Monthly Archives: June 2017

Protists, Pathogens, and Fungus… oh my!

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I’m using this blog post as an excuse to take a detour from my usual research and explore the tantalizing world of protists. Studying nothing but microbes and chemical compounds for the past year has given me an excitement for small aquatic critters of all kinds. You are officially about to become a sounding board to the army of thoughts and large confusing taxonomic names that are assaulting my brain. Bear with me and you might find yourself similarly enthralled!

It started with reading a paper on the ecology of Labyrinthulomycetes (Raghukumar 2002) as I was studying the topic of disease in eelgrass. Recently, I have been doing a lot of research on seagrass for classwork and personal interest (“NERD!”). I find seagrass meadows particularly fascinating since they are the most common coastal ecosystem on the planet, sequester 12x more carbon than terrestrial forests, provide habitat for thousands of species, and filter contaminated water in temperate AND tropical coastal/estuarine ecosystems. I think of seagrass meadows as “unsexy” coral reefs (“NERD!”).

Common eelgrass (Zostera marina) is a type of seagrass that often suffers from the parasitic disease called Eelgrass Wasting Disease. Labyrinthula zosterae is a marine protist that causes this disease by destroying the photosynthetic ability of eelgrass leaves through lesion formation. The L. zosterae protist is actually symbiotic if the host is unstressed. As soon as the host becomes stressed (due to any number of factors, such as salinity, temperature, light, etc.) L. zosterae quickly turns pathogenic and produces lesions on the plant. Labyrinthulomycota is the marine protist group under which L. zosterae is found, hence the interest in the Raghukumar paper.

Before we move on, let’s define protists. Protists are any eukaryotic organisms that are not plants, animals, or fungi – they are typically microscopic unicellular organisms. There are four groups that comprise protists: protozoa, slime molds, water molds, and algae. Labyrinthulomycetes are marine slime molds that produce a network of filaments or tubes (“ectoplasmic net”) which they use for movement or nutrient absorption. Interestingly, they are actually more closely related to algae (i.e. diatoms, other phytoplankton, and kelp) than they are to other slime molds.

Enter the chaos. Labyrinthulomycota comprises two groups of marine protists: labyrinthulids (e.g. L. zosterae) and thraustochytrids. Labyrinthulids are typically endobionts (organisms that live within another organism), while thraustochytrids are epibionts (organisms that live on the surface of another organism). My current research is interested in the effects of pharmaceutical contaminants on phytoplankton, so I started thinking about effects of contaminants on other non-algae protists as a trigger for diseases, such as Eelgrass Wasting Disease. My lab-mate, Lyle, who is also an awesomely passionate scientist, is culturing and studying chytrid parasites on phytoplankton. I thought, “Fantastic! A possible chance to study the effects of contaminants on a Labyrinthulomycete! Both chytrids and thraustochytrids are small circular epibionts that have “chytrids” in their name so they must be related… right?”. WRONG.

After a furious onslaught of text messages with [a very patient] Lyle arguing the difference between these two seemingly similar groups of organisms, I finally realized that chytrids are fungi, while thraustochytrids are protists. Now you may be thinking, “Protists and fungi… wait… aren’t those on opposite ends of the tree of life? Why are they both using the word “chytrid” in their names!?”. That’s a question that only taxonomists can answer, but one explanation is that thraustochytrids and labyrinthulids were variously placed under the fungi and protozoa groups before being consolidated into the Labyrinthulomycota protist group. Labyrinthulids look very similar to protozoa and thraustochytrids look very similar to fungi (e.g. chytrids). Similar morphology in combination with a seriously lacking fossil record makes it easy to see how taxonomists could have originally mistaken thraustochytrids for chytrids. It sure fooled me!

(above) Chytrids (left) vs. thraustochytrids (right)
(below) Protozoa (left) vs. labyrinthulids (right)
They look totally different… right?

Now that I understand that Lyle is NOT studying Labyrinthulomycetes, can I still explore the toxicology of protists in my lab? Actually… yes! Even though chytrids are fungi and thraustochytrids are protists, they employ similar life strategies (epibionts) and can be found simultaneously in the environment. For instance, chytrids and thraustochytrids colonize mangrove ecosystems by breaking down pollen spores and fallen leaves (Phuphumirat et al 2016). If they can be found co-occurring in the environment, and if they are hard to tell apart via microscopy, does that mean that Lyle might be unknowingly growing thraustochytrids as well as chytrids in his cultures? This is definitely a possibility, since he often spikes his cultures with actual material from the Columbia River Estuary.

