Genomics of deep‐sea and sub‐seafloor microbes

Abstract

Microbial BiotechnologyVolume 2, Issue 2 p. 157-163 Open Access Genomics of deep-sea and sub-seafloor microbes Roland J. Siezen, Corresponding Author Roland J. Siezen Kluyver Centre for Genomics of Industrial Fermentation; TI Food and Nutrition, 6700AN Wageningen, the Netherlands. NIZO Food Research, 6710BA Ede, The Netherlands. CMBI, Radboud University Nijmegen, 6500HB Nijmegen, the Netherlands. *E-mail r.siezen@cmbi.ru.nl; Tel. (+31) 24 3619559; Fax (+31) 24 3619395. Search for more papers by this authorGreer Wilson, Greer Wilson Science Consultant, Bowlespark 30, 6701DS Wageningen, the Netherlands.Search for more papers by this author Roland J. Siezen, Corresponding Author Roland J. Siezen Kluyver Centre for Genomics of Industrial Fermentation; TI Food and Nutrition, 6700AN Wageningen, the Netherlands. NIZO Food Research, 6710BA Ede, The Netherlands. CMBI, Radboud University Nijmegen, 6500HB Nijmegen, the Netherlands. *E-mail r.siezen@cmbi.ru.nl; Tel. (+31) 24 3619559; Fax (+31) 24 3619395. Search for more papers by this authorGreer Wilson, Greer Wilson Science Consultant, Bowlespark 30, 6701DS Wageningen, the Netherlands.Search for more papers by this author First published: 18 February 2009 https://doi.org/10.1111/j.1751-7915.2009.00092.xCitations: 7AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Over two-thirds of the surface of the earth is covered by oceans, which have an average depth of about 3800 m. As each drop of ocean water contains > 105 cells, the > 1030 microbial cells in the ocean represent the largest reservoir of microbes on earth (Whitman et al., 1998). Communities of bacteria, archaea, protists and unicellular fungi account for most of the oceanic biomass and metabolism. Marine microbes are known to play an essential role in the global cycling of nitrogen, carbon, oxygen, phosphorous, iron, sulfur and trace elements (Karl, 2007). The largest metagenome sequencing projects undertaken to date involved surface seawater samples from the Sargasso Sea (Venter et al., 2004) and the Global Ocean Sampling (GOS) (Yooseph et al., 2007) expeditions conducted by Craig Venter and colleagues. The GOS analysis has shown that the numbers of newly discovered protein families in microbes have not yet reached a plateau, and in fact the curve is still rising. This means that there are many more functionalities to be discovered. This surface seawater metagenome sequencing did not take into account the piezophiles (= pressure-loving) and so it would be reasonable to assume that this is still a large and generally untapped source of potentially useful enzymes and products. The microbes of the very deep differ from those isolated from shallow waters in several aspects. The GOS analysis suggests that near-surface microorganisms do not need chemotaxis, flagellae or pili to actively swim around in search of food, as they rely mostly on the plentiful O2, CO2 and sunlight for photosynthesis. Yet this is not the case for the deep-sea piezophilic psychrophiles. Deep-sea environments are characterized by low temperature (1–2°C), high pressure (1 MPa for every 100 m), high-salt and low-nutrient conditions. Pressure affects various aspects of metabolism in very different ways (Simonato et al., 2006). Little light penetrates below 500 m, the presence of food is scarce and many organisms have adapted to survive long periods without nutrition. Prokaryotic adaptation to deep sea habitats has been reviewed by Simonato and colleagues (2006) and Lauro and Bartlett (2008). It is assumed that life here will be heterotrophic and largely supported by influxes of nutrients coming down from the more ‘fertile’ waters above. Nutrients slowly reach the seabed in the