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Marine Genomics: at the Interface of Marine Microbial Microbial Biotechnology (2010) doi:10.1111/j.1751-7915.2010.00193.x Marine genomics: at the interface of marine microbial ecology and biodiscoverymbt_193 1..13 Karla B. Heidelberg,1* Jack A. Gilbert2† and a relatively minor aspect of oceanography during most of Ian Joint2 twentieth century. While epifluorescent microscopy of envi- 1Department of Biological Sciences, University of ronmental samples confirmed that bacteria were very Southern California, 3616 Trousdale Parkway, Los abundant (Hobbie et al., 1977), < 1–5% of bacteria could Angeles, CA 90089-0371, USA. be grown in culture (Staley and Konopka, 1985) and were 2Plymouth Marine Laboratory, Prospect Place, The Hoe, therefore very difficult to study. Specific filtration methods Plymouth PL1 3DH, UK. or the isolation and growth of a few organisms on a variety of different, and often complex, organic substrates were Summary developed mostly for clinical microbiology, but these limited methods were not well suited to studying the vast The composition and activities of microbes from complexity in natural environmental assemblages. Given diverse habitats have been the focus of intense this, many marine scientists turned to ‘black box’ ecological research during the past decade with this research approaches (e.g. Redfield, 1958; Carlson et al., 2001) to being spurred on largely by advances in molecular infer microbial roles in biogeochemical cycles. However, biology and genomic technologies. In recent years which microbes were responsible for specific bio- environmental microbiology has entered very firmly geochemical processes still remained largely a mystery. into the age of the ‘omics’ – (meta)genomics, proteom- While the invention of the microscope over 350 years ago ics, metabolomics, transcriptomics – with probably began to open up the richness of the microbial world, it is others on the rise. Microbes are essential participants the development of DNA sequencing tools in the past 30 in all biogeochemical processes on our planet, and the years that has truly changed how we understand microbial practical applications of what we are learning from the communities and their role in structuring ocean bio- use of molecular approaches has altered how we view geochemical dynamics. We are finding that the extent of biological systems. In addition, there is considerable marine microbial biodiversity, and consequently natural potential to use information about uncultured products potential, seems to be limitless and growing microbes in biodiscovery research as microbes larger as new techniques emerge to measure it. provide a rich source of discovery for novel genes, enzymes and metabolic pathways. This review explores the brief history of genomic and metage- How diverse is diverse? nomic approaches to study environmental microbial assemblages and describes some of the future chal- The first phylogeny-based studies of microbial life lenges involved in broadening our approaches – emerged from evaluation of the small subunit rRNA oligo- leading to new insights for understanding environ- nucleotide studies in the labs of Norman Pace, David mental problems and enabling biodiscovery research. Stahl and Carl Woese (Lane et al., 1985; Pace et al., 1985; Stahl et al., 1985; Woese, 1987; Turner et al., A brief history of marine microbiology 1989). Their advocacy for using rRNA for molecular phy- logenetic analysis revolutionized how scientists looked at Over the past two decades there has been an explosion in microbial diversity and evolution. understanding of how microbes – bacteria, protists and Initial findings were furthered to study microbial assem- viruses – critically influence the structure of and function of blages through the application of the polymerase chain the oceans. However, this was not always the case. The reaction (PCR) (Mullis, 1983) to allow for direct culture- study of microbial communities in marine environment was independent surveys of natural prokaryotic microbial assemblages (e.g. 16S rRNA: Giovannoni et al., 1990; Received 10 May, 2010; accepted 15 May, 2010. *For Correspon- dence. E-mail [email protected]; Tel. (+1) 310 510 4038; Fax (+1) Ward et al., 1990; Britschgi and Giovannoni, 1991; 310 510 1364. †Present address: Argonne National Laboratory, 9700 Schmidt et al., 1991). These surveys led to discoveries of South Cass Avenue Argonne, IL 60439, USA. extraordinarily unexpected levels of phylogenetic biodi- Re-use of this article is permitted in accordance with the Terms and Conditions set out at http://www3.interscience.wiley.com/ versity in natural systems (e.g. Pace, 1997; Head et al., authorresources/onlineopen.html 1998) and have resulted in a renewed interest in microbial © 2010 The Authors Journal compilation © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd 2 K. B. Heidelberg, J. A. Gilbert and I. Joint ecology for biodiscovery (Glöckner and Joint, 2010). A With either approach, diversity also depends on which case in point is one of the first applications of rRNA gene or which part of a gene is used in the analysis. For sequence analysis to study natural assemblages of bacte- example, a massively parallel tag 454 pyrosequencing rial lineages in the oceans (Giovannoni et al., 1990). They approach was used to evaluate the ‘rare biosphere’ diver- found that one group of closely related sequences was sity of 16S rRNA amplicons (Sogin et al., 2006). The very abundant in the Sargasso Sea. This group was code- technique uses internal primer sequences to produce named SAR11, and has subsequently been found in restriction-digest overhanging sequences, which greatly almost every marine province that has been sampled. improves the efficiency of serial analysis of ribosomal SAR11 accounts for a very significant proportion of bacte- sequence tags – SARST (Kysela et al., 2005). This pro- rioplankton in both surface and deep water (Morris et al., duced ~600 000 unique bacterial OTUs based on actual 2002) and has been described as the most abundant counts of sequence types from this study rather than bacterium on the planet. Another key outcome of the from extrapolated estimates (calculations made using the application of PCR was to show that Archaea, which were ICoMM database of ~40 marine microbial 16S rRNA originally thought to only inhabit extreme environments V6454 pyrosequencing projects – Pers. Comm. Sue such as hot springs or hypersaline ponds, could readily be Huse). Using this methodology, Huber and colleagues found in ocean environments (DeLong, 1992; Fuhrman (2007) also analysed > 900 000 16S rRNA amplicons et al., 1992). to evaluate hydrothermal vent microbial population There is no question that microbial diversity is vast, but structure. what is the true extent of diversity in the oceans. It has A global survey of 18S rRNA marine protistan eukary- been estimated that there are several hundred to several otic genes from diverse marine ecosystems was con- hundred thousand different phylogenetic species per ml of ducted using two fundamentally different high-throughput seawater with total diversity ranging between anything sequencing approaches on similar samples: traditional from 100 000 to more than a million (Curtis et al., 2002; Sanger ABI full length 18S rRNA sequencing (> 12 000 Huber et al., 2007). What we have learned about global contigs) and 454 pyrosequencing focused on the hyper- microbial diversity in the past decade from taxonomic variable V9 region of 18S rRNA genes (> 276 000 short gene surveys far exceeds our previous estimations. Fur- sequence tags). The Sanger approach (~1000 sequences thermore, we have seen tremendous genome wide diver- per sample) yielded non-parametric OTU diversity esti- sity within taxonomically identical phylogenetic groups. mates (e.g. Chao1, ACE1) that were substantially higher Even after two decades of concerted efforts to phylogen- than preliminary diversity analyses that were performed tically characterize microbial diversity, the discovery of several years earlier on some of the same samples but novel forms is common. The microbial species definition, with many fewer sequences (~150). The pyrosequenced despite its eminent practical significance for identification, V9 data revealed a substantial amount of ‘new’ 18S diver- diagnosis and diversity surveys, remains a very difficult sity in the samples (D.A. Caron and P.D. Countway, issue to advance (e.g. Hughes et al., 2001; Ward, 2002). unpubl. data). While pyrosequencing approaches can Currently, there are two common approaches to overestimate taxonomic richness as a result of PCR and measure diversity. First is a phylotype approach, which is sequencing errors (e.g. Quince et al., 2009), these based on assigning taxonomy based on results from an studies show that novel microbial diversity can be found at alignment to a sequence in a database that has the most every taxonomic level. However, even with exciting new statistically significant similarity a priori. Significant chal- technology, we are still massively under-sampling the lenges with this approach are that database searches diversity in marine ecosystems! may come back as undefined and that different databases (e.g. ribosomal database project II, SILVA, GreenGenes, Genome-based approaches Bergey’s culture db, NCBI’s nt or nr) can yield different taxonomies, many of which are based on ‘copycat’ assig- About the same time that PCR was becoming more com- nation whereby researchers have blindly accepted the monly used, technology for DNA sequencing of entire taxonomic assignation of the most homologous
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