Ratings

The field of metagenomics is revolutionizing quest into the adaptation and stratification of microbial functions in different unexplored niches of our planet and it has picked up quite at a big scale, ~100 publications within just 3 years. The present study, however, is the first one to explore deep-sea community genomics enlightening us about how temperature regulates the stratification and diversification of (deep-sea) Mediterranean plankton in the absence of light.

At the first glance itself I was convinced that we were looking through one of the top 1% of the community genomic studies, the only second ocean metagenomic effort after the Pacific ALOHA metagenomic study published sometimes back in Science by DeLong and colleagues. The paper was sent out for rigorous opinion by 3 known experts who dissected it out carefully and all of them recommended its publication without much modification. That conveys how balanced the authors framed their hypothesis, observations, arguments and interpretations from the beginning itself. This saved us a lot of time bringing out this landmark paper just in time. It was a great experience handling this amazing paper with its large data set and feasting discussions.

I am sure audience in the community genomics area will greatly benefit from this study as besides its subjective merit it provides in depth and unrestricted access to concerned methods, protocols, algorithms and genomic sequences. Also, I am convinced that this paper would provide a solid framework for the ensuing metagenomic studies involving other deep-sea communities to unravel important questions about their metabolism and lifestyle besides serving as a foundation for medical and agricultural animal metagenomic efforts.

Best,

Niyaz Ahmed

Academic Editor
PLoS ONE

Overall I like the paper for two reasons.

First there is some interesting science in here, which is not the case for all genomics or metagenomics papers. In particular I find the comparison to the ALOHA depth series metagenomic data to be most interesting. For example, they found that the deep Mediterranean communities' metagenome appears to be most similar to the metagenome of communities from closer to the surface in the ALOHA series. This suggests to the authors that temperature may be more related to microbial genomic diversity than depth (the ALOHA temperature profile drops off more quickly than the Mediterranean profile). I am not sure they are right in this but it is the right type of analysis to do --- just as in "normal" genomic sequencing, the power of metagenomics is going to come from comparative studies.

My second reason for liking the paper is they make appropriate caveats for many of the analyses. Such caveats are needed because we are in the infancy of metagenomics and the analysis required is quite complex and nobody is really sure exactly what to do or how to do it. In addition, the data sets we would like to compare to are not there yet ( e.g., they point out my own pet peeve - that the phylogenetic sampling of genomes of cultured organisms is very biased).

This paper was a remarkably enjoyable read. As someone who knows absolutely nothing about oceanography, I found that the introduction provided a fabulous framework for the interpretation of the results.

I had a difficult time rating the "reliability" of the article because I think the authors are analyzing their data in a relative vacuum (tough for a comparative study, but not their fault.) So, would I base my career upon their findings? No. But I have confidence in their methodology.

I'm excited that the era of comparative metagenomics is upon us, and I think that this study offers us an excellent peek at the power of such analyses. Not only can we describe the distribution of deep-ocean microbial communities, but we can begin to understand the metabolic capabilities that enable them to adapt to particular microenvironments. And, all of this by accumulating data represented by four letters, from organisms we've never seen, in an environment in which humans cannot survive. Mind-blowing!