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This page is work in progress.


We describe here research into the biogeochemical molecular nature of Organic Matter (OM) in the hydrosphere, particularly rivers and oceans. Owing to the complex nature of these molecules and the fact that they represent a dynamic carbon reservoir comparable to that in all living matter on earth, we see this area of research as a vital part of the global carbon cycle in the earth system. Incidentally Organic Matter is often subdivided into two classes based roughly on size: Dissolved and Particulate, hence DOM and POM respectively. Our focus in this research is largely on dissolved organic matter so we often say DOM to save a little typing.

To illustrate further consider this paradox: A tremendous amount of carbon is available in the marine environment from autotrophs fixing carbon from <math>CO_2</math> into sugars and more complex organic molecules via photosynthesis. This is the grocery store the marine food web is built upon. By quantity a mere 1% of that amount of carbon is imported to the specifically coastal marine environment via rivers, and thereupon into the world's oceans. And yet coastal waters are six times more productive than the deep ocean. Something about proximity to land is in play and an obvious hypothesis is that there is more to the terrestrial contribution story than just the 1% carbon. Perhaps nitrogen compounds are important, for example as we see in extreme cases of hypoxic dead zones. The system is complex with many factors involved; upwelling along the continental shelf plays an important role for example. But to keep matters simple for the moment let us state a question:

What is the role, importance, and fate of the terrestrial discharge of carbon and other dissolved/particulate matter in the ocean?

A second formative research question is forensic in nature: If certain organic molecules are reasonably stable over time can they be used to fingerprint the water in which they are dissolved? Can one see a characteristic signature from Point A in water from Point B and thus map the global ocean conveyor system in higher resolution?

Can DOM be used to fingerprint water sources and thereby map with great precision the global hydrological cycle?

This page is intended for general audiences; a more technical discussion is here. We proceed informally with a series of ideas intended to further frame this research.

Think Globally, Think Locally

Arctic GRO (Global Rivers Observatory) 6 Main Rivers

The scope of this research is global in nature: Fingerprinting the carbon in earth's oceans and rivers can be done anywhere and everywhere. However to make practical concrete progress in developing tools and datasets we necessarily focus on specific research problems and therefore specific locations. The focus involves particular standing research questions, networking with scientists and working within established programs under support from funding agencies. This is the practical side of how geoscience research proceeds.

In this case we take as our initial focus an initiative to consider the six primary rivers that contribute to the Arctic Ocean. The organizations involved in the so-called Arctic Global Rivers Observatory are PARTNERS, Arctic-GRO, CADIS, and AON. We will expand on this "six rivers" problem below to include a second course of research concerned with the watersheds of the northeast Pacific Ocean. Together the Arctic GRO and the northeast Pacific will provide more than enough pandemonium and mayhem to keep us perplexed and busy for some time.

The six great rivers that encircle and flow into the Arctic Ocean, by the way, are the Ob', the Kolyma, the Yukon (inhaled into the Arctic through the Bering Strait), the Mackenzie, the Lena and the Yenisey.

Introduction to DOM in the FOTO BGC project

First define acronyms! BGC is shorthand for biogeochemistry, an emergent discipline investigating the relationships between life and the earth substrate on a molecular level. FOTO stands for Fate Of Terrigenous Organics. DOM as noted above is Dissolved Organic Matter, i.e. carbon-based molecules that are small enough to qualify as dissolved in water.

The portmanteau biogeochemistry signals the trend in environmental science towards transdisciplinary -- really 'system' -- research. Consider the question of circum-Arctic rivers: Do they contribute organic molecules to the Arctic ocean? Absolutely. Is this supply of carbon and nitrogen and other elements important to life found in this ocean? If so: how? The pursuit of these questions has been ongoing for decades now, and we continue that process here by bringing together a collection of analytical methods under the inspiration of Dr. Aron Stubbins at Skidaway Institute for Oceanography.

We begin with data specific to the ArcticGRO rivers but we want to carry the story, the tools and the methods over to other datasets, other sample collections. For example we would like to look further into the northeast coast of the Pacific and the question of how terrestrial runoff changes as glaciers recede.

