The Sargasso Sea study had many important findings from the obvious, 1.3 million new genes and thousands of new species, to unique environmental biology with the discovery of over 800 new photoreceptors that could help explain the rich diversity of life in a nutrient-poor environment.  The paper also provided the first proof that scientists can use “whole environment” shotgun DNA sequencing to characterize complex environments. This paper demonstrated that the methods and algorithms that we developed for sequencing the human and other large genomes are equally applicable to complex mixtures of thousands of species. We have demonstrated that within one sample dataset we could uniquely assemble genomic DNA ranging from complete or nearly complete genomes of abundant organisms down to paired-end reads from organisms that are rare in the sample.

  Does it describe a new discovery or a new methodology that’s useful to others?

Our paper described new methods for characterizing the environment and more than 1.3 million new genes representing more gene diversity than in existing gene databases.

  Could you summarize the significance of your paper in layman’s terms?

We have learned that there is a remarkable diversity of organisms in the Sargasso Sea, an area that was previously thought to be relatively devoid of life compared with the rest of the world’s oceans. Our new methods build upon what is known about ocean microbes and provide significant evidence that there is still much to be learned about the diversity and abundance of life in the world’s oceans.

  How did you become involved in this research?

I’ve long been concerned by the state of our environment. It was obvious from our earliest shotgun sequencing of whole genomes[i] that there was a unique mathematical solution for each genome sequence.  In 1996, we sequenced a clinical isolate of a human pathogen that was contaminated by an additional species, something we did not realize until we attempted to assemble the genome.  The assembly algorithm assembled the two related species genomes completely separately with no false joins.  At that stage it was clear to all involved that we could assemble complex mixtures of genomic DNA into the correct species. Also starting with the Borrelia burgdorferi genome[ii] and the Deinococcus radiodurans genome sequencing project[iii] we discovered that many microbial species have multiple genomes and genomic elements. Borrelia had a single chromosome and multiple small but very similar plasmids while Deinococcus had four chromosomes and plasmids. These genomes probably were the first true environmental genome sequencing efforts.  Again it was obvious that the methods we developed were more than capable of sorting the DNA sequences into the correct structures.  Environmental genomics holds great potential to extend understanding of global ecology as well as basic science. Eventually, it may lead to novel ways to solve some of our most vexing environmental problems.  Now we can think not only of a community of microorganisms, but of the genes in that community. These genes, which we’re only beginning to identify, enable microbes to capture energy from the sun, remove carbon dioxide from the air, use organic carbon from other organisms, and cycle nitrogen through the ecosystem in its several forms. There is a vast untapped world of potentially useful microorganisms in our oceans that we are exploring with modern tools of genomics.

Dr. J. Craig Venter
President
J. Craig Venter Institute

Read a classic Science Watch^® interview with J. Craig Venter.