If we have a successful thraustochytrid culture in my lab, I can perform similar toxicology tests as with my phytoplankton. Effects of contaminants on thraustochytrids will give us insight into possible effects of contaminants on other Labyrinthulomycetes, such as Labyrinthulids, which could have ramifications for outbreaks of Eelgrass Wasting Disease. Of course, labyrinthulids are endobionts so their exposure to contaminants would be different. Nevertheless, disease ecology is a wonderful excuse to expand my research interests and enter through the gateway of non-algae protists. The world of Labyrinthulomycete toxicology awaits!

On a closing note, non-algae protists are particularly neglected in the world of microbial research. I can’t help but think that part of the reason scientists bypass these organisms is due to confusing taxonomy and terminology. But don’t let that deter you – all it takes is a few text messages to your scientist friends to start understanding protists in relation to other plants, animals, and fungi. In the meantime, oh, the possibilities that this negligence affords! This could be the beginning of a beautiful project for those of us who know…

 

References

Raghukumar S. (2002). Ecology of marine protists, the Labyrinthulomycetes (Thraustochytrids and Labyrinthulids). European Journal of Protistology 38: 127-145.

Phuphumirat W., Ferguson D. K., Gleason F. H. (2016). The colonization of palynomorphs by chytrids and thraustochytrids during pre–depositional taphonomic processes in tropical mangrove ecosystems. Fungal Ecol. 23: 11–19. 10.1016/j.funeco.2016.05.006

Seafood Processors and DEQ

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Since session started and elected officials have been for the most part confined to the capital I have attended various in district meetings on their behalf. One particular meeting, or series of meetings, were held by Department of Environmental Quality (DEQ) for Seafood Processors who are facing a looming permit change. This is everything I learned about that process;

In February DEQ came and met with the Coastal Caucus to discuss their plans to meet with the actual seafood processors to better understand the challenges facing processors, to discuss DEQ’s need to update permit requirements to reflect the most current water quality standards, and to outline next steps.  Since that time, DEQ and Business Oregon have been working closely with Oregon’s seafood processors to better understand their operational needs, identifying challenges as well as opportunities.

The process of discussion around reviewing the 900J general permit for renewal started in Astoria on April 18th, this permit governs the waste water allowed be discharged after the processors have taken whole sea creatures and turned them into saleable products. DEQ has established an internal project team that has been working to identify and better understand technical concerns to be addressed in this permit renewal, informed in part by the feedback they received during sites visits in 2016. DEQ has reviewed operational variables (such as species processed, discharge volumes, seasonality of operations, treatment technologies) and location variables specific to the receiving water (such as water quality characteristics, pollutant restrictions/limitations, availability of dilution) that must be considered when renewing the permits. These meeting run by members of DEQ’s project team with seafood processors were a concentrated effort to keep those who will be affected by this permit renewal informed of their progress. In addition, a series of public information meetings were held in coastal communities to provide an opportunity for other interested parties and members of the general public to learn about the renewal of the 900J, ask questions, and provide comments that will inform DEQ’s process.

DEQ is now ready to begin the early stages of the public engagement process. After these meetings with permitted facilities DEQ returned to headquarters to review its findings, discuss the issues and challenges that DEQ anticipates, and identify anything they may have overlooked. They are currently preparing to present a permit timeline that will include renewal of the 900J general permit, renewal of expired individual permits, and issuance of new individual permits, where applicable.

DEQ has established an internal project team that has been working to identify and better understand technical concerns to be addressed in this permit renewal, informed in part by the feedback we received during our visits with the processors. Permitting wastewater discharges for seafood processors is complex. Twenty-four seafood processing facilities maintain wastewater discharge permit coverage under either the 900J general or individual National Pollutant Discharge Elimination System permits. No two facilities are alike, and the water bodies receiving wastewater discharges vary greatly.

