//
you're reading...

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

taracatalog-01

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.

 

 

 

 

Discussion

No comments yet.

Post a Comment

Instagram

  • by oceanbites 1 day ago
    Leveling up - did you know that crabs have a larval phase? These are both porcelain crabs, but the one on the right is the earlier stage. It’s massive spine makes it both difficult to eat and quite conspicuous in
  • by oceanbites 1 week ago
    This week for  #WriterWednesday  on  #Oceanbites  we are featuring Cierra Braga. Cierra works ultraviolet c (UVC) to discover how this light can be used to combat biofouling, or the growth of living things, on the hulls of ships. Here, you
  • by oceanbites 2 weeks ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Elena Gadoutsis  @haysailor  These photos feature her “favorite marine research so far: From surveying tropical coral reefs, photographing dolphins and whales, and growing my own algae to expose it to different
  • by oceanbites 1 month ago
    This week for  #WriterWednesday  on Oceanbites we are featuring Eliza Oldach. According to Ellie, “I study coastal communities, and try to understand the policies and decisions and interactions and adaptations that communities use to navigate an ever-changing world. Most of
  • by oceanbites 1 month ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Jiwoon Park with a little photographic help from Ryan Tabata at the University of Hawaii. When asked about her research, Jiwoon wrote “Just like we need vitamins and minerals to stay
  • by oceanbites 2 months ago
    This week for  #WriterWednesday  on  #Oceanbites  we are featuring  @riley_henning  According to Riley, ”I am interested in studying small things that make a big impact in the ocean. Right now for my master's research at the University of San Diego,
  • by oceanbites 2 months ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Gabby Stedman. Gabby is interested in interested in understanding how many species of small-bodied animals there are in the deep-sea and where they live so we can better protect them from
  • by oceanbites 2 months ago
    This week for  #WriterWednesday  at  #Oceanbites  we are featuring Shawn Wang! Shawn is “an oceanographer that studies ocean conditions of the past. I use everything from microfossils to complex computer models to understand how climate has changed in the past
  • by oceanbites 2 months ago
    Today we are highlighting some of our awesome new authors for  #WriterWednesday  Today we have Daniel Speer! He says, “I am driven to investigate the interface of biology, chemistry, and physics, asking questions about how organisms or biological systems respond
  • by oceanbites 3 months ago
    Here at Oceanbites we love long-term datasets. So much happens in the ocean that sometimes it can be hard to tell if a trend is a part of a natural cycle or actually an anomaly, but as we gather more
  • by oceanbites 4 months ago
    Have you ever seen a lobster molt? Because lobsters have exoskeletons, every time they grow they have to climb out of their old shell, leaving them soft and vulnerable for a few days until their new shell hardens. Young, small
  • by oceanbites 4 months ago
    A lot of zooplankton are translucent, making it much easier to hide from predators. This juvenile mantis shrimp was almost impossible to spot floating in the water, but under a dissecting scope it’s features really come into view. See the
  • by oceanbites 4 months ago
    This is a clump of Dead Man’s Fingers, scientific name Codium fragile. It’s native to the Pacific Ocean and is invasive where I found it on the east coast of the US. It’s a bit velvety, and the coolest thing
  • by oceanbites 5 months ago
    You’ve probably heard of jellyfish, but have you heard of salps? These gelatinous sea creatures band together to form long chains, but they can also fall apart and will wash up onshore like tiny gemstones that squish. Have you seen
  • by oceanbites 6 months ago
    Check out what’s happening on a cool summer research cruise! On the  #neslter  summer transect cruise, we deployed a tow sled called the In Situ Icthyoplankton Imaging System. This can take pictures of gelatinous zooplankton (like jellyfish) that would be
  • by oceanbites 6 months ago
    Did you know horseshoe crabs have more than just two eyes? In these juveniles you can see another set in the middle of the shell. Check out our website to learn about some awesome horseshoe crab research.  #oceanbites   #plankton   #horseshoecrabs 
  • by oceanbites 7 months ago
    Feeling a bit flattened by the week? So are these summer flounder larvae. Fun fact: flounder larvae start out with their eyes set like normal fish, but as they grow one of their eyes migrates to meet the other and
  • by oceanbites 7 months ago
    Have you seen a remote working setup like this? This is a photo from one of our Oceanbites team members Anne Hartwell. “A view from inside the control can of an underwater robot we used to explore the deep parts
  • by oceanbites 8 months ago
    Today is the day of  #shutdownacademia  and  #shutdownstem  and many of us at the Oceanbites team are taking the day to plan solid actions for how we can make our organization and the institutions we work at a better place
  • by oceanbites 8 months ago
    Black lives matter. The recent murders of Ahmaud Arbery, Breonna Taylor, and George Floyd have once again brought to light the racism in our country. All of us at Oceanbites stand with our Black colleagues, friends, readers, and family. The
WP2Social Auto Publish Powered By : XYZScripts.com