Publication Summaries

Here I am posting short summaries for my published manuscripts, written for folks who are not scientists (or are not in the same scientific field). My hope is to increase public outreach and education. Please feel free to contact me with any questions. This idea was inspired by Jeff Clements.

Regional patterns in ammonia-oxidizing communities throughout Chukchi Sea waters from the Bering Strait to the Beaufort Sea

Julian Damashek, Kade P. Pettie, Zach W. Brown, Matt M. Mills, Kevin R. Arrigo, and Chris A. Francis. Published in Aquatic Microbial Ecology, 2017.

The Chukchi Sea (west of Alaska) is a shallow and dynamic region of the Arctic Ocean. This region is highly productive – lots of phytoplankton growth and associated animal activity (birds, fish, etc.). Rates of nitrogen (N) cycling processes are very high, and due to how the water moves around the Arctic, N cycling in the Chukchi has impacts on nutrient distributions throughout much of the Arctic Sea – which then affects nutrient distributions of water entering the North Atlantic. However, little is known about many of the important N-cycling microbes, including ammonia oxidizers.

We investigated ammonia-oxidizing archaea (“AOA,” or “Thaumarchaeota“) and ammonia-oxidizing bacteria (“AOB”) in two regions of the Chukchi Sea: (1) the coastal Chukchi Sea, from the Bering Strait along the Alaska coast; and (2) the deeper Beaufort shelf, just north of Alaska, where water depth rapidly increases into the deep central basin of the Arctic Ocean. Ammonia oxidizers live by oxidizing ammonia to nitrite, an important step in the marine N cycle. We determined the abundance of AOA and AOB by measuring the number of their genes and RNA transcripts present in the water. Gene abundance gives an idea of how many of these microbes there are, and RNA transcript abundance gives an idea of how active they are, it least in terms of transcribing genes into messenger RNA transcripts for the specific genes we looked for.

Zach happily collecting some freezing-cold water

Based on previous coastal ocean studies, we anticipated finding high AOA abundance and low AOB abundance, but this was not what we found. In deeper Beaufort shelf waters (off the northern coast of Alaska, closer to the central Arctic Sea), we indeed saw far more AOA genes than AOB genes, as expected. But throughout the shallow and nutrient-rich coastal Chukchi Sea, we found a high number of AOB genes, and found high abundances of a specific AOA clade that is typically abundant only in deep ocean waters.

Ascribing mechanistic causes for these patterns is challenging, but we hypothesized: (1) AOB thrive in Chukchi Sea waters when they get “trapped” by currents at the bottom of the water column, where ammonium builds up over time due to decomposition of dead phytoplankton; and (2) “deep-ocean” microbes were transported into the Chukchi Sea from the north by upwelling currents that bring deep water from the Beaufort Sea into shallower regions. Surprisingly, transcript abundances of different archaeal clades were similar, suggested both types were active: even when transported out of what we think is their “happy zone,” the deep-ocean archaea may still be active – though we don’t know how this translates into growth or biogeochemical impacts.

In all, we found distinct ammonia-oxidizing communities between these two Arctic regions, and our data suggest local physical processes (currents, upwelling, decomposition of organic material) have substantial impacts on microbial populations. There is a lot we still don’t know about ammonia oxidizers in the Chukchi Sea, but this study helped fill out the picture of their population structure and activity across a large section of this part of the ocean.

(photo: Zach Brown)

Variable nitrification rates across environmental gradients in turbid, nutrient-rich waters of San Francisco Bay

Julian Damashek, Karen L. Casciotti, and Chris A. Francis. Published in Estuaries and Coasts, 2016.

My PhD work was predominantly on San Francisco Bay, which is a really fascinating ecosystem and a great place to take samples – it’s really beautiful and you can get off the boat and go get pizza at the end of the day. Compared to other estuaries, relatively little was known about nitrogen (N) cycling in San Francisco Bay, despite this estuary being absolutely loaded with N mostly due to inputs of treated wastewater or runoff from agricultural land: San Francisco Bay both drains a massive, agriculture-rich watershed (including all of the Central Valley) and has over 40 wastewater treatment plants that directly discharge treated wastewater into the bay.

Not a bad office

One of the knowledge gaps I decided to work on was measuring rates of nitrification – the microbial oxidation of ammonium (NH4+) to nitrite and nitrate (NOX) – in the water column. Nitrification is a central step in the N cycle of any ecosystem: it takes N coming from decomposition of organic matter (ammonium) and converts it into the oxidized forms (NOX), which are required for loss processes (“denitrification” and “anammox”) that convert NOX into N2 gas, which then diffuses back into the atmosphere and is therefore lost from the ecosystem. So, nitrification is the key pathway that links inputs and outputs of N in any ecosystem and was an important part of getting a handle on how the high amounts of N in San Francisco Bay were getting recycled (and eventually lost, though we didn’t measure those processes).

We measured nitrification rates by adding small amounts of NH4+ that contained a heavier stable isotope of N: 15N instead of the common 14N. We then let the water incubate for a while and measured how much heavy 15NH4+ got converted into heavy 15NOX over time, by freezing small samples from incubation bottles and then measuring the isotopic value of NOX back in the lab to see how much NOX was 15N vs. 14N.

Isotope methods in the lab. So many sharp needles.

Since this process hadn’t been measured in the San Francisco Bay water column yet, we took samples from across the different regions of the bay and at different depths in the water to try to get a broad picture of nitrification rates across the whole ecosystem. We saw two strong correlations: there were high nitrification rates in waters with high NH4+ concentrations, which were mostly in the Sacramento River, and there were high nitrification rates in deep waters where there were high concentrations of suspended sediment (basically mud in the water).

In general, nitrification rates in San Francisco Bay were higher than in the coastal Pacific Ocean but lower than other N-rich estuaries around the world. By comparing our data with dozens of other studies measuring nitrification in estuaries, we found that nitrification rates were also correlated with NH4+ and/or suspended sediment in many other ecosystems around the globe, suggesting these correlations are general trends in a range of diverse estuaries.

Sunrise, lower Sacramento River. Bagel and coffee not pictured but definitely there