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One of the projects you were working on during the cruise focused on microbial communities in low-oxygen zones. Can you give us the context?

Yes, so one of the areas we visited, off the coast of northern Chile, right next to the Atacama desert, is characterized by ocean upwelling — water from below is brought up to the surface by local wind and currents. Because of this upwelling, phytoplankton are highly abundant on the surface. When that biomass sinks, it's degraded by microbes, which consume a lot of oxygen. This creates an oxygen-deficient zone. Some people call them dead zones — though that phrase is more often in reference to anthropogenically driven impacts in coastal areas. What we have here occurs naturally in the open ocean.

The problem is that these areas are expanding and becoming more intense because of warming in the ocean. There have been a few studies showing this, and they have also predicted further expansion with global warming. Low oxygen is a big stressor for marine life. So if these areas are becoming larger, that means that the habitat of certain organisms is shrinking.

But these areas are also home to some very unique microbial communities. Unlike other life forms, these organisms don’t rely on oxygen to drive their metabolisms. Instead, they gain energy by breaking down nitrogen-containing compounds into inert nitrogen gas and water. This process removes nitrogen from the ecosystem. So, these microbial communities are very important on a global scale, because they can basically control how much oxygen and nitrogen is available in the ocean.��

Julio �����ú������岹 logs data at a work station aboard the Sonne. (Courtesy)

What kind of data did you collect on these microbial communities and what questions are you investigating?

We're trying to understand how these communities can adapt to multiple environmental stressors, including ocean warming, ocean acidification, and deoxygenation. How do we do this? We study the fats, or lipids, found in the cell membranes of these organisms. Why? Because organisms are able to change the chemistry of their cell membranes in order to adapt to environmental factors.

Imagine a stick of butter in a cool room, versus a bottle of olive oil. The butter is solid, because it is a saturated fat, while the olive oil is liquid, because it is an unsaturated fat. Organisms that live in warmer waters produce more butter-like fats to keep their cell membranes sturdy, while organisms that live in colder environments produce more olive oil-like fats, to keep their cell membranes flexible. If, all of the sudden, you put an organism that lives in warm waters in the Arctic, it will freeze to death unless it can adjust the ratio of fats it is producing — and the same vice versa.

So, what we do is collect large volumes of sea water at different depths using instruments known as in situ pumps. That allows us to capture a large swath of suspended particles coming from organisms in the ocean. Then we concentrate this material using large filters, freeze it, and bring it to the lab. In the lab, we can study the chemical composition of the entire microbial community at a particular water depth.

This approach is called environmental lipidomics. Basically, we’re able to see all of the fats produced in a given ecosystem. It allows us to do chemical fingerprinting, where we link certain fats back to the organisms that produce them. We also try to figure out which of these chemical signatures are unique to which systems and which signatures represent adaptations to environmental stressors.

Another part of the work we did was to filter smaller volumes of sea water to analyze DNA, which basically allows us to get a better sense of who's there, and look at the genetic potential of certain organisms to produce certain lipids. Finally, we also filtered samples for RNA, which allows us to see which genes are actually being expressed.

So, now we know which lipids are present, which organisms are present, and which genes they are expressing. This allows us to look at how the entire system is adapting to change. Is the makeup of species in the community shifting, or are the existing species genetically equipped to adapt to these changes, for instance? The integration of these genomics techniques with lipidomics is called meta-omics.

Why are these important questions?

If the chemistry of these organisms changes, that influences the quality of the organic matter consumed by all of the organisms in the marine trophic web. If you, for instance, reduce the number of unsaturated fats, that will have huge implications for animals. Animals cannot produce omega-3 and omega-6 fatty acids, we have to get them from eating primary producers like plants and phytoplankton, or from animals that feed on them like fish. So if the composition of phytoplankton changes, that has implications for zooplankton and then fish and eventually all the way up to us. It impacts the nutritional value at the very base of the food web.

This can also have big impacts on fish physiology — fish will struggle if they don't have the right proportion of good fatty acids. It could impact reproduction and potentially even lead to the collapse of some fisheries around the world. Now, this is speculation beyond the current research, obviously, but these are things that we care about, and that's where we study how these ecosystems are changing.

What’s next?

One of the things that I would love to do in the near future is to team up with some biogeochemical modelers or ecological modelers or climate modelers, people we have in-house, like [INSTAAR director Nicole Lovenduski]. Modelers may be able to put all of this data that we’re parsing into more complex numerical models or statistical analyses that allow us to get a much more quantitative idea of what drives change in these communities —what are the lipids telling us?

The long-term objective is to use some of these chemical signatures as indicators of the status of marine ecosystems. If we can infer which organisms are present, how they are adapting, and which adaptations might occur in response to certain environmental stressors, we might be able to see when and how an ecosystem is experiencing environmental pressure, just from analyzing a water sample.

We may also be able to use these tools to power predictive models of future ecological and chemical changes. It could help us go from models of things like temperature and dissolved oxygen to the future conditions of trophic webs, ocean chemistry, and fisheries. This is really thinking a lot further in time, but I guess those are the kinds of things that get me and others in my group excited about the work we do. We're trying to make stronger connections between what we find and what's really critical for us as humanity to understand.

Lastly, we plan to apply the information gathered from the water column to study changes in microbial processes associated with the expansion of oxygen-deficient zones during glacial-interglacial cycles. Stay tuned.