137 Marine Microbial Genomes from Cultured Samples are Sequenced
News Nov 18, 2010
Researchers at the J. Craig Venter Institute (JCVI), a not-for-profit genomic research organization, published results today describing the sequencing and analysis of 137 marine microbial genomes living in the global ocean surface. The research was published by JCVI lead authors Shibu Yooseph and Kenneth Nealson and colleagues in Nature.
The results give clearer insights into life in this region of the ocean by showing that the microbes there, called picoplankton, can be classified into two main groups that are very different in their genetic make-up, physical qualities and metabolic abilities.
The first group (dubbed “cosmopolitan” by the team), has only a few dominant but abundant members who have small genomes, low gene content, and are capable only of slow growth and survival in low energy environments. The other group consists of many different families of microbes that are not abundant, but whose inhabitants have higher gene content and more developed systems allowing them to better adapt to “feast or famine” situations because of their ability for rapid or slow growth depending on their environments.
The team theorizes that the “cosmopolitan” microbe group is more successful in the surface oceans because of their large population consisting of organisms with small genomes and smaller mass thereby making them less attractive as a food source to potential predators and to viruses. They called this theory cryptic escape.
The 137 sequenced genomes were analyzed in the context of 10.97 million sequences of JCVI’s Sorcerer II Global Ocean Sampling (GOS) metagenomic data and thousands of 16S rRNA sequences. The marine genomes were collected as part of the Gordon and Betty Moore Foundation-funded Marine Microbial Genome Sequencing Project (MMGSP), a project coordinated by JCVI that has a primary goal of obtaining whole genome sequences of ecologically important microbes from a variety of diverse, global marine environments.
The MMGSP genomes and the GOS metagenomic data are both predominantly from the surface ocean and were useful as comparative datasets. When comparing these data the group found that only 24.5% of the 10.97 million GOS sequences overlapped with 197 sequenced genomes: 137 genomes sequenced by JCVI as part of the MMGSP and another 60 genomes sequenced by others.
According to Shibu Yooseph, “This work highlights an important example of combining metagenomic data with sequenced genomes data to study microbial communities and to generate testable hypotheses in microbial ecology.” He added, “This could be a model for future environmental genomic studies.”
The GOS metagenomic data were collected onboard the Sorcerer II from the Northwest Atlantic to the Tropical Pacific and from the Indian Ocean. The sampling protocol onboard Sorcerer II consists of taking 200 to 400 liters of seawater approximately every 200 miles and filtering this water through increasingly smaller filters--20.0 μm, 3.0 μm, 0.8 μm, and 0.1 μm filters. The microbes in the 0.1 μm to 3.0 μm size range are what the JCVI research team termed marine surface picoplankton. The GOS data used as part of this research were primarily from the 0.1 μm filter along with representative samples from the 0.8 μm and 3.0 μm filters.
Funding for this research came from the following: The Gordon and Betty Moore Foundation; the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research; National Science Foundation. More than 60 collaborators worldwide provided the 137 microbes analyzed as part of this study.