Ocean’s microbiome has incredible diversity – and human likeness

We’re a step closer to understanding the microbial community that inhabits the ocean – and it has some striking similarities to the community that lives inside our guts. The microbiome of the world’s biggest ecosystem and one of the smallest appear to function in surprisingly similar ways.

Microscopic plankton produce a large proportion of the oxygen in the atmosphere – amounting to half of all oxygen produced by photosynthesis – but we know very little about these organisms. The data collected by researchers aboard the schooner Tara will change that. Between 2009 and 2013, the ship sailed the world’s seas and oceans, collecting 35,000 plankton samples – both microbial and multicellular – from the upper layers of the water.

The first batch of the Tara studies is published today, and it reveals that planktonic marine life is far more diverse than anyone expected. For example, we already knew of about 4350 species of microalgae, 1350 species of protists and 5500 species of tiny animals, based on direct studies of their appearance. But the new genetic evidence suggests that there are probably three to eight times as many distinct species in each group as currently recognised.

40 million genes

Shinichi Sunagawaat the European Molecular Biology Laboratory in Heidelberg, Germany, and his colleagues used the genetic samples from the Tara voyage to create the Ocean Microbial Reference Gene Catalogue. It contains over 40 million genes from more than 35,000 species.

They then used the catalogue to establish the core genetic features of the global ocean microbiome. That core turned out to be relatively small: the researchers considered only the subset of genes found in every one of the 139 ocean microbe samples they studied, and those genes fell into just 5755 gene families.

Only one other microbiome – that of the human gut - known in a comparable level of detail. The two clearly occupy very different environments: the gut lacks oxygen, for example, and has a stable temperature, while shallow ocean water is aerobic and fluctuates in temperature.

Even so, the genetic studies show there is a significant overlap in the way the two microbiomes function.

In both, there was an almost identical abundance of genes involved in replication, ion transport and cell motility.

“This certainly was rather a big surprise to us because we expected different ecosystems would have microbial communities with functions that would be completely different,” Sunagawa said at a press conference this week.

Universal features

There were some differences, though: genes involved in defence mechanisms and carbohydrate transport were present in both microbiomes, but were more abundant in the human gut. Also, genes involved in energy production – including photosynthesis – were present in both but were more abundant in the ocean.

Jens Walter at the University of Alberta in Edmonton, Canada – who was involved in a recent analysis of the unusual microbiome of hunter - gatherers in the remote Venezuelan rainforest – says it is not surprising that two very different microbiomes would function in broadly similar ways.

This is because the fundamental way in which many microbes function has not changed much during their evolution, and it is the functions they do not share with others that helps define the ecology of any given microbiome, Walter says.

For instance, all forms of E. coli bacteria function in an essentially similar way, but some are benign and some are pathogens. “The first live in the gut of healthy people, and the latter kill you,” he says.

Future Tara studies should hopefully give a more detailed picture of these differences – as well as revealing more about how the ocean’s microbial community might be affected by climate change.

It is too early to say if the similarities are coincidental or are characteristics shared by all microbiomes. But the results hint that microbial systems in general may behave in a similar way regardless of exactly what environment they occupy; something that other researchers could now begin to test, Sunagawa says.