form of dead whales, crustaceans, fish, kelp, wood and their debris. These all carry the microbiota that was associated with them as they sank to the ocean bed (Egan et al., 2008). These surface-associated microbes can to a certain extent also adapt to the changing conditions in which they now find themselves. Microbial isolates or communities of some deep-sea ‘oases’ such as hydrothermal vents in the seafloor (Nakagawa and Takai, 2008) or whale falls (Tringe et al., 2005) have been sampled and studied, but these are exceptions which we do not address here. Databases and computing tools Marine microbe researchers are highly organized with respect to storing and sharing their data. The Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) aims to develop global methods for monitoring microbial communities in the ocean and their response to environmental changes. The CAMERA's database (http://camera.calit2.net) includes environmental metagenomic and genomic sequence data, associated environmental parameters (‘metadata’), pre-computed search results, and software tools to support powerful cross-analysis of environmental samples (Seshadri et al., 2007) (Fig. 1). The CAMERA includes the Sargasso Sea and GOS expedition data, as well as a vertical profile of marine microbial communities collected at the Hawaii Ocean Time-Series station ALOHA by Ed DeLong and his research team at MIT. In addition, the MetaLook software has been developed for visualisation, analysis and comparison of marine ecological genomic and metagenomic data with respect to habitat parameters (http://www.megx.net/metalook) (Fig. 2). Figure 1Open in figure viewerPowerPoint Example of a blast search by CAMERA. Figure 2Open in figure viewerPowerPoint The starting point of MetaLook: the world map showing genomics and metagenomics sampling sites. Clicking on a location will provide all genomics and meta data. (Meta)genome sequencing of deep-sea microbes Thanks to initiatives by the Gordon and Betty Moore Foundation, nearly 200 genomes of culturable marine bacteria have been sequenced since 2004 (http://www.moore.org/microgenome/). Table 1 summarizes deep-sea and sediment (meta)genome sequencing projects. Table 1. Deep-sea and sediment genome sequencing projects. Phylum Order Organism Isolation Depth (m) Reference/data Euryarchaeota Methanococci Methanococcus aeolicus Nankai-3 Deep marine sediment, Nankai Trough Japan NC_009635 Euryarchaeota Methanomicrobia Methanoculleus marisnigri JR1 Sediment, Black Sea NC_009051 Chlorobi Chlorobia Chlorobium phaeobacteroides BS1 Chemocline, Black Sea NC_010831 Proteobacteria Gammaproteobacteria Shewanella piezotolerans WP3 Sediment, west Pacific 1914 Wang et al. (2008) Proteobacteria Gammaproteobacteria Alteromonas macleodii DSM 17117 Seawater, Urania Basin, Mediterranean 3500 NC_011138 Proteobacteria Gammaproteobacteria Moritella sp. PE36 Patton escarpment, off San Diego, Pacific NZ_ABCQ00000000 Proteobacteria Gammaproteobacteria Psychromonas sp. CNPT3 Central north Pacific 5800 NZ_AAPG00000000 Proteobacteria Gammaproteobacteria Shewanella benthica KT99, PT99 Tonga-Kermadec Trench, Pacific 9000 NZ_ABIC00000000 Proteobacteria Gammaproteobacteria Shewanella woodyi MS32 Sediment, Strait of Gibraltar, Mediterranean 5110 NC_010506 Proteobacteria Gammaproteobacteria Shewanella loihica PV-4 Iron-rich mat, Naha Vents, Hawaii 1325 NC_009092 Proteobacteria Gammaproteobacteria Shewanella sp. W3-18-1 Sediment, Washington, Pacific 997 NC_008750 Proteobacteria Gammaproteobacteria Shewanella violacea DSS12 Sediment, Ryukyu Trench, Philippine Sea 5110 nakasone@hiro.kindai.ac.jp Proteobacteria Gammaproteobacteria Photobacterium profundum SS9 Sulu Trough 2500 Vezzi et al. (2005) Proteobacteria Alphaproteobacteria Roseobacter