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  • Climate warming is rapidly melting temperate (warm) glaciers thereby changing watershed landscapes along the Northeast Pacific. Search for glacier retreat on YouTube for interesting image comparisons.
  • The chemical composition of water runoff from these watersheds is changing, correspondingly, and this trend will apparently.
  • Coastal waters are highly productive, responsible for as much as one eighth of the earth's annual gross primary production.
  • Estuarine ecosystems depend upon carbon and nutrients in runoff.


  • How will climate change impact the health of the highly productive coastal marine ecosystem?


Standing on the shoreline we notice that the rain coming down; it pools and flows over the ground and through the ground, across terrain to reach tributary streams and rivers. We imagine this water entrains decayed plant and animal matter as it passes. On this wiki we have reproduced some remarks on the mysteries of rainfall. But willy-nilly, eventually this laden water flows from the river back into coastal marine water where it mixes with the salt water.

Let's take next a look at the bottom of the ocean food web. That base is primary producers or autotrophs: Algae that turn carbon dioxide and water and sunlight into sugar and amino acids and protein and so forth, and then the rest of the food web builds from there. Where does the carbon in the sugar come from? From carbon dioxide on hand. Where does this carbon dioxide come from? It dissolves into the ocean directly from the atmosphere. The land runoff isn't involved. In fact the oceanic carbon in sugar exceeds the terrestrial runoff source of carbon by a factor of 100. Why, therefore, be concerned with runoff water if it is at best a supplier of 1% of the sugar?

To examine the question more carefully we can note that 'why be concerned?' is really a question of influence and impact on a system, it is not a question of supply of 'raw' fixed carbon. By analogy: If the workers in an automobile factory all contract a microscopic flu virus, the factory may shut down despite the fact that there are still lots of car parts waiting to be assembled.

Some factual remarks:

  • Nitrogen, sodium, iron, phosphorous, sulfur, magnesium: All important to life processes in addition to carbon, hydrogen and oxygen.
  • The transport and use of chemical energy is locked up in chemical bonds; so carbon-based molecules, not individual carbon atoms, are the important functional units.
  • Carbon-based molecules flowing from land into the ocean -- once possibly considered rather inert and useless -- are now understood to be chemically active.
    • Some of this chemical activity involves light (photo) degredation of these molecules
    • Some organic molecules of terrestrial origin are available for use by autotrophs and heterotrophs

At this point should follow some estimates of carbon mass based on C-bar, R, %Water and D-bar.

At the next point it is important to describe estuarine production < estuarine respiration.

Temperature, pH and Salinity

Three qualities of water deserve first attention since they change drastically as water flows from the land into the sea: temperature, pH, and salinity.

Riverine pH can often be acidic, even very acidic (pH as low as 4) whereas the pH of the ocean is around 8; ocean water is a base. Hence ocean acidification describes a trend, a process that lowers the ocean pH. It does not say that the oceans are acidic.

Second, as water comes off the land it is typically pretty fresh; the salt concentration is down below a couple parts per thousand usually. This will vary from one river to another of course. Out in the ocean the salinity goes up to about 35 ppt. Somewhere in between, as estuary water mixes with ocean water, the salinity varies accordingly. Oceanographers often say that salinity is conservative meaning that chemical or biological processes do not tend to change salt concentration, so that it is predominantly driven by physical mixing. Hence we have a first important measurement tool: You can tell how a given water sample is mixed by measuring its salinity. That is: If you know the salinity of a river end member (the water flowing into but above the area of tidal influence) and you know the salinity of the water out beyond the estuary then you measure a salinity (say in an estuary) and simply interpolate to determine how much of that water is from the ocean and how much from the land. pH it should be noted is not conservative, and is a generally much less stable thing to measure. You can leave a bottle of seawater out for a short amount of time and its pH will change as the microbial processes modify the water chemistry.

