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Microbiology

Prokaryotes are prokaryotes: a sneak peak at the microbial oceans courtesy DNA  

Sunagawa et al. Structure and function of the global ocean microbiome. Science 348. (2015). DOI: 10.1126/science.1261359

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Seawater has a lot of little organisms floating about in it busily recycling nutrients and discreetly running planet earth. Perhaps most famously to aerobic life like us, some 70 percent of the oxygen we breathe comes from photosynthetic free-floating (“planktonic”) microalgae that occupy the upper layers of the ocean. Of course, microbes also do so much more than make oxygen. They also recycle the elements that are essential to life, while taking care of their own business of survival. The structure of the “microbiome” (the world of microbial life) is determined by the physical and chemical environments that microorganisms inhabit, which in the oceans varies with depth and geography, inevitably leading to interdependencies among specialists (kind of like a city banker and country farmer both need each other despite occupying distinct habitats). While scientists know that microbes run the show in element and mineral cycling, practically nothing is known about the diversity and structure of microbial communities on a global scale.

To get at the microbial oceans, scientists from the Tara Oceans consortium undertook the brave task of conquering the microbiome of the world’s oceans. From 2009 to 2013 the consortium sampled water from all the world’s major ocean basins (minus the Arctic) bringing back 579 samples from 79 locations. They sampled from several depths allowing for a structured global comparison including useful physical (e.g. temperature) and chemical (e.g. oxygen concentration) measurements. They sorted these samples on the basis of size to separate out viruses, prokaryotes (bacteria and archaea), and eukaryotic cells using fancy filters, and performed “deep sequencing” on these samples to infer community composition (who’s there?), and community function (what are they doing?). Each of these “fractions” formed the basis for a distinct scientific narrative published in a special issue in the journal Science. The focus of the article described here by Sunagawa and about fifty other authors (demonstrating the vast team effort involved in this survey) is on what they found in the prokaryotic fraction, perhaps the most interesting (in my humble opinion) given the metabolic versatility and abundance of prokaryotes that do most of the heavy lifting in life.

A vast sampling of the world's oceans.

A seriously vast sampling of the world’s oceans. Sampling locations of  58 out of the over 200 sample sites surveyed for which data was collected at multiple depths and environmental data were measured. Image Courtesy Sunagawa y muchos otros, Science, 2015.

The fruits of their sequencing efforts culminated in a gene catalog of some 40 million distinct genes, over 80 percent from this study, and just under 60 percent prokaryotic, and the majority of whose functions could not be predicted. Impressively, the Tara team, according to statistics, achieved a near comprehensive assessment of the diversity of pelagic (open ocean) microbiota from around the world.

A whole lot of genes. A) Pie charts showing breakdown of the non-redundant gene catalog curated (and mostly contributed) by the Tara oceans consortium by contributing initiative (top) and taxonomy (bottom). Also shown is the catalog of genes from the human gut microbiome for comparison. B) A “rarefaction” curve showing just how good a job Tara did of sampling. As sub-sampling of the data set increases the rate of increase of new genes detected decreases (curve flattens out), implying that there isn’t much more to sample. Image courtesy Sunagawa et al., Science, 2015.

Combining metagenomic and physical data, the Tara team was able to interpret trends consistent with theories of ocean ecology. For example, they found more genes for swimming among the members of the mesopelagic layer (just below the epiplagic layer, where food comes from eating rather than light and carbon dioxide), which one might expect to allow bacteria in this nutrient-deficient zone to avoid grazing as well as colonization of sinking particulates carrying nutrients from above. Significantly, they found that the diversity of the community (who was there) was explained more by temperature than the geographic location of sampling, which could have important implications as temperatures of the global oceans change due to global warming.

The team also sorted genes into functional categories, and zeroed in on a core set of conserved functional groups common to all geographic locations. They next sought to compare this core to that of a similarly sized microbiome dataset. As it happens the dataset of the largest magnitude to-date corresponds to the human gut microbiome. Amazingly, despite the dramatically different environments posed by the human gut as compared to the open ocean, researchers found that a majority of core functional abundance (greater than 73 percent) is shared between the two datasets.

Lastly, the researchers looked at the ecological concept of functional redundancy, which is the idea that ecosystems buffer themselves by employing multiple members of the community to perform the same job. As with the human gut, they found that despite great variability in community composition across samples, the core functionalities of the ocean’s microbes were fairly stable. Where variability comes in, they suggest, is in the creative ways that microbes around that world find to adapt to their local environments, while their jobs remain essentially the same from one end of the globe to the other—prokaryotes are prokaryotes.

The Tara oceans project has produced a dataset at least as grand in importance as it is in scale that promises to revolutionize our understanding of earth as a system. Although the researchers are quick to admit that they really don’t know quite what will come out of the vast amounts of data they collected, it is clear that an unprecedented level of understanding awaits as the scientific community begins to make use of this tremendous resource in combination with further efforts to understand community function and structure through sequencing combined with environmental data. Without a doubt, we live in truly exciting times for biology where the potential for discovery is practically without bound.

 

What questions do you have about the ocean microbiome? Leave a comment.

 

Find out more about the remarkable Tara Expeditions here.

 

 

 

 

Abrahim El Gamal
Abrahim is a PhD student at Scripps Institution of Oceanography in San Diego where he studies marine chemical biology.

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