. New production and the f ratio around the Crozet Plateau in austral summer 2004–2005 diagnosed from seasonal changes in inorganic nutrient levels. DeepSea Res. Part II Top. Stud. Oceanogr. 2007, 54, 2191–2207, doi:10.1016/j.dsr2.2007.06.007.
[21]
Turley, C. Bacteria in the cold deep-sea benthic boundary layer and sediment-water interface of the NE Atlantic. FEMS Microbiol. Ecol. 2000, 33, 89–99.
[22]
Jamieson, R.E.; Rogers, A.D.; Billett, D.S.M.; Pearce, D.A. Bacterial biodiversity in deep-sea sediments from two regions of contrasting surface water productivity near the Crozet Islands, Southern Ocean. Deep Sea Res. Part A Oceanogr. Res. Pap. 2013. in press.
[23]
Danovaro, R.; Corinaldesi, C.; Luna, G.M.; Magagnini, M.; Manini, E.; Pusceddu, A. Prokaryote diversity and viral production in deep-sea sediments and seamounts. DeepSea Res. Part II Top. Stud. Oceanogr. 2009, 56, 738–747, doi:10.1016/j.dsr2.2008.10.011.
[24]
Bendtsen, J.; Lundsgaard, C.; Middelboe, M.; Archer, D. Influence of bacterial uptake on deep-ocean dissolved organic carbon. Glob. Biogeochem. Cycle 2002, 16, 74:1–74:12.
[25]
Danovaro, R.; della Croce, N.; Dell’Anno, A.; Pusceddu, A. A depocenter of organic matter at 7800 m depth in the SE Pacific Ocean. DeepSea Res. Part I Oceanogr. Res. Pap. 2003, 50, 1411–1420, doi:10.1016/j.dsr.2003.07.001.
[26]
Fang, J.; Zhang, L.; Bazylinski, D.A. Deep-sea piezosphere and piezophiles: Geomicrobiology and biogeochemistry. Trends Microbiol. 2010, 18, 413–422, doi:10.1016/j.tim.2010.06.006.
[27]
Forney, L.J.; Zhou, X.; Brown, C.J. Molecular microbial ecology: Land of the one-eyed king. Curr. Opin. Microbiol. 2004, 7, 210–220, doi:10.1016/j.mib.2004.04.015.
[28]
Grossart, H.P.; Gust, G. Hydrostatic pressure affects physiology and community structure of marine bacteria during settling to 4000 m: An experimental approach. Mar. Ecol. Prog. Ser. 2009, 390, 97–104, doi:10.3354/meps08201.
[29]
Muyzer, G.; de Waal, E.C.; Uitterlinden, A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 1993, 59, 695–700.
[30]
Fromin, N.; Hamelin, J.; Tarnawski, S.; Roesti, D.; Jourdain-Miserez, K.; Forestier, N.; Teyssier-Cuvelle, S.; Gillet, F.; Aragno, M.; Rossi, P. Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ. Microbiol. 2002, 4, 634–643, doi:10.1046/j.1462-2920.2002.00358.x.
[31]
Rink, B.; Seeberger, S.; Martens, T.; Duerselen, C.D.; Simon, M.; Brinkhoff, T. Effects of phytoplankton bloom in a coastal ecosystem on the composition of bacterial communities. Aquat. Microb. Ecol. 2007, 48, 47–60, doi:10.3354/ame048047.
[32]
Yoshida, A.; Nishimura, M.; Kogure, K. Bacterial community structure in the Sulu Sea and adjacent areas. DeepSea Res. Part II Top. Stud. Oceanogr. 2007, 54, 103–113, doi:10.1016/j.dsr2.2006.01.030.
[33]
Wu, L.; Yu, Y.; Zhang, T.; Feng, W.; Zhang, X.; Li, W. PCR-DGGE fingerprinting analysis of plankton communities and its relationship to lake trophic status. Int. Rev. Hydrobiol. 2009, 94, 528–541, doi:10.1002/iroh.200911129.