sp. SK209-2-6 Arabian Sea 2500 NZ_AAYC00000000 Proteobacteria Epsilonproteobacteria Sulfurimonas autotrophica OK10 Deep-sea sediment, Mid-Okinawa Trough, Japan microbes@cuba.jgi-psf.org Proteobacteria Zetaproteobacteria Mariprofundus ferrooxydans PV-1 Loihi Seamount, Hawaii 1100 NZ_AATS00000000 Firmicutes Bacilli Oceanobacillus iheyensis HTE831 Deep sea mud, Iheya ridge, Okinawa Japan 1050 Takami et al. (2002) Firmicutes Bacilli Carnobacterium sp. AT7 Aleutian Trench 2500 NZ_ABHH00000000 Firmicutes Clostridia Carboxydibrachium pacificum JM Okinawa Trough 1500 NZ_ABXP00000000 Metagenomes Unclassified Unclassified Marine anammox community Deep sea sgtringe@lbl.gov Unclassified Unclassified Marine archaeal anaerobic oxidation of methane communities Sediment, Eel River Basin, Mendocino California 520 Hallam et al. (2004) Unclassified Unclassified Marine planktonic communities North Pacific Ocean, ALOHA station, Hawaii 500–4000 DeLong et al. (2006) Unclassified Unclassified Marine microbial communities Seep water masses of the North Atlantic 500–4121 Sogin et al. (2006) Unclassified Unclassified Marine planktonic communities Mediterranean Sea, Ionian Km3 Station 3010 Martin-Cuadrado et al. (2007) Unclassified Unclassified Sediment microbial communities Sub-seafloor, Peru Margin 1229 Biddle et al. (2008) Adapted from the GOLD database (http://www.genomesonline.org; December 2008). Most of the sequenced culturable microorganisms from the deep-sea are Alteromonadales from the Gammaproteobacteria. Unique properties of sequenced deep-sea microbes are that they all have a high ratio of rRNA operon copies per genome size, and that their intergenic regions are larger than average (Lauro and Bartlett, 2008). These properties are characteristic of bacteria with an opportunistic lifestyle and a high degree of gene regulation to respond rapidly to environmental changes when searching for food. A large number of genes are found for synthesis of mono- and poly-unsaturated fatty acids and membrane unsaturation in these deep dwelling microorganisms, as they need to maintain membrane fluidity at low temperature and high pressure (Simonato et al., 2006). They also contain a larger than average repertoire of transport proteins for scavenging different types of food. Large numbers of proteins are encoded for chemotaxis, flagellar assembly and motor function to allow them to hunt for dissolved and particulate organic matter, also called ‘marine snow’ (Azam and Long, 2001; Kiorboe and Jackson, 2001). The latter consists mainly of diffuse gels with a variety of organisms living together in biofilms and communities highly dependent upon each other for survival. The marine snow can sink thousands of metres into the sea. This brings down to the seabed a lot of organic material, nitrogen and phosphorus, helping to sustain the communities present at depth (for a review see Azam and Malfatti, 2007). In order to make use of this food source the microorganisms have fine-tuned hydrolytic enzymes and nutrient uptake systems. Very few metagenomics studies of deep-sea communities have been reported so far, and include only deep water samples from the North Pacific Gyre ALOHA station (DeLong et al., 2006) and the Ionian Sea in the Mediterranean (Martin-Cuadrado et al., 2007), and (sub)seafloor samples from the Peru Margin (Biddle et al., 2008) and the Eel Basin off the coast of California (Hallam et al., 2004) (Table 1). The cold (2–5°C) North Pacific deep waters were found to contain Deferribacteres, Planctomycetaceae, Acidobacteriales, Gemmatomonadaceae, Nitrospira, Alteromondaceae, and SAR11, SAR202 and Agg47 bacterial clades (DeLong et al., 2006); these microbial communities were enriched in genes encoding transposases, pilus synthesis, protein