Although emerging evidence indicates that deep-sea water contains an untapped reservoir of high metabolic and genetic diversity, this realm has not been studied well compared with surface sea water. The study provided the first integrated meta-genomic and -transcriptomic analysis of the microbial communities in deep-sea water of North Pacific Ocean. DNA/RNA amplifications and simultaneous metagenomic and metatranscriptomic analyses were employed to discover information concerning deep-sea microbial communities from four different deep-sea sites ranging from the mesopelagic to pelagic ocean. Within the prokaryotic community, bacteria is absolutely dominant (~90%) over archaea in both metagenomic and metatranscriptomic data pools. The emergence of archaeal phyla Crenarchaeota, Euryarchaeota, Thaumarchaeota, bacterial phyla Actinobacteria, Firmicutes, sub-phyla Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria, and the decrease of bacterial phyla Bacteroidetes and Alphaproteobacteria are the main composition changes of prokaryotic communities in the deep-sea water, when compared with the reference Global Ocean Sampling Expedition (GOS) surface water. Photosynthetic Cyanobacteria exist in all four metagenomic libraries and two metatranscriptomic libraries. In Eukaryota community, decreased abundance of fungi and algae in deep sea was observed. RNA/DNA ratio was employed as an index to show metabolic activity strength of microbes in deep sea. Functional analysis indicated that deep-sea microbes are leading a defensive lifestyle.
References
[1]
Orcutt, B.N.; Sylvan, J.B.; Knab, N.J.; Edwards, K.J. Microbial ecology of the dark ocean above, at, and below the Seafloor. Microbiol. Mol. Biol. Rev. 2011, 75, 361–422, doi:10.1128/MMBR.00039-10.
[2]
Aristegui, J.; Gasol, J.M.; Duarte, C.M.; Herndl, G.J. Microbial oceanography of the dark ocean’s pelagic realm. Limnol. Oceanogr. 2009, 54, 1501–1529, doi:10.4319/lo.2009.54.5.1501.
[3]
Arístegui, J.; Duarte, C.M.; Agustí, S.; Doval, M.; Alvarez-Salgado, X.A.; Hansell, D.A. Dissolved organic carbon support of respiration in the dark ocean. Science 2002, 298, 1967, doi:10.1126/science.1076746.
[4]
Arístegui, J.; Duarte, C.M.; Gasol, J.M.; Alonso-Sáez, L. Active mesopelagic prokaryotes support high respiration in the subtropical northeast Atlantic Ocean. Geophys. Res. Lett. 2005, 32, doi:10.1029/2004GL021863.
[5]
Teske, A.; Durbin, A.; Ziervogel, K.; Cox, C.; Arnosti, C. Microbial community composition and function in permanently cold seawater and sediments from an arctic fjord of Svalbard. Appl. Environ. Microbiol. 2011, 77, 2008–2018, doi:10.1128/AEM.01507-10.
[6]
Haefner, B. Drugs from the deep: Marine natural products as drug candidates. Drug Discov. Today 2003, 8, 536–544, doi:10.1016/S1359-6446(03)02713-2.
[7]
Fenical, W.; Jensen, P.R. Developing a new resource for drug discovery: Marine actinomycete bacteria. Nat. Chem. Biol. 2006, 2, 666–673, doi:10.1038/nchembio841.
[8]
Schattenhofer, M.; Fuchs, B.M.; Amann, R.; Zubkov, M.V.; Tarran, G.A.; Pernthaler, J. Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean. Environ. Microbiol. 2009, 11, 2078–2093, doi:10.1111/j.1462-2920.2009.01929.x.
[9]
Massana, R.; Pedrós-Alió, C. Unveiling new microbial eukaryotes in the surface ocean. Curr. Opin. Microbiol. 2008, 11, 213–218, doi:10.1016/j.mib.2008.04.004.
[10]
Díez, B.; Pedrós-Alió, C.; Massana, R. Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing. Appl. Environ. Microbiol. 2001, 67, 2932–2941, doi:10.1128/AEM.67.7.2932-2941.2001.
[11]
Frias-Lopez, J.; Shi, Y.; Tyson, G.W.; Coleman, M.L.; Schuster, S.C.; Chisholm, S.W.; Delong, E.F. Microbial community gene expression in ocean surface waters. Proc. Natl. Acad. Sci. USA 2008, 105, 3805–3810.
[12]
Gilbert, J.A.; Field, D.; Huang, Y.; Edwards, R.; Li, W.; Gilna, P.; Joint, I. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 2008, 3, e3042, doi:10.1371/journal.pone.0003042.