[34]
Bonin, P.C.; Michotey, V.D.; Mouzdahir, A.; Rontani, J.-F. Anaerobic biodegradation of squalene: Using DGGE to monitor the isolation of denitrifying Bacteria taken from enrichment cultures. FEMS Microbiol. Ecol. 2002, 42, 37–49, doi:10.1111/j.1574-6941.2002.tb00993.x.
[35]
Nakagawa, T.; Fukui, M. Phylogenetic characterization of microbial mats and streamers from a Japanese alkaline hot spring with a thermal gradient. J. Gen. Appl. Microbiol. 2002, 48, 211–222, doi:10.2323/jgam.48.211.
[36]
Stephen, J.R.; Chang, Y.-J.; Gan, Y.D.; Peacock, A.; Pfiffner, S.M.; Barcelona, M.J.; White, D.C.; Macnaughton, S.J. Microbial characterization of a JP-4 fuel-contaminated site using a combined lipid biomarker/polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)-based approach. Environ. Microbiol. 1999, 1, 231–241, doi:10.1046/j.1462-2920.1999.00030.x.
[37]
Murray, A.E.; Preston, C.M.; Massana, R.; Taylor, L.T.; Blakis, A.; Wu, K.; DeLong, E.F. Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl. Environ. Microbiol. 1998, 64, 2585–2595.
[38]
Spiegelman, D.; Whissell, G.; Greer, C.W. A survey of the methods for the characterization of microbial consortia and communities. Can. J. Microbiol. 2005, 51, 355–386, doi:10.1139/w05-003.
[39]
Grossi, V.; Yakimov, M.M.; Al Ali, B.; Tapilatu, Y.; Cuny, P.; Goutx, M.; La Cono, V.; Giuliano, L.; Tamburini, C. Hydrostatic pressure affects membrane and storage lipid compositions of the piezotolerant hydrocarbon-degrading Marinobacter hydrocarbonoclasticus strain #5. Environ. Microbiol. 2010, 12, 2020–2033, doi:10.1111/j.1462-2920.2010.02213.x.
[40]
Yayanos, A.A.; Dietz, A.S. Death of a hadal deep-sea bacterium after decompression. Science 1983, 220, 497–498.
[41]
Chastain, R.A.; Yayanos, A.A. Ultrastructural changes in an obligately barophilic marine bacterium after decompression. Appl. Environ. Microbiol. 1991, 57, 1489–1497.
[42]
Park, C.B.; Clark, D.S. Rupture of the cell envelope by decompression of the deep-sea methanogen methanococcus jannaschii. Appl. Environ. Microbiol. 2002, 68, 1458–1463, doi:10.1128/AEM.68.3.1458-1463.2002.
[43]
Yayanos, A.A.; Dietz, A.S. Thermal inactivation of a deep-sea barophilic bacterium, isolate CNPT-3. Appl. Environ. Microbiol. 1982, 43, 1481–1489.
[44]
Patching, J.W.; Eardly, D. Bacterial biomass and activity in the deep waters of the eastern Atlantic—Evidence of a barophilic community. Deep Sea Res. Part I Oceanogr. Res. Pap. 1997, 44, 1655–1670, doi:10.1016/S0967-0637(97)00040-X.
[45]
Eardly, D.F.; Carton, M.W.; Gallagher, J.M.; Patching, J.W. Bacterial abundance and activity in deep-sea sediments from the eastern North Atlantic. Prog. Oceanog. 2001, 50, 245–259, doi:10.1016/S0079-6611(01)00056-8.
[46]
Nagata, T.; Fukuda, H.; Fukuda, R.; Koike, I. Bacterioplankton distribution and production in deep Pacific waters: Large-Scale geographic variations and possible coupling with sinking particle fluxes. Limnol. Oceanogr. 2000, 45, 426–435, doi:10.4319/lo.2000.45.2.0426.