transport, polysaccharide and antibiotic synthesis, the glyoxylate cycle, and urea metabolism, relative to surface communities. The warmer (14°C) deep Mediterranean waters contained mainly Proteobacteria, but also Actinobacteria, Firmicutes, Planctomycetales, Chloroflexi, Bacteroidetes, Acidobacteria, and also Crenarchaeota (Martin-Cuadrado et al., 2007). Enriched functional categories were again for pilus, polysaccharide and antibiotic synthesis, as well as peptide and amino acid transporters, while genes involved in degradation of complex biopolymers and xenobiotics were also abundant. The high percentage of genes encoding dehydrogenases, and among them cox genes, suggested that aerobic CO oxidation may play a role in deep seas as additional energy source. The marine subsurface at great depths is a distinct microbial habitat. Metagenomics analysis (GS20 pyrosequencing) of ng amounts of DNA extracted from 1–50 m below the seafloor at an Ocean Drilling Program Site (seafloor depth is 1229 m) on the Peru Margin showed that only ∼10% of the sequences had a detectable homology to known sequences (Biddle et al., 2008). Archaea, and particularly Crenachaeota, appear to be the dominant microbes in these environments, and could be a source of as yet completely undiscovered enzymes with unique properties. Discovery of novel enzymes from deep-sea microbes Marine enzyme biotechnology can offer novel biocatalysts with properties like high salt tolerance, hyperthermostability, barophilicity, cold adaptivity, and ease in large-scale cultivation (reviewed by Debashish et al., 2005). Metagenomics strategies are powerful tools to identify enzymes with novel biocatalytic properties from unculturable members of microbial communities (Ferrer et al., 2009; Steele et al., 2009). The GOS project discovered hundreds of truly novel protein and enzyme families from marine surface microbes for which no function is yet known (Yooseph et al., 2007). Deep-sea and sediment microbes should provide an enormous reservoir of low-temperature and high-pressure adapted enzymes. Both sequence-based and function-based screening approaches have been used to identify enzymes with potentially interesting biocatalytic activities from cultured deep-sea microbes as well as uncultured metagenomes (Kennedy et al., 2008; Kobayashi et al., 2008) (Table 2). Table 2. Enzymes from deep-sea microbes. Enzyme(s) Producing organism(s) Isolation Reference α-Amylase Nocardiopsis sp. Deep sea sediment Zhang and Zeng (2008) Alkane hydroxylases Metagenome Deep-sea sediment Xu et al. (2008) β-Lactamases Metagenome Cold-seep sediment of seamount Song et al. (2005) Cellulase Pseudoaltermonas sp. DY3 Deep-sea sediment Zeng et al. (2006) Esterases Metagenome Deep-sea hypersaline anoxic basin Ferrer et al. (2005) Esterase (alkaline) Metagenome Deep-sea sediment Park et al. (2007) Lipase Metagenome Deep-sea sediment Hardeman and Sjoling (2007) Lipase Metagenome Deep-sea sediment Jeon et al. (2009) Quinol oxidase Shewanella sp. strain DB-172F Deep-sea sediment Qureshi et al. (1998) Protease (alkaline) Pseudomonas strain DY-A Deep-sea sediment Zeng et al. (2003) Proteases (neutral, alkaline) Pseudoaltermonas sp. Deep-sea sediment Xiong et al. (2007) Protease (alkaline) Pseudoaltermonas sp. SM9913 Deep-sea sediment Chen et al. (2007) Various Metagenome Deep sub-seafloor sediment core Kobayashi et al. (2008) Adapted from Kennedy and colleagues (2008). For instance, highly salt-tolerant and pressure-tolerant esterases were identified in a metagenome expression library generated from microbes isolated from a deep-sea hypersaline anoxic basin in the Eastern Mediterranean (Ferrer et al., 2005). The amino acid content of proteins in psychrophilic piezophiles is also