Jonathan Zehr


 

zehr_jonMuch of your work addresses nitrogen cycling. We’ve made big strides in the last couple of decades in understanding the pools and drivers of the nitrogen cycle, but do you think it’s possible there’s something we’re missing? Some big player or driver of the nitrogen cycle that we’re just not aware of yet?

I think it would be silly to make a statement that we’re not missing anything, given that we continue to find new surprises in the last 5 and 10 years. I’m sure we’re not at the end of this yet.

We still don’t know how the nitrogen budget balances on short time scales or long time scales. We don’t really understand the space and time variables of the organisms that we do know about and that’s largely because the oceans are so large, and our sampling of the oceans in time and space is so small, that there are pretty large degrees of uncertainty associated with our estimates of the abundance and activities of different types of microorganisms.

So we still can’t be sure we have a full picture of the nitrogen cycle?

Two types of information in the marine nitrogen cycle are still open questions: one is identifying all the transformations and the organisms that catalyze them, and the second is addressing the issues of time and space. We’re really constrained in oceanography by taking ships out, which end up providing anecdotal information which we try to extrapolate over very large time and space scales using models. One of the areas of research we’ve been focusing on is trying to develop tools that allow us to increase the resolution of information that we get from the ocean. We’ve always studied the nitrogen cycle from the perspective of the organisms and the genes involved, and we are extending that to use these types of approaches to measure the abundance and the activities of organisms using remote instrumentation machines that can sit in the water and sample for DNA and RNA over time so you can capture info on relevant time scales and figure out how the microbiology coincides with the environmental chemistry and physics.

Microbial ecology seems to find huge diversity wherever we look: soils, oceans, the human gut, etc. Study after study seems to find that, in any given environment, there’s a lot of genomic diversity within bacterial taxa. In one of your recent papers, however, you and your colleagues found that a nitrogen-fixing cyanobacterium showed very little genomic diversity. Why should Crocosphaera watsonii be the exception to the diversity rule?

I think it’s going to turn out not to be the exception to the diversity rule. It is, when you compare it to really abundant organisms like Prochlorococcus and Pelagibacter. Some of the organisms involved in the nitrogen cycle are key, but their abundance is relatively small – orders of magnitude less than the organisms studied by the people who have been doing metagenomics. An organism that has such low abundance and grows in a boom or bust phase probably needs a different evolutionary strategy and may be more affected by things like population sweeps.

What we see is that C. watsonii is highly conserved in DNA sequence, but it does maintain genetic diversity by rearranging its chromosome, so there’s a lot of transposases in this genome.

There’s this other cyanobacterium we discovered: it was a nitrogen fixing cyanobacterium that we assumed was going to be like C. watsonii, but we were able to sequence its genome, and and it lacks photosystem II. This is the first cyanobacterium ever described that lacks the oxygen-evolving apparatus of photosynthesis, and it also lacks carbon fixation. It turns out that its genome was highly conserved as well. We found DNA sequences in the GOS (Global Ocean Sampling) dataset from this genome, and they’re 99% identical. So it appears that the genome sequence conservation is a feature of things that maintain relatively small population sizes.

If you had to change careers today and you could do anything, what would you do?

I threatened to sell Harley parts. Seriously, though, I’m not sure I would change fields because it’s been an exciting place to be in the last ten years, and I think it’s going to continue to be exciting as we change what we can do, particularly with environmental organisms.

What’s your favorite science book?

I would say A Field Guide to Bacteria by Betsey Dyer and An Inconvenient Truth by Gore. These are both good books as they bring science and education together and make it reachable for the public. The field guide is particularly nice because it brings the microbial world into the macroscopic, enabling microbiology and microbial ecology education.

What is something about you that most people don’t know?

I own a ten year old, 3 foot long, blue and gold macaw, named Darwin.


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