[47]
Thingstad, T.F. Elements of a theory for the mechanisms controlling abundance, diversity and biogeochemical role of lytic viruses in aquatic systems. Limnol. Oceanogr. 2000, 45, 1320–1328, doi:10.4319/lo.2000.45.6.1320.
[48]
Pernthaler, J. Predation on prokaryotes in the water column and its ecological implications. Nat. Rev. Microbiol. 2005, 3, 537–536, doi:10.1038/nrmicro1180.
[49]
Hyun, J.H.; Kim, K.H. Bacterial abundance and production during the unique spring phytoplankton bloom in the central Yellow Sea. Mar. Ecol. Prog. Ser. 2003, 252, 77–88, doi:10.3354/meps252077.
[50]
Guixa-Boixereu, N.; Lysnes, K.; Pedros-Alio, C. Viral lysis and bacterivory during a phytoplankton bloom in a coastal water microcosm. Appl. Environ. Microbiol. 1999, 65, 1949–1958.
[51]
Pinhassi, J.; Sala, M.M.; Havskum, H.; Peters, F.; Guadayol, O.; Malits, A.; Marrase, C. Changes in bacterioplankton composition under different phytoplankton regimens. Appl. Environ. Microbiol. 2004, 70, 6753–6766, doi:10.1128/AEM.70.11.6753-6766.2004.
[52]
Jurgens, K.; Matz, C. Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria. Antonie Leeuwenhoek 2002, 81, 413–434, doi:10.1023/A:1020505204959.
[53]
ZoBell, C.E.; Anderson, D.Q. Observations on the multiplication of bacteria in different volumes of sea water and the influence of oxygen tension and solid surfaces. Biol. Bull. (Woods Hole) 1936, 71, 324–342, doi:10.2307/1537438.
[54]
Zobell, C.E. The effect of solid surfaces upon bacterial activity. J. Bacteriol. 1943, 46, 39–56.
[55]
Kato, C.; Bartlett, D.H. The molecular biology of barophilic bacteria. Extremophiles 1997, 1, 111–116, doi:10.1007/s007920050023.
Bent, S.J.; Forney, L.J. The tragedy of the uncommon: Understanding limitations in the analysis of microbial diversity. ISME J. 2008, 2, 689–695, doi:10.1038/ismej.2008.44.
[58]
Sogin, M.L.; Morrison, H.G.; Huber, J.A.; Welch, D.M.; Huse, S.M.; Neal, P.R.; Arrieta, J.M.; Herndl, G.J. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc. Natl. Acad. Sci. USA 2006, 103, 12115–12120, doi:10.1073/pnas.0605127103.
[59]
Fuhrman, J.A. Microbial community structure and its functional implications. Nature 2009, 459, 193–199, doi:10.1038/nature08058.
[60]
Muylaert, K.; VanDerGucht, K.; Vloemans, N.; Meester, L.; Gillis, M.; Vyverman, W. Relationship between bacterial community composition and bottom-up versus top-down variables in four eutrophic shallow lakes. Appl. Environ. Microbiol. 2002, 68, 4740–4750, doi:10.1128/AEM.68.10.4740-4750.2002.
[61]
Zwart, G.; Kamst-van Agterveld, M.P.; van der Werff-Staverman, I.; Hagen, F.; Hoogveld, H.L.; Gons, H.J. Molecular characterization of cyanobacterial diversity in a shallow eutrophic lake. Environ. Microbiol. 2005, 7, 365–377, doi:10.1111/j.1462-2920.2005.00715.x.
[62]
Park, J.W.; Crowley, D.E. Nested PCR bias: A case study of Pseudomonas spp in soil microcosms. J. Environ. Monit. 1039, 12, 985–988, doi:10.1039/b924160d.
Bianchi, A.; Garcin, J. Bacterial response to hydrostatic-pressure in seawater samples collected in mixed-water and stratified-water conditions. Mar. Ecol. Prog. Ser. 1994, 111, 137–141, doi:10.3354/meps111137.