different from that in mesophiles. There are more polar amino acids in the proteins, resulting in a loss of rigidity and increased structural flexibility for enhanced catalytic activity. The adaptive properties of psychrophilic enzymes are high specific activity, relatively low temperature optima and high thermolability (Gomes and Steiner, 2004). A major challenge will be to develop alternative hosts and their associated vectors for heterologous expression of genes from the diverse phyla existing in the deep-sea ecosystem (Ferrer et al., 2009). Applications Cold-adapted enzymes are advantageous for waste decomposition in cold environments, for food processing, flavour enhancement (He et al., 2004) and preservation, and for processes that require the rapid inactivation of enzymatic reactions (Huston et al., 2000; O'Brien et al., 2004). Piezophilic enzymes could be useful for food sterilization at high pressure and low temperature, improving preservation of flavour and colour. Halophilic enzymes can be applied for non-aquatic reactions, as they have better thermostability and other unique properties in organic solvents, and could be used in anti-fouling coating and paint industries (Yebra et al., 2004), but also for synthesis of optically active substances. Finally, many deep-sea bacteria can synthesize interesting chemical compounds, such as omega-3 polyunsaturated fatty acids that are considered useful in reducing the risk of cardiovascular disease, and polyketides (Siezen and Khayatt, 2008) which could be used as novel antibiotics. Acknowledgements This project was carried out within the research programme of the Kluyver Centre for Genomics of Industrial Fermentation which is part of the Netherlands Genomics Initiative/Netherlands Organization for Scientific Research. References Azam, F., and Long, R.A. (2001) Sea snow microcosms. Nature 414: 497– 498. CrossrefCASWeb of Science®Google Scholar Azam, F., and Malfatti, F. (2007) Microbial structuring of marine ecosystems. Nat Rev Microbiol 5: 782– 791. CrossrefCASPubMedWeb of Science®Google Scholar Biddle, J.F., Fitz-Gibbon, S., Schuster, S.C., Brenchley, J.E., and House, C.H. (2008) Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc Natl Acad Sci USA 105: 10583– 10588. CrossrefCASPubMedWeb of Science®Google Scholar Chen, X.L., Xie, B.B., Lu, J.T., He, H.L., and Zhang, Y. (2007) A novel type of subtilase from the psychrotolerant bacterium Pseudoalteromonas sp. SM9913: catalytic and structural properties of deseasin MCP-01. Microbiology 153: 2116– 2125. CrossrefCASPubMedWeb of Science®Google Scholar DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496– 503. Wiley Online LibraryCASPubMedWeb of Science®Google Scholar Debashish, G., Malay, S., Barindra, S., and Joydeep, M. (2005) Marine enzymes. Adv Biochem Eng Biotechnol 96: 189– 218. CrossrefCASPubMedWeb of Science®Google Scholar Egan, S., Thomas, T., and Kjelleberg, S. (2008) Unlocking the diversity and biotechnological potential of marine surface associated microbial communities. Curr Opin Microbiol 11: 219– 225. CrossrefCASPubMedWeb of Science®Google Scholar Ferrer, M., Golyshina, O.V., Chernikova, T.N., Khachane, A.N., Martins Dos Santos, V.A., Yakimov, M.M., et al. (2005) Microbial enzymes mined from the Urania deep-sea hypersaline anoxic basin. Chem Biol 12: 895– 904. CrossrefCASPubMedWeb of Science®Google Scholar Ferrer, M., Beloqui, A., Timmis, K.N., and Golyshin, P.N. (2009) Metagenomics for mining new genetic resources of microbial communities. J Mol Microbiol Biotechnol 16: 109– 123. CrossrefCASPubMedWeb of Science®Google Scholar Gomes, J., and Steiner, W. (2004) The biocatalytic potential of extremophiles and extremozymes. Food Tech Biotechnol 42: 223– 235. CASWeb of Science®Google Scholar