© 2005 Nature Publishing Group Division of Biological Engineering and Department of Civil and Environmental Engineering, Room 48-427, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA. e-mail: [email protected]:10.1038/nrmicro1158Published online 10 May 2005Molecular approaches for characterizing microbial species and assemblages have significantly influenced our understanding of microbial diversity and ecology. In particular, ribosomal RNA (rRNA) gene sequence comparisons have provided a revolutionary approach for interpreting microbial evolutionary relationships1. In a logical extension of this technique, extraction of phylogenetically informative genes (like rRNAs) directly from naturally occurring microorganisms represented another important development in micro-bial biology, opening up the natural microbial world to closer scrutiny2,3. Resulting discoveries include the recognition of new phylogenetic lineages4–6, distri-butional mapping of taxa in sometimes unsuspected habitats7,8 and the fundamental realization that most extant microbial diversity had eluded detection by traditional cultivation approaches3,5.Advances in genome sequencing technologies have similarly had great impact on microbial biology, pro-viding new insights into microbial evolution, biochem-istry, physiology and diversity. Genomic technologies are now also extending their influence to microbial ecology and environmental science. With respect to ocean science, several marine microbial whole genome sequences have been completed TABLE 1. The first sequenced marine microorganism was that of a marine archaeon, Methanocaldococcus jannaschii, which was isolated from deep-sea hydrothermal vents9, and the list of sequenced marine microorganisms now includes marine viruses (see also the article by R.A. Edwards and F. Rohwer in this issue), cyanobac-teria10–12, bacteria13–22, archaea9,23–30 and protists31 from the EUPHOTIC ZONE, deep water, BENTHIC habitats and hydrothermal vents. Many more marine bacterial, archaeal and protistan genome sequencing projects are now underway. As these new sequencing initiatives progress (see Online links box), the database of refer-ence sequences from ecologically relevant organisms will expand rapidly. This is a crucial consideration in cultivation-independent genomic projects, as whole genome sequences from relevant organisms provide the foundations for interpretation and annotation of environmental genomic data.Most recently, the merging of cultivation-independent gene sequences with contemporary genomic approaches (such as whole-genome shotgun sequencing) is providing a more com-prehensive picture of the structure and function of indigenous microbial communities. Genomic approaches for studying natural microbial assem-blages have been variously dubbed environmental genomics, population genomics, metagenomics or ecogenomics. Regardless of the moniker, all these approaches involve cultivation-independent genomic MICROBIAL COMMUNITY GENOMICS IN THE OCEANEdward F. DeLongAbstract | Marine microbial communities were among the first microbial communities to be studied using cultivation-independent genomic approaches. Ocean-going genomic studies are now providing a more comprehensive description of the organisms and processes that shape microbial community structure, function and dynamics in the sea. Through the lens of microbial community genomics, a more comprehensive view of uncultivated microbial species, gene and biochemical pathway distributions, and naturally occurring genomic variability is being brought into sharper focus. Besides providing new perspectives on oceanic microbial communities, these new studies are now poised to reveal the fundamental principles that drive microbial ecological and evolutionary processes.EUPHOTIC ZONE The uppermost stratum of the water column that receives sufficient light for photosynthesis.BENTHIC Living in, or on the bottom of, a body of water.NATURE REVIEWS | MICROBIOLOGY VOLUME 3 | JUNE 2005 | 459REVIEWS FOCUS ON METAGENOMICS© 2005 Nature Publishing Group Table 1 | Published whole genomes from marine microorganismsSpecies Genome size ReferencesBacteriaPhotobacterium profundum 6,400 kb 21Vibrio fischeri 4,284 kb 22Silicibacter pomeroyi 4,109 kb 14Idiomarina loihiensis 2,839 kb 13Desulfotalea psychrophila 3,659 kb 18Vibrio vulnificus 5,211 kb 15Prochlorococcus marinus subsp. Pastoris MED4 1,657 kb 11Prochlorococcus marinus MIT9313 2,410 kb 11Synechococcus sp. 2,434 kb 12Prochlorococcus marinus SS120 1,751 kb 10Rhodopirellula baltica 7,145 kb 19Vibrio parahaemolyticus 5,165 kb 16Oceanobacillus iheyensis 3,630 kb 20ArchaeaMethanococcus maripaludis 1,661 kb 25Methanosarcina acetivorans 5,751 kb 24Methanopyrus kandleri 1,694 kb 30Pyrococcus furiosus 1,908 kb 29Pyrobaculum aerophilum 2,222 kb 113Pyrococcus abyssi 1,765 kb 23Thermotoga maritima 1,860 kb 17Aeropyrum pernix 1,669 kb 27Pyrococcus horikoshii 1,738 kb 26Archaeoglobus fulgidus 2,178 kb 28Methanocaldococcus jannaschii 1,664 kb 9EukaryaThalassiosira pseudonana 25,000 kb 31analysis of DNA extracted from naturally occur-ring microbial biomass. These techniques were first applied to marine plankton to characterize uncultivated marine bacterial and archaeal spe-cies32,33, and are now becoming a common method to characterize microbial assemblages. Applications include the genome analysis of uncharacterized taxa34–49, expression of novel genes or pathways from uncultured environmental microorganisms34,48,50–53, elucidation of community-specific metabolism54,55 and comparison of different community gene con-tents. Several recent reviews and commentaries have summarized the history and potential applications of cultivation-independent genomic surveys50,51,56–62. Here, the development, application and potential of ocean-going microbial genomics is explored.Practical approaches Large-insert bacterial artificial chromosome and fosmid libraries. Several strategies for cultivation-independent genomic survey of marine microbial communities have been used (FIG. 1). One of the earliest examples used bacteriophage-λ cloning techniques to produce genomic libraries from marine picoplankton32. More recently, fosmids and bacterial artificial chromosomes63,64 (BACs) have been applied in genomic analyses of naturally occur-ring marine microorganisms34,35,38–40,49,54,65 (FIG. 1a). These vectors are particularly useful for stable,
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