DEQ staff has compiled wastewater discharge and operations data from seafood processors currently covered by either the expired General Permit or individual NPDES permits.  DEQ has reviewed operational variables (such as species processed, discharge volumes, seasonality of operations, treatment technologies) and location variables specific to the receiving water (such as water quality characteristics, pollutant restrictions/limitations, availability of dilution) that must be considered when renewing the permits.  DEQ plans to continue with some combination of individual and general permit coverage.  This may result in some seafood processors operating on a different type of permit.

Rockfish Research Cruise

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From May 26 to June 2nd I was aboard the NOAA research vessel the Reuben Lasker to help out with NOAA’s Pre-Recruit survey to help with federal fishery research and to collect samples for my own research. Below is a description of the cruise and a daily log of my time on the cruise)

The Pre-Recruit Survey is part of the National Marine Fisheries Service’s (NMFS) effort to improve stock assessment estimates of rockfish recruitment. Let’s see if I can break this down. Federal fisheries scientists (who work for NMFS) are tasked with tracking commercially harvested fish stocks and determining the appropriate amount that fisherman should catch in a given year to ensure the population persists and produces fish in future years. To give fisherman an accurate number, NMFS scientists need to be able to predict how their specific fish populations will change in size from year to year. Most commercially harvested fishes produce prodigious numbers of young every year, with relatively few surviving to adulthood.

  • I’ll define recruits as fish that survive to adulthood
  • I’ll define recruitment as the total number of fish that survive to adulthood from a cohort born in a given year.

Recruitment can be high or low for a given year depending on survival of the early life stages. The Pre-Recruit Survey collects Pre-Recruit rockfishes (a.k.a. young rockfishes that haven’t reached adulthood, but have passed through most of the gauntlet of high mortality associated with the larval stages) so stock assessment scientists can try to get a sneak preview of what recruitment in a given year will look like. Otherwise, stock assessment scientists have to wait several years for these fish to mature to adulthood and then be caught by fishermen (or fishery independent fish surveys) to know how many survived (isn’t it weird that fish have to be caught for scientists to know that they lived? Some groups are working on using remotely operated vehicles and other camera systems to get non-destructive estimates of fish abundance).

I am on this cruise to help sort fishes and will be using juvenile rockfishes collected in the cruise as part of my PhD research. My work aims to give us a better understanding of how environmental conditions (water temperature, food availability, and patterns of water movement) affect survival of the young life stages of rockfish.

 

Sea-date 1 :

Today I boarded the NOAA Research Vessel Reuben Lasker. To get to the ship was quite a trip. I drove from Newport, OR to Eureka, CA where I met up with another NOAA scientist, Paul Chittaro, who was going on the cruise. Paul and I have been on several research cruises together and are pumped for this cruise.

To get to the ship, we had to get picked up at the docks of the Eureka Harbor on a small skiff and cruise out to meet the Lasker. Every other time I’ve been on a research cruise, I’ve met the vessel at the dock, but this year to save time (it takes a full day to bring a large vessel into a port to load and offload passengers) the ship’s commanding officer decided to do an at sea transfer.
The weather and sea conditions were pretty exciting. The waves crossing the bar at the mouth of the harbor were a good 6-10 feet tall and outside the harbor the seas had been whipped up by some storm winds creating crisscrossing swells.

Approaching the RV Lasker from their transfer skiff. Photo: Will Fennie

This made an already exciting boat ride almost too exciting when we got picked up by the Lasker. The Lasker has a device much like a claw that slides down the side of the ship to pick up its skiff. Our boat driver had to maneuver the skiff alongside the Lasker and hold it in position, in choppy seas, so the ship’s claw could grab the skiff and pull it onboard. I am having trouble describing how weird it felt to be in a boat, lifted out of the water, and land on a larger ship, but anyway I’m on board and ready to start catching fishes.

Unfortunately the weather off Eureka wasn’t conducive to sampling, so the chief scientist decided to steam up to Newport Oregon where the weather was better. My first day aboard consisted of eating, and trying to adjust my sleep schedule over to the night shift. Juvenile fishes spend the daytime in deep water and come closer to the surface at night to feed. It is much easier to collect juvenile fish at nighttime because they are concentrated near layers of zooplankton (tiny planktonic animals) that they feed on, so all my work occurs from 9pm to 6am. “Adjusting” my sleep schedule to get used to the night shift really means that I spent most of the first day trying to sleep in my bunk and battling nausea.

