Taking metagenomic studies in context.

Today we are witnessing an explosion in interest in marine microbial communities, including Bacteria, Archaea, protists and viruses. Recent advances in genomic science have helped scientists to study microorganisms with much greater precision than ever before and provided new ways to evaluate ecosystem diversity and functional potential. In their article ‘Metagenomic marine nitrogen fixation – feast or famine?’, published in this issue of TIM, Johnston et al. have focused on one specific area – the nitrogen cycle – and have attempted to draw conclusions from the lack of particular N2-fixing genes in the Sargasso Sea metagenomic data described by us (1). We wish to clarify that a key piece of context from our study [1xEnvironmental genome shotgun sequencing of the Sargasso Sea. Venter, J.C. et al. Science. 2004; 304: 66–74Crossref | PubMed | Scopus (2237)See all References[1] is unaccounted for by Johnston et al., and cannot be neglected if accurate conclusions are to be drawn.The failure of the their effort to detect key elements of biological nitrogen fixation in the Sargasso Sea database (SSDB) cannot be taken to infer, as the authors do, the ‘patchiness’ of the nif genes in marine samples. The Sargasso study was not designed to fully elucidate the nitrogen cycle from the Sargasso Sea ecosystem, but rather to describe the gene complement found within a particular biological size fraction extracted from the filtered samples. Owing to their size, many nitrogen fixing cyanobacteria potentially present in the samples collected would not be represented in the size fraction examined in the Sargasso study, which focused on microbes captured on a 0.1μm filter after passing through a 0.8μm prefilter (Table S1 in Ref. [1xEnvironmental genome shotgun sequencing of the Sargasso Sea. Venter, J.C. et al. Science. 2004; 304: 66–74Crossref | PubMed | Scopus (2237)See all References[1]). Clearly, many nitrogen-fixing cyanobacteria could well be found on the larger size fractions, which have yet to be analyzed.Johnston et al. rightly point out that metagenomic databases are rich resources leading to intriguing questions, not only of the genes and pathway components identified as being present in particular samples, but also which genes are conspicuously absent. It is crucial, however, to take great care to consider the full context of the samples being analyzed before any conclusions are drawn.