[13]
Poretsky, R.S.; Gifford, S.; Rinta-Kanto, J.; Vila-Costa, M.; Moran, M.A. Analyzing gene expression from marine microbial communities using environmental transcriptomics. J. Vis. Exp. JoVE 2009, 24, doi:10.3791/1086.
[14]
Vila-Costa, M.; Rinta-Kanto, J.M.; Sun, S.; Sharma, S.; Poretsky, R.; Moran, M.A. Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate. ISME J. 2010, 4, 1410–1420, doi:10.1038/ismej.2010.62.
Eloe, E.A.; Fadrosh, D.W.; Novotny, M.; Zeigler Allen, L.; Kim, M.; Lombardo, M.-J.; Yee-Greenbaum, J.; Yooseph, S.; Allen, E.E.; Lasken, R.; Williamson, S.J.; Bartlett, D.H. Going deeper: Metagenome of a hadopelagic microbial community. PLoS One 2011, 6, e20388, doi:10.1371/journal.pone.0020388.
[22]
Kawagucci, S.; Yoshida, Y.T.; Noguchi, T.; Honda, M.C.; Uchida, H.; Ishibashi, H.; Nakagawa, F.; Tsunogai, U.; Okamura, K.; Takaki, Y.; Nunoura, T.; Miyazaki, J.; Hirai, M.; Lin, W.; Kitazato, H.; Takai, K. Disturbance of deep-sea environments induced by the M9.0 Tohoku Earthquake. Sci. Rep. 2012, 2, doi:10.1038/srep00270.
[23]
Danovaro, R.; Dell’anno, A.; Pusceddu, A.; Fabiano, M. Nucleic acid concentrations (DNA, RNA) in the continental and deep-sea sediments of the eastern Mediterranean: Relationships with seasonally varying organic inputs and bacterial dynamics. Deep Sea Res. Part Ocean. Res. Pap. 1999, 46, 1077–1094, doi:10.1016/S0967-0637(98)00101-0.
[24]
Wu, J.; Gao, W.; Zhang, W.; Meldrum, D.R. Optimization of whole-transcriptome amplification from low cell density deep-sea microbial samples for metatranscriptomic analysis. J. Microbiol. Methods 2011, 84, 88–93, doi:10.1016/j.mimet.2010.10.018.
[25]
Urich, T.; Lanzén, A.; Qi, J.; Huson, D.H.; Schleper, C.; Schuster, S.C. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One 2008, 3, e2527.
[26]
Morse, A.M.; Carballo, V.; Baldwin, D.A.; Taylor, C.G.; McIntyre, L.M. Comparison between NuGEN’s WT-Ovation Pico and one-direct amplification systems. J. Biomol. Tech. 2010, 21, 141–147.
[27]
Skalitzky, C.; Watt, M.-A. Evaluation of RNA Amplification Methods for NimbleGen Gene Expression Microarray Analysis, 2010. Roche NimbleGen. Available online: http://www.nimblegen.com/products/lit/NG_GeneExp_TechNote_RNAAmplification_101310.pdf (accessed on 5 May 2013).
[28]
DeLong, E.F.; Preston, C.M.; Mincer, T.; Rich, V.; Hallam, S.J.; Frigaard, N.-U.; Martinez, A.; Sullivan, M.B.; Edwards, R.; Brito, B.R.; et al. Community genomics among stratified microbial assemblages in the ocean’s interior. Science 2006, 311, 496–503, doi:10.1126/science.1120250.
[29]
Rusch, D.B.; Halpern, A.L.; Sutton, G.; Heidelberg, K.B.; Williamson, S.; Yooseph, S.; Wu, D.; Eisen, J.A.; Hoffman, J.M.; Remington, K.; et al. The sorcerer II global ocean sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biol. 2007, 5, e77, doi:10.1371/journal.pbio.0050077.
[30]
Brown, M.V.; Philip, G.K.; Bunge, J.A.; Smith, M.C.; Bissett, A.; Lauro, F.M.; Fuhrman, J.A.; Donachie, S.P. Microbial community structure in the North Pacific ocean. ISME J. 2009, 3, 1374–1386, doi:10.1038/ismej.2009.86.
[31]
Liao, L.; Xu, X.-W.; Jiang, X.-W.; Wang, C.-S.; Zhang, D.-S.; Ni, J.-Y.; Wu, M. Microbial diversity in deep-sea sediment from the cobalt-rich crust deposit region in the Pacific Ocean. FEMS Microbiol. Ecol. 2011, 78, 565–585, doi:10.1111/j.1574-6941.2011.01186.x.