 

Sea-date 2:

 

Bucket o’ pyrosomes. We had to rinse the pyrosomes in seawater to clean off any fish or other important organisms from the pyrosomes to figure out what else was in the water. Photo: Will Fennie

We arrived on station just south of Newport this afternoon and began our first night of sampling. Our sampling plan is to run transects of midwater trawls at specific location along Oregon’s coast. We starting sampling our shallow depth/nearshore stations at the beginning of the night, and move offshore to
deeper water as the night progresses. The idea is to get a long-term view of fish communities and see how they vary with distance from shore (bottom depth) and latitude. We use a mid-water trawl to get density estimates of fish and other organisms.
There is pretty high variability in the abundance and composition of our catches from year to year, but this year is pretty weird. Normally we catch lots of juvenile rockfishes (yellowtail, widow, shortbelly,

Sorting fish and krill from the pyrosomes. Looks like we caught some myctophids (lantern fish) and a king of the salmon (the long, skinny, red and silvery fish in the bottom right).

canary, dark blotched, bocaccio, blue, and black rockfishes), Pacific hake, several species of lantern fish, quite a few species of larval flat fishes, and some adult anchovy.
Tonight we mainly caught gelatinous zooplankton and in particular colonial tunicates called pyrosomes. Pyrosomes are typically found in more tropical waters, but with the warm blob in 2015 and the el Niño of 2016, waters off Oregon have been unusually warm and many tropical species are showing up far north or their normal ranges. While pyrosomes are pretty cool to see in the water, they are bioluminescent, they are a real bummer to sort through and have almost broken are net!

 

Sea-date 3:

 

We sampled off of the Columbia River mouth tonight. This is an interesting place because there is a huge source of freshwater that dramatically affects the oceanographic conditions for hundreds of miles. Freshwater is much less dense than salt water, so it sits on top of it (think oil and water, but less dense water and denser water…). As the Columbia River empties into the Pacific Ocean it punches through the surrounding saltwater creating a wedge in the ocean. Oceanic water moving towards shore smashes into this freshwater wedge and sinks beneath it (like a tectonic subduction zone). This concentrates plankton at the interface between these two types of water, which attracts zooplankton, then juvenile fishes, then larger fishes and birds, then marine mammals and so on. The marine mammal and bird observer on the ship said he saw more birds in that area than he has seen almost anywhere else (this observer has been on research cruises for 30+ years all around the globe).

This is Paul who is pumped for our huge catch of pyrosomes. We lost a little enthusiasm when we learned that this catch had ripped the net. (Photo: Will Fennie)

Last year we caught hundreds of rockfishes along this transect, so I was very excited to see what we caught this year. Unfortunately for me, our nearshore station was dominated by adult anchovies, many of which were pregnant females, and there were very few rockfishes. Our second station was so full of pyrosomes that it ripped the net (see attached image of our net almost bursting with pyrosomes). We cancelled our furthest offshore station because we were afraid that we wouldn’t get any fish and needed time to repair the net.

 

Sea-date 4

 

Tonight we sampled off the Tillamook line. We had decent rockfish catches here last year, but like the Columbia River line, pyrosomes dominated this year’s catch. I am starting to get sick of wading through buckets of those things. However, we did collect several rockfishes. I wasn’t quick enough to take a picture of them, but we caught a couple of species: yellowtail rockfish (S. flavidus), shortbelly (Sebastes jordani), bocaccio (S. paucispinis), canary (S. pinniger), and widow rockfish (S. entomelas). At least this cruise is starting to live up to its name (Rockfish Pre-Recruit Survey)!

 

Sea-date 5

 

Tonight was our last night of fishing. We managed to catch quite a few rockfishes! We didn’t collect nearly as many as I was hoping, but certainly better than catching zero. I also saw a salmon shark while we were collecting larval fishes (click the link to
view, sorry it isn’t the best quality video!): https://media.oregonstate.edu/media/t/0_94ypdre8

While we didn’t catch as many rockfish as I hoped for, we still
found some, and it made the cruise worthwhile. I am looking forward to planning the next steps in my research which involve free diving and SCUBA diving to collect juvenile rockfishes that have moved from their offshore life stage (the one being sampled in this cruise) to their nearshore benthic stage where they grow up to become the adults that everyone loves to fish for.

