The genes of the ocean microbiome are similar to those of human gut microbiota

This discovery was made by an international research consortium, including FAPESP-funded researcher, based on data from Tara Oceans circumglobal scientific expedition.

By Elton Alisson

Agência FAPESP – The genes of marine microorganisms are similar to those of the microbes that inhabit the human gut microbiota.

This discovery was made by an international team of researchers during the Tara Oceans scientific expedition around the world. The 36-meter French schooner TARA’s 140,000 km circumnavigation lasted three and a half years and cost some 16 million euros.

The expedition’s first results were reported in five articles published in the latest issue of Science.

“Never before has such an exhaustive survey of marine microbial diversity been performed,” said Hugo Sarmento, a professor in the Hydrobiology Department of the Federal University of São Carlos (UFSCar), São Paulo State, Brazil, and co-author of one of the studies.

“The amount of ocean samples and data collected is the largest ever,” Sarmento told Agência FAPESP. He took part in the first stage of the expedition and is currently engaged in a research project supported by FAPESP under its Young Investigators Grants program.

According to Sarmento, the purpose of the expedition was to study plankton ecosystems in the world’s oceans. Plankton include a diverse group of microorganisms, such as viruses, algae and bacteria, as well as animals of various sizes. They float on the surface of the ocean and provide a crucial source of food to many large aquatic organisms.

Backed by an international consortium of 160 scientists from 40 countries, Tara Oceans collected some 35,000 plankton and water samples at depths of up to 2,000 meters between 2009 and 2013. The expedition visited 210 oceanic regions around the world, including the Brazilian coast.

Genome sequencing of the molecular plankton samples resulted in a database of 12.581 gigabases (trillions of DNA base pairs), which is equivalent to approximately 135 fully sequenced human genomes.

“It’s the biggest DNA sequencing effort ever performed not only in oceanography but also in other areas, such as health, including recent initiatives like the sequencing of the human gut microbiome,” Sarmento said.

For example, the Human Microbiome Project funded by the US National Institutes of Health (NIH) resulted in 1.5 terabases (Tb) of sequenced metagenomic data. The European Union’s Metagenomics of the Human Intestinal Tract Project (MetaHIT) resulted in 3.8 Tb.

By contrast, 243 samples of bacteria collected from 68 ocean locations around the world by Tara Oceans generated 7.2 Tb of metagenomic data. “It was only possible to generate such a large amount of data thanks to recent advances in genetic sequencing and computational analysis,” Sarmento said. “Enhanced techniques in both areas afford access to the taxonomic and genomic content of ocean microbial communities, so that we can study their structural patterns, diversity and functional potential.”

Genetic similarities

By analyzing the 7.2 Tb of metagenomic data from these 243 bacterial samples, Sarmento and fellow researchers in the consortium generated an ocean microbial reference gene catalogue with more than 40 million genes. Based on the catalogue, which is publicly available on the internet for use by the scientific community free of charge, the researchers identified a core set of gene families that are the most common in marine microorganisms.

A comparison with the genes sequenced by the Human Microbiome Project and MetaHIT shows that over 73% of the functional genes in marine microorganisms are shared with the human gut microbiome, despite the physicochemical differences between these two ecosystems. “Genetic sequencing of the plankton samples collected during the expedition could result in the identification of tens of thousands of new species of bacteria, single-cell organisms and marine viruses,” Sarmento said.

Another discovery made by the consortium was that temperature is the key environmental factor in determining the composition of the ocean microbiome. Global climate change could therefore have a major impact on the diversity of these microorganisms, which rapidly react to ocean warming and acidification. “One of the motivations for the project is to evaluate how the changes that are now occurring in the oceans, such as pollution, overfishing and rising temperatures, are affecting marine microorganisms,” Sarmento said.

Microorganisms are ubiquitous in the ocean environment, where they have key roles in biogeochemical processes such as carbon and nutrient cycling, he explained. They are as important as tropical rainforests to the Earth’s ecosystems, providing over half the oxygen that is produced through photosynthesis and absorbing CO2 from the atmosphere. “Oceans cover two-thirds of the planet’s surface and represent the largest active carbon sink. Moreover, microorganisms are responsible for almost all of the photosynthesis that takes place in the oceans,” Sarmento said.

The researchers also found that the ocean microbiome varies from one region to another according to location, temperature and water composition. For example, there are viruses and bacteria found in the Atlantic that are not found in the Pacific: they are kept separate by fast-moving ocean currents. “Given the ability of microorganisms to disperse throughout the ocean, scientists used to believe biogeography and geographic distribution played no role, but today’s advanced genetic sequencing technology shows that microorganisms are biogeographic and that plankton biodiversity isn’t the same in the various ocean regions,” Sarmento said.

There are approximately 1 million bacteria and 10 million viruses in 1 milliliter of water, which is equivalent to three drops. “Generally speaking, microbial biodiversity is higher than animal and plant biodiversity,” he noted.

As part of his research project funded by FAPESP, Sarmento plans to conduct a survey of microbial diversity in aquatic environments in São Paulo State, possibly using the 64-meter Alpha Crucis and the smaller Alpha Delphini, the first oceanographic vessel built entirely in Brazil. Both ships were bought by FAPESP for the University of São Paulo’s Oceanography Institute.