Water temperature in rivers is highly variable, rising and falling on a daily basis. In contrast deep ocean water tends to have a stable temperature for longer periods. Furthermore the ocean tends to be at a different average temperature than the rivers flowing in. In Alaska a glacier-fed stream can be near 0 deg Celsius while the ocean nearby is much warmer. Temperature sensors (thermometers combined with data loggers) are fairly cheap and easy to use; so measuring water temperature is a straightforward and common way to characterize what water came from where, or for that matter how big a mass of coherent water is.

This leads to the notion of water mixing and water density, which is determined largely by salinity and to a lesser degree by temperature. Salt water is dense and will tend to sink; fresh water is quite buoyant and so runoff often flows over the top of salt water making a thin fresh water lens. At the salt/fresh interface some sort of mixing will cause the freshwater to become saline and eventually sink. The rate of mixing is often driven by wave action, in turn driven by currents and wind, in turn driven by prevailing atmospheric conditions moderated by land (acting as a wind barrier). So already in a few short sentences we see a complex interdependent relationship between land, sea and air. It is tempting to give up at this point, to say 'this is so complicated and messy how can we ever hope to make progress towards some sort of simplifying set of rules?' Fortunately we have time on our side, so that while moment-to-moment rules may be so complex as to be not worth the bother, time-averaged behavior is well within our capacity to understand.

FerryMon data graphic needed


  • Concerning programs and their websites
  • Concerning the dependency of estuaries on runoff water (autotrophic production less than gross respiration)
    • Frankignoulle, M and Borges, A.V.: European continental shelf as a significant sink for atmospheric carbon dioxide, Global Biogeochemical Cycles, 15(3), 569--576, 2001.
    • Smith, S. V. and Hollibaugh, J. T.: Coastal metabolism and the oceanic organic carbon balance, Rev. Geophys., 31, 75–89, 1993.
    • Cole, J. J. and Caraco, N. F.: Carbon in catchments: connecting terrestrial carbon losses with aquatic metabolism, Mar. Freshwater Res., 52, 101–110, 2001.
    • Cai, W.-J. and Wang, Y.: The chemistry, fluxes, and sources of carbon dioxide in the estuarine waters of the Satilla and Altamaha Rivers, Georgia. Limnol. Oceanogr. 43, 657–668, 1998.
    • Raymond, P.A., Bauer, J.E., and Cole J.J.: Atmospheric CO2 evasion, dissolved inorganic carbon production, and net heterotrophy in the York River estuary. Limnol. Oceanogr, 45, 1707–1717, 2000.

20 Science Questions

To recapitulate from the above discussion I will state 20 scientific questions. It is important to observe at the outset that this is one of may "sets of 20". Another set of 20, for example, might concern the acquisition and analysis of specific types of data. There is no definitive set of 20 questions; rather there are many sets of 20 questions which are interrelated to one another.

  • How will climate change impact the health of the highly productive coastal marine ecosystem?
  • How does a given estuary support its respiration (taken to exceed primary production) using runoff?
  • Concerns conservative mixing and transition to marine coastal water outside of a plume.
  • Concerns the glacial percentage and the corresponding characterization of the water.
  • Concerns a computer aggregate of the answer to 4 across many watersheds.
  • Concerns nutrients from Redfield to iron and the auto/hetero balance.
  • Concerns the build up of the food web above the microbial; salmon and crab populations.

Research Direction: Reduction of complex methods to in situ observation

This section describes in situ sensing technology as data generating method (or shortcut, or proxy) for some facet of intensive DOM-related analysis. The idea is to find a tractable research problem that requires a lot of observations, more than could reasonably be done in the laboratory, where the needed observations can be condensed into a small set of field measurements that can be repeated many times. Suppose for example that three fluorescence excitation / emission pairs are particularly useful for discriminating lignin concentration in estuarine water. One could custom build a dedicated sensor bundle (throw in dissolved oxygen, conductivity, temperature, pH) and map lignin discharge from a set of rivers over the course of a year or two or ten.

Often a bootstrapping approach is taken: Measure something of interest in the labor-intensive laboratory manner where the result is known to be accurate. Measure the same samples with a hypothetical proxy method and (possibly using a model) chart the known result against the hypothetical observations. If you get a high degree of correlation you have an important step towards a new proxy method.

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