Discovering the diversity and importance of marine microbes
In the early 1700s Anton van Leeuwenhoek developed a microscope with which he observed and described the “microscopic” life in a drop of water. Ever since then, scientists have used plankton nets and microscopes to collect and name thousands of diatoms and other ocean drifters. For 200 years, those phytoplankton (ten to 200 microns in size) got credit for much of the ocean's primary production and the key role in the ocean food chain. Then in the 1970s, scientists using DNA analysis discovered even tinier creatures floating in the ocean—so small they can’t be caught in plankton nets. These one-celled organisms which range from 0.2 to 2 microns in size are called picoplankton, and include archaea, bacteria, and blue-green algae. Scientists believe there are probably thousands of additional species of plankton that have yet to be discovered or named.
What are all those kinds of plankton doing in the open ocean? That is the sort of question that MBARI researchers have been trying to answer. And in addition to using high-powered microscopes and culturing some species, Chris Scholin’s research team analyzes DNA from marine plankton to determine what types are present and what biochemical tricks they use to survive. The team has developed techniques to identify and quantify plankton, including picoplankton, algae and invertebrates in the ocean. By demonstrating that harmful algal blooms and toxins can be detected in real time, their methods can reduce risks to human health and economic impacts on fisheries and recreation.
Even though only a small fraction of the plankton have been studied in detail, MBARI researchers have learned a lot by analyzing the combined DNA of all the marine microbes in a sample of seawater. The resulting data can give scientists an overview of entire microbial communities using a technique first pioneered years ago by microbiologist Ed DeLong who conducted his research at MBARI for several years. More recent technological advances in genomics have made it possible for scientists to sequence really large quantities of DNA in a matter of weeks or months. This allows biologists to study not just microbial communities as a whole, but individual groups of microbes within those communities.
One of the research goals of MBARI researchers has been to determine how the microbes near the surface are different from those that live thousands of meters down. Not surprisingly, in samples from the sunlit waters within about 100 meters of the surface, the researchers have found a lot of microbial DNA sequences that were associated with photosynthesis. This means many microbes in these waters were probably using sunlight as a source of energy. Surface samples also contained microbial DNA that was associated with movement and propulsion. This suggests that movement is important for these microbes, perhaps helping them follow chemical gradients or move from food particle to food particle.
Perhaps the most surprising finding of this study was the large amount of DNA that came from viruses, especially in near-surface waters. Since the researchers excluded free-living viruses from their initial sample, they believe that this viral DNA must have come from viruses that had infected living bacteria. Such viruses can lie dormant and reproduce within bacterial cells, and can actually transfer DNA from one bacterium to another. Although microscopic inhabitants of the ocean are poorly understood, we now know they play a central role in the cycling of carbon, sulfur, nitrogen, and metals in the ocean. And scientists now estimate that half of the primary productivity is cycled through picoplankton via the so-called “microbial loop”.
In 2007, microbiologist Alex Worden joined the MBARI staff to continue developing new tools, assays, and methods for identifying, quantifying and characterizing marine plankton. Her goal is to characterize the community structure and functional significance of the tiny picoplankton, to gain a better understanding of the multiple roles that these organisms play in the ecosystem.
MBARI contributors: Oded Béjà, Lynne Christianson, Ed Delong, Peter Girguis, Steve Hallam, Roman Marin III, Ed Mellinger, Peter Miller, Christina Preston, Farley Shane, Chris Scholin, Grieg Steward, Marcelino Suzuki, John Tyrrell.
- Microbial oceanography group web page
- DNA from the deep
- DNA analysis shows how some deep-sea microbes limit global warming
- Scientists identify methane-consuming microbes from ocean depths