What can a single drop of seawater tell us about the ocean?
A surprising amount, as it turns out.
Genetic information taken from a small sample of seawater reveals the diversity of microorganisms present, their global distribution, and new information about certain species. Researchers at the Bigelow Laboratory for Ocean Sciences in Maine recently discovered that the microbial life within a teaspoon of water from the Sargasso Sea could be representative of the vast genetic diversity of marine microorganisms around the globe. Their study, published in Cell in December 2019, may provide a new approach to examining the complex communities of microorganisms.
These communities, called microbiomes, are made up of thousands of different types of bacteria and other types of microorganisms. Because they are too small to reliably identify simply by examining them under a microscope, researchers use genetic information to learn which species of microorganisms are present in a sample. It’s a little bit like if scientists chose thousands of people at random from one big city and had them take a DNA test — the result would be a glimpse of the population’s diversity.
“In the same way that we think of New York City as a melting pot, every teaspoon of the ocean is a microbial melting pot,” said Ramunas Stepanauskas, research scientist and senior author of the paper, in Bigelow’s press release. “The ocean is huge, and it’s amazing how complex ecological and evolutionary processes take place in each tiny drop.”
Using genomes — the set of genes present in an organism’s cells — the researchers employed a method of DNA sequencing called single-cell genomics. By isolating just one cell, they can “zoom in” on a microorganism’s entire genome, revealing important details about the species. This is useful in myriad ways for microbiologists hoping to better understand complex microbiomes, such as that of a river or the human gut, which may contain thousands of different kinds of microorganisms.
In their study of the marine microbiome, the researchers at Bigelow used 28 water samples from the tropic and subtropical regions of the Atlantic and Pacific Oceans to analyze more than 12,000 different microbial genomes. The data generated was used to create a database called the Global Ocean Reference Genomes Tropics (GORG-Tropics).
“One of our main goals with the GORG initiative was to produce a powerful resource for the marine microbiology research community,” said Julia Brown, bioinformatician at Bigelow Laboratories and an author of the study, in the press release. “We hope that scientists will be able to use this dataset in follow-up studies to answer questions no one has even thought of yet.”
The researchers were looking at the global dispersal of an organism called prokaryoplankton. Plankton are very, very small marine organisms used as a food source by other creatures, such as whales and fish. They are generally separated into two groups: phytoplankton, an algae, and zooplankton, which are animal-like and resemble miniscule mythological sea creatures. Prokaryoplankton are prokaryotic bacteria, which means they’re more like plants than animals. Some of them are decomposers feeding off dead animals and waste in the water, and some of them are photosynthesizers, which make their own energy using sunlight.
Each of these microorganisms are too small to see with the naked eye. But while they may be small, they play a key role in marine ecosystems. Prochlorococcus marinus, a marine blue-green algae (or cyanobacteria) that the scientists at Bigelow looked at during their research, is thought to be the most abundant photosynthetic organism on our planet.
Scientists can mine the GORG database to learn more about the global prokaryplankton pangenome, or the genes found in all strains of a species. They do this using metagenomics, in which DNA extracted from a single sample from the environment — such as the teaspoon of water from the Sargasso Sea — to look at all the microbial genomes present. The result is a more detailed picture of the extraordinary diversity inherent to microbiomes.
But this complexity can also present challenges for researchers interested in studying microbiomes. Generating, and subsequently sifting through, large amounts of data is time-consuming and expensive. Now, thanks to advances in genomic technologies and methods such as single-cell genomics, scientists looking at microbiomes can generate and analyze significant amounts of data in a shorter amount of time. It’s a big data approach to microbiology. This allows them to examine microbiomes — whether that of the ocean, or soil, or the human gut — in unprecedented detail.
As a result, there can be new discoveries about microorganisms. While analyzing data on the ocean’s most abundant photosynthetic organism, Prochlorococcus, the researchers uncovered the ability to photosynthesize within the genes of a group of proteobacteria, a previously unknown detail about the microorganism. These kinds of surprises can help scientists learn more about microorganisms and also gather data on species about which little is known.
“Genetic information can teach us a lot about ecology, and these may be photosynthetic organisms that were unnoticed before,” said Maria Pachiadaki, a study author and assistant scientist at Woods Hole Oceanographic Institution who did her postdoctoral studies at Bigelow, in the press release.
Why does it matter that we understand these microorganisms better? Because researchers hope to discover whether the chemicals they produce could have potential applications for biotechnology, climate change adaptation, even new antibiotics and cancer treatments. The researchers collaborated with scientists from the University of California San Diego to explore some of these possibilities.
Though it may be some time before significant developments are made, but thanks to the researchers’ novel single-cell genomics approach, the next steps are clearer. And moving forward, Stepanauskas and his team hope to expand from the tropics to look at polar regions and the deep ocean, where different — but very important — microorganisms lurk.