 

 

The tales we tell…

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Stories are a near universal aspect of human existence. They define who we are as a people, illustrate the values we hold as individuals, and provide a common medium by which to communicate the shared human experience. The more that I delve into my work and examine myself, the more I realize how integral storytelling is. On any given day, any single aspect of my work can ultimately be related back to some form of narrative, whether that is looking for a shared narrative or spinning some of my own novel yarns.

One way that we use stories is to connect the public, or some subset of it, to the places, resources, and activities that the Oregon Department of Fish and Wildlife (ODFW) manages on their behalf. By invoking imagery, cultural values, and common experiences associated with the resources that we manage, we are able to better communicate the results of our stewardship and inform the public.

A great example of this is the outreach and education materials that the Marine Reserves Program produces.You can check out some of their work on their website. Some of this material describes the structure of the program or the status of recent monitoring trips while others communicate issues of concern, like Ocean Acidification (OA). They have produced a wonderful the wonderful video below where you can learn about what causes it and how it relates to the Oregon coast and see many of the great people that I work with.

 

Sometimes the stories we tell are not to convey new information but demonstrate involvement and commitment to an issue. This last week, Cat Dayger and I have been editing press releases describing the work of the Ocean Acidification Alliance (alliance). The alliance is the nonprofit we helped launch to elevate OA on the international stage. The press releases are intended to highlight the West Coast regional efforts to address OA in light of the alliance attending the Ocean Conference hosted by the United Nations in New York this upcoming week.

The alliance, as well as California, Oregon, and Washington, are all making voluntary commitments towards Sustainable Development Goal 14.3 to continue their work on global ocean change and OA. The narrative here was not to tell a new story about OA but to keep the spotlight on the issue and communicate that work is underway to understand and address it. Sometimes the issues or status of a topic can be more effectively told not with words or other traditional media but through other means…

Everyone has heard the adage that “a picture is worth a thousand words.” Most people, however, don’t usually bring charts, tables, or maps to mind when they hear this phrase, let alone matrices or databases. But data is essentially the building block, or base-unit, that scientists work with. Every dataset has a story that it can tell and part of what scientists do is to use visual, mathematical, and statistical tools to piece together the plot points of a dataset’s story, identify its main characters, and expose the details hidden beneath the surface.

During my time with ODFW, I have been hard at work creating an interactive toolset to illustrate the story behind  the Ocean Acidification and Hypoxia (OAH) Monitoring Inventory which is one of the main projects I work on. The OAH Monitoring Inventory is a catalog of monitoring assets (buoys, moorings, sensors, etc.) and research projects related to OAH that helps determine where OAH is already being monitored and where it needs to be monitored more. This is very similar to the inventory a restaurant manager takes at the end of a week before ordering more supplies. However, before we can decide where to place new instruments, we must understand the “lay of the land,” as it were, by identifying where assets are located, what they are collecting, and how long have they been there. These are are just a handful of the 70+ odd bits of descriptive information that were recorded. To communicate the complexities of this in a typical narrative would be almost certainly lose some of the finer details of the inventory’s story. Unfortunately, this interactive web app still needs some refining but I hope to be able to share it soon.

Storytelling is an innate practice permeating nearly every facet of our lives. When we are at home playing a game, reading a book, or watching netflix we are ‘listening’ to the tales presented before us. Moving out into the real world to telling stories with friends around a bonfire, tall tales on social media, or drafting a press release we move from consuming to weaving our own tapestries. Framing and polishing a narrative to reflect either how we want to be perceived or best fits the situational context. Medium is yet another facet that can change the experience. Some elements of a story will be more apparent in one format and lost via another. When watching a movie of a popular book your favorite character can take on an entirely new light due to how they are portrayed. With technical information this is no less true. The takeaways one has looking at a table of values will be far different than those represented on a map or plotted in a chart. All of these differences demonstrate how deeply saturated we are in stories and how they color our perceptions and, in turn, our own personal narratives.

I look forward to the opportunity to continue to ‘tell my tales’ here to you and to the audience of my professional work.