[32]
Schippers, A.; Kock, D.; H？ft, C.; K？weker, G.; Siegert, M. Quantification of Microbial Communities in Subsurface Marine Sediments of the Black Sea and off Namibia. Front. Microbiol. 2012, 3, doi:10.3389/fmicb.2012.00016.
[33]
Karner, M.B.; DeLong, E.F.; Karl, D.M. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 2001, 409, 507–510, doi:10.1038/35054051.
[34]
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.
[35]
Pester, M.; Rattei, T.; Flechl, S.; Gr？ngr？ft, A.; Richter, A.; Overmann, J.; Reinhold-Hurek, B.; Loy, A.; Wagner, M. amoA-Based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions. Environ. Microbiol. 2012, 14, 525–539, doi:10.1111/j.1462-2920.2011.02666.x.
[36]
Gruber, N.; Galloway, J.N. An earth-system perspective of the global nitrogen cycle. Nature 2008, 451, 293–296, doi:10.1038/nature06592.
[37]
Purkhold, U.; Pommerening-R？ser, A.; Juretschko, S.; Schmid, M.C.; Koops, H.P.; Wagner, M. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl. Environ. Microbiol. 2000, 66, 5368–5382, doi:10.1128/AEM.66.12.5368-5382.2000.
Pester, M.; Schleper, C.; Wagner, M. The Thaumarchaeota: An emerging view of their phylogeny and ecophysiology. Curr. Opin. Microbiol. 2011, 14, 300–306, doi:10.1016/j.mib.2011.04.007.
[40]
Kirkpatrick, J.; Oakley, B.; Fuchsman, C.; Srinivasan, S.; Staley, J.T.; Murray, J.W. Diversity and distribution of planctomycetes and related bacteria in the suboxic zone of the Black Sea. Appl. Environ. Microbiol. 2006, 72, 3079–3083, doi:10.1128/AEM.72.4.3079-3083.2006.
[41]
Byrne, N.; Strous, M.; Crépeau, V.; Kartal, B.; Birrien, J.-L.; Schmid, M.; Lesongeur, F.; Schouten, S.; Jaeschke, A.; Jetten, M.; et al. Presence and activity of anaerobic ammonium-oxidizing bacteria at deep-sea hydrothermal vents. ISME J. 2009, 3, 117–123, doi:10.1038/ismej.2008.72.
[42]
Fuerst, J.A.; Webb, R.I.; van Niftrik, L.; Jetten, M.S.M.; Strous, M. Anammoxosomes of anaerobic ammonium-oxidizing planctomycetes. Microbiol. Monogr. 2006, 2, 259–283, doi:10.1007/7171_028.
[43]
Kuypers, M.M.M.; Lavik, G.; Woebken, D.; Schmid, M.; Fuchs, B.M.; Amann, R.; J？rgensen, B.B.; Jetten, M.S.M. Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proc. Natl. Acad. Sci. USA 2005, 102, 6478–6483, doi:10.1073/pnas.0502088102.
[44]
G？rtner, A.; Blümel, M.; Wiese, J.; Imhoff, J.F. Isolation and characterisation of bacteria from the Eastern Mediterranean deep sea. Antonie Van Leeuwenhoek 2011, 100, 421–435, doi:10.1007/s10482-011-9599-5.
[45]
Simon, C.; Wiezer, A.; Strittmatter, A.W.; Daniel, R. Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome. Appl. Environ. Microbiol. 2009, 75, 7519–7526, doi:10.1128/AEM.00946-09.
[46]
Sun, J.; Steindler, L.; Thrash, J.C.; Halsey, K.H.; Smith, D.P.; Carter, A.E.; Landry, Z.C.; Giovannoni, S.J. One carbon metabolism in SAR11 pelagic marine bacteria. PLoS One 2011, 6, e23973, doi:10.1371/journal.pone.0023973.
[47]
Viklund, J.; Ettema, T.J.G.; Andersson, S.G.E. Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 Clade. Mol. Biol. Evol. 2012, 29, 599–615, doi:10.1093/molbev/msr203.
[48]
Laghdass, M.; Catala, P.; Caparros, J.; Oriol, L.; Lebaron, P.; Obernosterer, I. High contribution of SAR11 to microbial activity in the North West Mediterranean Sea. Microb. Ecol. 2012, 63, 324–333, doi:10.1007/s00248-011-9915-7.
