April 2009 Archives

Forecast update

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Our copepod forecasts are now appearing in habitat assessment reports produced by the Provincetown Center for Coastal Studies.  The PCCS runs cruises approximately weekly to characterize the prey resource for right whales in Cape Cod Bay.  Our forecasts include their samples from the previous week, coupling them with physical data to project into the upcoming week.

Here are a couple of our forecasts, with comparison to the actual data collected around the same time.

This plot shows a forecast for April 11th, for total copepodid zooplankton in the bay.
SEASCAPEapr11.png

This plot shows the distribution based on data collected on April 10th.
PCCSapr10.png
The higher concentration in the southern part of the bay matches fairly well, though our prediction put this patch further south than where it was observed.  Our forecast also predicted two strong patches near the tip of the cape, which didn't appear in the samples.  Note that the color bars are not quite the same in the two images.

This plot shows our forecast for April 15, for all copepodid zooplankton.
SEASCAPEapr15.jpg
Below is the distribution from the survey on April 14.
PCCSapr14.jpg
The spatial pattern of abundance matched well, with a low concentration in the northern part of Cape Cod Bay, and a higher concentration to the south.  As in the plots above, note that the color bars are not quite the same in the two images.

In both the forecasts and the sampled data, regions of zooplankton abundance were dominated by Calanus finmarchicus at this time of year, marking a shift from earlier in the year, when C.fin. was low, and Pseudocalanus spp. and Centropages spp. were higher.

Carbon in the Ocean

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A few weeks back a paper by Wilson et al. (2009) caught my attention. It was on the contribution of fish to the Inorganic carbon cycle, but busy ensuring my undergraduate degree was official,I glanced at the abstract, thought it was pretty cool, and kept going with other things. Two days ago, Andy put the paper on my desk and I had a second opportunity to look at it.
     The paper, Contribution of Fish to the Marine Inorganic Carbon Cycle, discusses, as its title suggests, the significant contribution to the inorganic carbon made by fish. First, let's quickly touch on why the inorganic carbon cycle is important, then we'll look at how the fish are incorporated into the cycle. This review will assume little to no biogeochemical background, so if you're biogeochemically savy, feel free to jump ahead. If the word biogeochemical scares you, don't worry, it's pretty neat once you get through all those syllables.

Carbon in the Ocean
     The oceans contain about 60 times more carbon than the atmosphere, and as such the oceanic carbon cycle exerts a strong control over atmospheric carbon dioxide, CO2 (Sarmiento and Gruber 2006). Therefore in order to fully understand the changes in atmospheric carbon (which are relevant to global warming, for example), we need to understand what is happening with carbon in the ocean.
      Most of the carbon in the ocean is in the form of dissolved inorganic carbon (DIC) (see below for brief discussion of organic/inorganic carbon). There is organic carbon in the ocean, too: fish, whales, plankton-- any living or dead tissue is organic. Most of the organic carbon, though, is in a dissolved state known as dissolved organic carbon (DOC). The non-dissolved (and non-colloidal) carbon is called particulate organic carbon (POC); POC is made up of living or dead particulate matter. Some key forms of DOC include carbohydrates, sugars, and amino and fatty acids (Valiela 1995). Photosynthesis is perhaps the largest single source of DOC in aerobic (non-oxygen depleted) zones of the ocean (Skirrow 1975). In terms of the world ocean, photosynthesis wins again as the largest contributing mechanism to the creation of organic carbon (Valiela 1995).
     So, what does all this boil down to? Basically, we (people, fish, other heterotrophs) consume organic carbon to generate energy and release inorganic carbon (e.g. CO2) as a byproduct. Plants and other autotrophs can take the inorganic carbon, like CO2 and with the help of sunlight (or a chemical energy source), they make organic carbon. It's all tied together. Carbon is on your dinner plate, it's in the atmosphere, it's in rocks (don't eat that carbon, unless you're a rockbiter); carbon is everywhere.  Now, back to the fish and the Wilson et al. paper.