Hallam, S.J., Putnam, N., Preston, C.M., Detter, J.C., Rokhsar, D., Richardson, P.M., and DeLong, E.F. (2004) Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305: 1457– 1462. CrossrefCASPubMedWeb of Science®Google Scholar Hardeman, F., and Sjoling, S. (2007) Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment. FEMS Microbiol Ecol 59: 524– 534. Wiley Online LibraryCASPubMedWeb of Science®Google Scholar He, H., Chen, X.L., Li, J., Zhang, Y., and Gao, P. (2004) Taste improvement of refrigerated meat treated with cold-adapted protease. Food Chemistry 84: 307– 311. CrossrefCASWeb of Science®Google Scholar Huston, A.L., Krieger-Brockett, B.B., and Deming, J.W. (2000) Remarkably low temperature optima for extracellular enzyme activity from Arctic bacteria and sea ice. Environ Microbiol 2: 383– 388. Wiley Online LibraryCASPubMedWeb of Science®Google Scholar Jeon, J.H., Kim, J.T., Kim, Y.J., Kim, H.K., Lee, H.S., Kang, S.G., et al. (2009) Cloning and characterization of a new cold-active lipase from a deep-sea sediment metagenome. Appl Microbiol Biotechnol 81: 865– 874. CrossrefCASPubMedWeb of Science®Google Scholar Karl, D.M. (2007) Microbial oceanography: paradigms, processes and promise. Nat Rev Microbiol 5: 759– 769. CrossrefCASPubMedWeb of Science®Google Scholar Kennedy, J., Marchesi, J.R., and Dobson, A.D. (2008) Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microb Cell Fact 7: 27. CrossrefCASPubMedWeb of Science®Google Scholar Kiorboe, T., and Jackson, G. (2001) Marine snow, organic solute plumes, and optimal chemosensory behaviour of bacteria. Limnol Oceanogr 46: 1309– 1318. Wiley Online LibraryCASWeb of Science®Google Scholar Kobayashi, T., Koide, O., Mori, K., Shimamura, S., Matsuura, T., Miura, T., et al. (2008) Phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off Shimokita Peninsula. Extremophiles 12: 519– 527. CrossrefCASPubMedWeb of Science®Google Scholar Lauro, F.M., and Bartlett, D.H. (2008) Prokaryotic lifestyles in deep sea habitats. Extremophiles 12: 15– 25. CrossrefPubMedWeb of Science®Google Scholar Martin-Cuadrado, A.B., Lopez-Garcia, P., Alba, J.C., Moreira, D., Monticelli, L., Strittmatter, A., et al. (2007) Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS ONE 2: . e914. CrossrefGoogle Scholar Nakagawa, S., and Takai, K. (2008) Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance. FEMS Microbiol Ecol 65: 1– 14. Wiley Online LibraryCASPubMedWeb of Science®Google Scholar O'Brien, A., Sharp, R., Russell, N., and Roller, S. (2004) Antarctic bacteria inhibit growth of food-borne microorganisms at low temperatures. FEMS Microbiol Ecol 48: 157– 167. Wiley Online LibraryCASPubMedWeb of Science®Google Scholar Park, H.J., Jeon, J.H., Kang, S.G., Lee, J.H., Lee, S.A., and Kim, H.K. (2007) Functional expression and refolding of new alkaline esterase, EM2L8 from deep-sea sediment metagenome. Protein Expr Purif 52: 340– 347. CrossrefCASPubMedWeb of Science®Google Scholar Qureshi, M.H., Kato, C., and Horikoshi, K. (1998) Purification of a ccb-type quinol oxidase specifically induced in a deep-sea barophilic bacterium, Shewanella sp. strain DB-172F. Extremophiles 2: 93– 99. CrossrefCASPubMedWeb of Science®Google Scholar Seshadri, R., Kravitz, S.A., Smarr, L., Gilna, P., and Frazier, M. (2007) CAMERA: a community resource for metagenomics. PLoS Biol 5: e75. CrossrefCASPubMedWeb of Science®Google Scholar Siezen, R.J., and Khayatt, B.I. (2008) Natural products genomics. Microbial Biotechnol 1: 275– 282. Wiley Online LibraryCASPubMedWeb of Science®Google Scholar Simonato, F., Campanaro, S., Lauro, F.M., Vezzi, A., D'Angelo, M., Vitulo, N., et al. (2006) Piezophilic adaptation: a genomic point of view. J Biotechnol 126: 11– 25. CrossrefCASPubMedWeb of Science®Google Scholar