[49]
Meyer, F.; Paarmann, D.; D’Souza, M.; Olson, R.; Glass, E.M.; Kubal, M.; Paczian, T.; Rodriguez, A.; Stevens, R.; Wilke, A.; et al. The metagenomics RAST server—A public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinforma. 2008, 9, doi:10.1186/1471-2105-9-386.
[50]
Wang, F.; Zhou, H.; Meng, J.; Peng, X.; Jiang, L.; Sun, P.; Zhang, C.; Van Nostrand, J.D.; Deng, Y.; He, Z.; et al. GeoChip-Based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc. Natl. Acad. Sci.USA 2009, 106, 4840–4845, doi:10.1073/pnas.0810418106.
[51]
Schrenk, M.O.; Kelley, D.S.; Delaney, J.R.; Baross, J.A. Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Appl. Environ. Microbiol. 2003, 69, 3580–3592, doi:10.1128/AEM.69.6.3580-3592.2003.
[52]
Xie, W.; Wang, F.; Guo, L.; Chen, Z.; Sievert, S.M.; Meng, J.; Huang, G.; Li, Y.; Yan, Q.; Wu, S.; et al. Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries. ISME J. 2010, 5, 414–426.
[53]
El-Hajj, Z.W.; Tryfona, T.; Allcock, D.J.; Hasan, F.; Lauro, F.M.; Sawyer, L.; Bartlett, D.H.; Ferguson, G.P. Importance of proteins controlling initiation of DNA replication in the growth of the high-pressure-loving bacterium Photobacterium profundum SS9. J. Bacteriol. 2009, 191, 6383–6393, doi:10.1128/JB.00576-09.
Wolanin, P.M.; Thomason, P.A.; Stock, J.B. Histidine protein kinases: Key signal transducers outside the animal kingdom. Genome Biol. 2002, 3, doi:10.1186/gb-2002-3-10-reviews3013.
[56]
Taylor, B.L.; Zhulin, I.B. PAS domains: Internal sensors of oxygen, redox potential, and light. Microbiol. Mol. Biol. Rev. 1999, 63, 479–506.
[57]
Heusipp, G.; F？lker, S.; Schmidt, M.A. DNA adenine methylation and bacterial pathogenesis. Int. J. Med. Microbiol. 2007, 297, 1–7, doi:10.1016/j.ijmm.2006.10.002.
[58]
Nakai, R.; Abe, T.; Takeyama, H.; Naganuma, T. Metagenomic analysis of 0.2-μm-passable microorganisms in deep-sea hydrothermal fluid. Mar. Biotechnol. 2011, 13, 900–908, doi:10.1007/s10126-010-9351-6.
[59]
Braun, V.; Braun, M. Active transport of iron and siderophore antibiotics. Curr. Opin. Microbiol. 2002, 5, 194–201, doi:10.1016/S1369-5274(02)00298-9.
[60]
Jannasch, H. Microbial Interactions with Hydrothermal Fluids. In Seafloor Hydrothermal Systems: Physical, Chemical, Biological, and Geological Interactions; American Geophysical Union: Washington, DC, USA, 1995; pp. 273–296.
[61]
Konstantinidis, K.T.; Braff, J.; Karl, D.M.; DeLong, E.F. Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre. Appl. Environ. Microbiol. 2009, 75, 5345–5355, doi:10.1128/AEM.00473-09.
[62]
Herndl, G.J.; Agogu, H.; Baltar, F.; Reinthaler, T.; Sintes, E.; Varela, M.M. Regulation of aquatic microbial processes: The “microbial loop” of the sunlit surface waters and the dark ocean dissected. Aquat. Microb. Ecol. 2008, 53, 59–68, doi:10.3354/ame01225.
[63]
Walsh, D.A.; Zaikova, E.; Howes, C.G.; Song, Y.C.; Wright, J.J.; Tringe, S.G.; Tortell, P.D.; Hallam, S.J. Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science 2009, 326, 578–582, doi:10.1126/science.1175309.
[64]
Vilibi？, I.; ？anti？, D. Deep water ventilation traced by Synechococcus cyanobacteria. Ocean Dyn. 2008, 58, 119–125, doi:10.1007/s10236-008-0135-8.
[65]
Gao, W.; Shi, X.; Wu, J.; Jin, Y.; Zhang, W.; Meldrum, D.R. Phylogenetic and gene expression analysis of cyanobacteria and diatoms in the twilight waters of the temperate northeast Pacific Ocean. Microb. Ecol. 2011, 62, 765–775, doi:10.1007/s00248-011-9891-y.