The Paper
     In order for fish to survive in the salty conditions of the ocean they need to osmoregulate the water they bring into their system. Part of this process involves the secretion of bicarbonate ions HCO3- as the seawater passes through the gut. These bicarbonate ions supersaturate the imbibed seawater and as a result the bicarbonate ions bond with calcium,Ca2+, and less frequently magnesium, Mg2+, cations to form insoluble precipitates (insoluble at the temperature and depth of their production).
     Basically, the chemistry of the fish gut in seawater is just right for solid pieces of calcite, CaCO3, to form in the guts of fish. Why is this cool? They poop it out and now instead of dissolved inorgaic carbon (DIC) in the seawater, we have a solid particulate organic carbon (POC) in the form of calcite. For reasons I won't go into here, the amount of bicarbonate and calcite in the ocean is important to how the carbon cycle (see Chapters 8-9 in Sarmient and Gruber 2006 for a nice explaination).
    The amount of calcite produced per fish (see the Wilson et al. paper for the numbers) was extrapolated to estimates of total fish biomass for all of the worlds oceans. The conservative estimates suggest that 2.7 to 15.4% of total global new CaCO3 production may come from fish intestines! Before this paper, the world was missing out on this piece of the inorganic carbon cycle!
     Wilson et al. take it a step further and look at the amounts of calcite and bicarbonate (as well as carbonate) relative to depth. As a function of pressure and temperature, seawater becomes undersaturated with respect to HCO3- and CO32- at a specific depth. Along the gradient approaching this depth, one would expect to see [HCO3]- and [CO3]2- increase with depth. However, for a long time oceanographers observed higher [HCO3]- and [CO3]2- than predicted based on temperature and pressure alone. This suggested that there was a more soluble form of calcite that was unknown. While Wilson et al. cannot account for all of the [HCO3]- and [CO3]2- observed at higher values, their discovery explains perhaps as much as 26% of the observed phenomenon.
    There's more, but this post is long enough already. The meat (or should I say the carbon) of it is there. Thanks for sticking it out. Comments or questions from all paries, biogeochemically inclined or otherwise, are encouraged.



And for those who got lost in the biogeochemical sweetness above, here's the punchline:
Fish contribute significantly to the carbon cycle in the ocean, more so than previously thought. They poop out a different form of carbon than they take in, which is important for the chemistry of the seawater they inhabit. This discovery means scientists have yet another piece of the puzzle that will help us better understand things like changes in atmospheric CO2,  for example.



Organic vs Inorganic Carbon:
     Any molecules that contain a carbon-carbon bond are organic; all other molecules are inorganic. Taking the definition one step further, an organic compound is "any compound containing carbon and hydrogen, and usually containing carbon-carbon bonds" (Freeman 2002). Heterotrophic organisms consume, in one form or another, organic molecules and remineralize them, releasing energy and producing inorganic molecules as a wasteproduct. Autotrophs use these inorganic compounds (e.g. CO2 or CH4) in a photo- or chemosynthetic process to synthesize food (organic molecules, e.g. glucose, C6H12O6).



works cited
  • Freeman, S. 2002. Biological Science. Pp. 31,G-14. Prentice Hall.
  • Valiela, I. 1995. Marine Ecological Processes, 2nd ed. Pp. 318-390. Springer.
  • Sarmiento, J. L. and N. Gruber. 2006. Ocean Biogeochemical Dynamics. Pp. 318-388.  Princeton University Press.
  • Skirrow, G. 1975. The dissolved gases--carbon dioxide. Pp. 1-192 in J.P. Wiley and G. Skirrow (eds.), Chemical Oceanography, Vol. 2. Academic.
  • Wilson, R.W., Millero, F.J., Taylor, J.R., Walsh, P.J., Christensen, V., Jennings, S. and M. Grosell. 2009. Contribution of Fish to the Marine Inorganic Carbon Cycle. Science 323:359-362.

Forecast 4/6/09

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I created a new hindcast/forecast run. The key inputs are the satellite data (SST & chlorophyll), flow fields, and the PCCS zooplankton data.  The availability of the data changes throughout the  period. Here's what I used:
  • 1/1/2009-3/22/2009--FVCOM 2009 flow fields (high res), assimilating PCCS data
  • 3/22/2009-4/6/2009--climatological FVCOM fields (lower res), no assimilation
  • 4/6/2009-4/15/2009--climatological FVCOM fields, climatological satellite data
I mapped the adult abundances for Calanus, Pseudocalanus, and Centropages for the 10d assimilation windows and uploaded the images to Picassa.  You should be able to click through the figures.  Each figure contains three panels.  The two on the left are the initial conditions for the 10d period.  The leftmost is the initial guess (usually, the output from the previous 10d window).  The second, labeled "post" (for posterior) is the initial condition estimated by the EnKS algorithm.  The panel on the right is at the end of the 10d period.  OK, here are the images:

Calanus:

Pseudocalanus:

Centropages:


Some comments on the figures:
  • If the two initial conditions look the same, there was likely no PCCS cruise in that period
  • If the two initial conditions are similar, then the PCCS data and model agree well in that period
  • If the two initial conditions are wildly different, then the model required significant adjustment to reproduce the data.
We plan to try a few things to try to minimize the "case 3" situations.  In particular, using better parameters from Nick's genetic algorithm work, using BCs from our Gulf of Maine model (esp. for Calanus), and trying different analysis intervals.

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