Sogin, M.L., Morrison, H.G., Huber, J.A., Mark Welch, D., Huse, S.M., Neal, P.R., et al. (2006) Microbial diversity in the deep sea and the underexplored ‘rare biosphere. Proc Natl Acad Sci USA 103: 12115– 12120. CrossrefCASPubMedWeb of Science®Google Scholar Song, J.S., Jeon, J.H., Lee, J.H., Jeong, S.H., Jeong, B.C., Kim, S.J., et al. (2005) Molecular characterization of TEM-type beta-lactamases identified in cold-seep sediments of Edison Seamount (south of Lihir Island, Papua New Guinea). J Microbiol 43: 172– 178. CASPubMedWeb of Science®Google Scholar Steele, H.L., Jaeger, K.E., Daniel, R., and Streit, W.R. (2009) Advances in recovery of novel biocatalysts from metagenomes. J Mol Microbiol Biotechnol 16: 25– 37. CrossrefCASPubMedWeb of Science®Google Scholar Takami, H., Takaki, Y., and Uchiyama, I. (2002) Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments. Nucleic Acids Res 30: 3927– 3935. CrossrefCASPubMedWeb of Science®Google Scholar Tringe, S.G., Von Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H.W., et al. (2005) Comparative metagenomics of microbial communities. Science 308: 554– 557. CrossrefCASPubMedWeb of Science®Google Scholar Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66– 74. CrossrefCASPubMedWeb of Science®Google Scholar Vezzi, A., Campanaro, S., D'Angelo, M., Simonato, F., Vitulo, N., Lauro, F.M., et al. (2005) Life at depth: Photobacterium profundum genome sequence and expression analysis. Science 307: 1459– 1461. CrossrefCASPubMedWeb of Science®Google Scholar Wang, F., Wang, J., Jian, H., Zhang, B., Li, S., Wang, F., et al. (2008) Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3. PLoS ONE 3: . e1937. CrossrefCASPubMedWeb of Science®Google Scholar Whitman, W.B., Coleman, D.C., and Wiebe, W.J. (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95: 6578– 6583. CrossrefCASPubMedWeb of Science®Google Scholar Xiong, H., Song, L., Xu, Y., Tsoi, M.Y., Dobretsov, S., and Qian, P.Y. (2007) Characterization of proteolytic bacteria from the Aleutian deep-sea and their proteases. J Ind Microbiol Biotechnol 34: 63– 71. CrossrefCASPubMedWeb of Science®Google Scholar Xu, M., Xiao, X., and Wang, F. (2008) Isolation and characterization of alkane hydroxylases from a metagenomic library of Pacific deep-sea sediment. Extremophiles 12: 255– 262. CrossrefCASPubMedWeb of Science®Google Scholar Yebra, D., Kiil, S., and Dam-Johansen, K. (2004) Antifouling techniques – past, present and future steps towards efficient and environmentally friendly antifouling coatings. Prog Org Coat 50: 75– 104. CrossrefCASWeb of Science®Google Scholar Yooseph, S., Sutton, G., Rusch, D.B., Halpern, A.L., Williamson, S.J., Remington, K., et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 5: . e16. CrossrefCASPubMedWeb of Science®Google Scholar Zeng, R., Zhang, R., Zhao, J., and Lin, N. (2003) Cold-active serine alkaline protease from the psychrophilic bacterium Pseudomonas strain DY-A: enzyme purification and characterization. Extremophiles 7: 335– 337. CrossrefCASPubMedWeb of Science®Google Scholar Zeng, R., Xiong, P., and Wen, J. (2006) Characterization and gene cloning of a cold-active cellulase from a deep-sea psychrotrophic bacterium Pseudoalteromonas sp. DY3. Extremophiles 10: 79– 82. CrossrefCASPubMedWeb of Science®Google Scholar Zhang, J.W., and Zeng, R.Y. (2008) Purification and characterization of a cold-adapted alpha-amylase produced by Nocardiopsis sp 7326 isolated from Prydz Bay, Antarctic. Mar Biotechnol (NY) 10: 75– 82. CrossrefCASPubMedWeb of Science®Google Scholar Citing Literature Volume2, Issue2Special Issue: Bioremediation. With guest editors Jan Roelof van der Meer, Thomas Wood, Hideaki Nojiri, Pieter van DillewijnMarch 2009Pages 157-163 FiguresReferencesRelatedInformation