[66]
Koblí？ek, M.; Komenda, J.; Masojídek, J.; Pechar, L. Cell aggregation of the cyanobacterium Synechococcus elongatus: Role of the electron transport chain. J. Phycol. 2001, 36, 662–668.
[67]
Amacher, J.; Neuer, S.; Lomas, M. DNA-based molecular fingerprinting of eukaryotic protists and cyanobacteria contributing to sinking particle flux at the Bermuda Atlantic time-series study. Deep Sea Res. Part II 2013, 93, 71–83, doi:10.1016/j.dsr2.2013.01.001.
[68]
Bass, D.; Howe, A.; Brown, N.; Barton, H.; Demidova, M.; Michelle, H.; Li, L.; Sanders, H.; Watkinson, S.C.; Willcock, S.; Richards, T.A. Yeast forms dominate fungal diversity in the deep oceans. Proc. Biol. Sci. 2007, 274, 3069–3077, doi:10.1098/rspb.2007.1067.
[69]
Gestal, C.; Pascual, S.; Hochberg, F.G. Aggregata bathytherma sp. nov. (Apicomplexa: Aggregatidae), a new coccidian parasite associated with a deep-sea hydrothermal vent octopus. Dis. Aquat. Organ. 2010, 91, 237–242, doi:10.3354/dao02264.
[70]
Takishita, K.; Yubuki, N.; Kakizoe, N.; Inagaki, Y.; Maruyama, T. Diversity of microbial eukaryotes in sediment at a deep-sea methane cold seep: Surveys of ribosomal DNA libraries from raw sediment samples and two enrichment cultures. Extremophiles Life Extreme Cond. 2007, 11, 563–576, doi:10.1007/s00792-007-0068-z.
[71]
De Buron, I.; Morand, S. Deep-Sea hydrothermal vent parasites: Why do we not find more? Parasitology 2004, 128, 1–6, doi:10.1017/S0031182003004347.
[72]
Lambshead, P.J.D.; Boucher, G. Marine nematode deep-sea biodiversity—Hyperdiverse or hype? J. Biogeogr. 2003, 30, 475–485, doi:10.1046/j.1365-2699.2003.00843.x.
[73]
Merckx, B.; Goethals, P.; Steyaert, M.; Vanreusel, A.; Vincx, M.; Vanaverbeke, J. Predictability of marine nematode biodiversity. Ecol. Model. 2009, 220, 1449–1458, doi:10.1016/j.ecolmodel.2009.03.016.
[74]
Vanreusel, A.; de Groote, A.; Gollner, S.; Bright, M. Ecology and biogeography of free-living nematodes associated with chemosynthetic environments in the deep sea: A review. PLoS One 2010, 5, e12449.
[75]
Schierwater, B.; de Jong, D.; Desalle, R. Placozoa and the evolution of Metazoa and intrasomatic cell differentiation. Int. J. Biochem. Cell Biol. 2009, 41, 370–379, doi:10.1016/j.biocel.2008.09.023.
[76]
Eitel, M.; Schierwater, B.; Eitel, M.; Schierwater, B. The phylogeography of the Placozoa suggests a taxon-rich phylum in tropical and subtropical waters. Mol. Ecol. 2010, 19, 2315–2327, doi:10.1111/j.1365-294X.2010.04617.x.
[77]
Maruyama, Y.K. Occurrence in the field of a long-term, year-round, stable population of placozoans. Biol. Bull. 2004, 206, 55–60, doi:10.2307/1543198.
[78]
Le Calvez, T.; Burgaud, G.; Mahé, S.; Barbier, G.; Vandenkoornhuyse, P. Fungal diversity in deep-sea hydrothermal ecosystems. Appl. Environ. Microbiol. 2009, 75, 6415–6421, doi:10.1128/AEM.00653-09.
[79]
Bhadury, P.; Bik, H.; Lambshead, J.D.; Austen, M.C.; Smerdon, G.R.; Rogers, A.D. Molecular diversity of fungal phylotypes co-amplified alongside nematodes from coastal and deep-sea marine environments. PLoS One 2011, 6, doi:10.1371/journal.pone.0026445.
[80]
Takishita, K.; Tsuchiya, M.; Reimer, J.D.; Maruyama, T. Molecular evidence demonstrating the basidiomycetous fungus Cryptococcus curvatus is the dominant microbial eukaryote in sediment at the Kuroshima Knoll methane seep. Extremophiles Life Extreme Cond. 2006, 10, 165–169, doi:10.1007/s00792-005-0495-7.