[65]
Jannasch, H.W.; Wirsen, C.O.; Taylor, C.D. Deep-Sea Bacteria: Isolation in the Absence of Decompression. Science 1982, 216, 1315–1317.
[66]
Herndl, G.J.; Reinthaler, T.; Teira, E.; van Aken, H.; Veth, C.; Pernthaler, A.; Pernthaler, J. Contribution of archaea to total prokaryotic production in the deep Atlantic Ocean. Appl. Environ. Microbiol. 2005, 71, 2303–2309, doi:10.1128/AEM.71.5.2303-2309.2005.
[67]
Ingalls, A.E.; Shah, S.R.; Hansman, R.L.; Aluwihere, L.I.; Santos, G.R.; Druffel, E.R.M.; Pearson, A. Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. Proc. Natl. Acad. Sci. USA 2006, 103, 6442–6447, doi:10.1073/pnas.0510157103.
[68]
Oger, P.M.; Jebbar, M. The many ways of coping with pressure. Res. Microbiol. 2010, 161, 799–809, doi:10.1016/j.resmic.2010.09.017.
[69]
Parkes, R.J.; Cragg, B.A.; Getliff, J.M.; Harvey, S.M.; Fry, J.C.; Lewis, C.A.; Rowland, S.J. A quantitative study of microbial decomposition of biopolymers in Recent sediments from the Peru Margin. Mar. Geol. 1993, 113, 55–66, doi:10.1016/0025-3227(93)90149-P.
Achenbach, L.; Woese, C.R. 16S and 23S rRNA-like Primers. In Archaea—A Laboratory Manual; Sower, K.R., Schreier, H.J., Eds.; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, USA, 1995; pp. 521–523.
[72]
DeLong, E.F. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 1992, 89, 5685–5689, doi:10.1073/pnas.89.12.5685.
[73]
Ovreas, L.; Forney, L.; Daae, F.; Torsvik, V. Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 1997, 63, 3367–3373.
[74]
Sheffield, V.C.; Cox, D.R.; Lerman, L.S.; Myers, R.M. Attachment of a 40 base-pair G+C-rich sequence to genomic DNA fragments by the polymerase chain reaction results in improved detection of single base changes. Proc. Natl. Acad. Sci. USA 1989, 86, 232–236, doi:10.1073/pnas.86.1.232.
[75]
Kovach, W. MVSP-A Multivariate Statistical Package for Windows, ver. 3.13q; Kovach Computing Services: Pentraeth, Wales, UK, 1998.
[76]
Simpson, E.H. Measurement of diversity. Nature 1949, 163, 688, doi:10.1038/163688a0.
[77]
Shannon, C.E.; Weaver, W. The Mathematical Theory of Communication; University of Illinois Press: Urbana, IL, USA, 1963; p. 29.
[78]
Altschul, S.F.; Madden, T.L.; Schaffer, A.A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D.J. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 1997, 25, 3389–3402, doi:10.1093/nar/25.17.3389.
[79]
Johnson, M.; Zaretskaya, I.; Raytselis, Y.; Merezhuk, Y.; McGinnis, S.; Madden, T.L. NCBI BLAST: A better web interface. Nucleic Acids Res. 2008, 36, W5–W9, doi:10.1093/nar/gkn201.
[80]
Chenna, R.; Sugawara, H.; Koike, T.; Lopez, R.; Gibson, T.J.; Higgins, D.G.; Thompson, J.D. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 2003, 31, 3497–3500, doi:10.1093/nar/gkg500.
[81]
Tamura, K.; Peterson, D.; Peterson, N.; Stecher, G.; Nei, M.; Kumar, S. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol. 2011, 28, 2731–2739, doi:10.1093/molbev/msr121.
[82]
Saitou, N.; Nei, N. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4, 406–425.
[83]
Felsenstein, J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985, 39, 783–791, doi:10.2307/2408678.
[84]
Kimura, M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 1980, 16, 111–120, doi:10.1007/BF01731581.
