Biogeochemical Cycles
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Francisco P. Chavez

Biogeochemical Cycles

Some of the first principles in biological oceanography are that phytoplankton primary production supports the pelagic and benthic ecosystems and determines the rate of accumulation of organic material in the sediments. The so-called biological "pump" moves the energy harvested from sunlight by phytoplankton to the deep ocean. Phytoplankton, because they exist at the ocean-atmosphere interface, are directly affected by changes in climate. The biological pump, and therefore the biogeochemical cycling of chemical elements, are then also strongly influenced by climate and the large-scale ocean circulation. The global-scale patterns of the primary production-pelagic-benthic-sedimentary coupling support the aforementioned first principles. Coastal regions have higher phytoplankton biomass and production, higher biomass and production of pelagic and benthic heterotrophic organisms, and greater accumulation of organic material in the sediments. Open ocean regions have lower values of all of these properties. Theoretical models have been developed in an attempt to synthesize coastal and open ocean vertical fluxes of primary production, however, models that are consistent with the observations have been difficult to establish. How and how much of the primary production is transferred through the food web as well as vertically and horizontally has been difficult to determine and is still poorly known. Bishop (1989) succinctly described one aspect of the problem: "a major term missing in linking primary production and particulate flux appears to be one describing the consumption of particles by macrozooplankton and other large animals."

Researchers at MBARI hope to contribute to resolving the inconsistencies between theory and observation with studies of the primary production-pelagic-benthic-sedimentary coupling in the waters of Monterey Bay, those in the California Current and beyond. This region is well suited for these studies because of the large dynamic range in primary production. Inshore waters are affected by coastal upwelling and are highly productive. Productivity decreases rapidly as one travels offshore and after several hundred kilometers oligotrophic conditions of the subtropical gyre are found. Complex circulation is found in between these two regions where strong jets and eddies are prevalent. These jets and eddies tend to reoccur in the same general geographic location year after year and therefore there is, significant but coherent alongshore variability in oceanographic conditions. The comparative study of subsurface consequences of the spatial variability in upper ocean productivity should provide valuable insight about the pathways of production export in the ocean.

Over the past several years research groups at MBARI have focused on various aspects of the climate-primary production-pelagic-benthic-sedimentary coupling in Monterey Bay. These include studies of the climate-ocean physics-marine chemistry-primary productivity relationships, composition and flux of marine snow, mid-water biology, benthic community structure and geological/biological coupling. This focus has led to significant advances in each of these fields and we may now be ready to integrate many of these studies in order to develop a more complete view of the system. Our preliminary attempts suggested the need to expand our near-shore work further from shore, both to increase our dynamic range (by providing comparisons between productivity domains) and to track the export of the inshore productivity. Our questions will likely expand from ones like: What are the trophic relationships of the heterotrophic organisms in mid-water and benthic communities? To include others like: What does the biomass and production of mid-water and benthic organisms tell us about the supply of food and how does this relate to primary production above and particulate flux?


We strive for a better understanding of the causes of temporal and spatial variability in phytoplankton biomass, composition and production at meso to large scales, and to relating the variations to climate, ocean variability and upper ocean biogeochemical cycles. Our studies have focused on the meso-scale seasonal coastal upwelling system off Monterey as well as on global large-scale basin-wide ocean circulation. Research in each of these areas is driven by similar hypotheses and questions and they share a set of technological limitations. The scientific rationale and the technological solutions are discussed separately with some obvious overlap.

Coastal Central California 

Some of the questions we seek to answer are: 1) what are the mean and fluctuating components of phytoplankton primary production, biomass and species composition on time scales ranging from days to years; 2) what are the physical, chemical and biological processes responsible for the mean and fluctuating components; 3) what is the role of phytoplankton in the carbon cycle and 4) what is the fate of the primary production?

Phytoplankton have growth and mortality rates on the order of hours to days so a primary focus has been to foster the development of new instruments and systems for continuous, high-frequency observation of the upper ocean pelagic ecosystem. The need for high-frequency observation is especially true in the coastal ocean where variability is much greater than in the open ocean. While high-frequency time series of physical properties are common, concurrent time series of biological and chemical properties are rare. Realizing that advances in ocean sciences are limited by the lack of instrumentation and systems capable of collecting these time series we have established a vigorous developmental program geared at making these observations possible. The strategy of our time series work has been to utilize a combination of shipboard, moored and satellite observations with the long term goal of requiring less of the more expensive shipboard measurements.

Figure 1. 3D contours of temperature (top panel) at 9.5°C and salinity (bottom panel) at 33.75 ppt. This data is from the 1995 Coastal Ocean Processes (CoOP95) cruise that took place in the Monterey Bay between April 18 and May 8, 1995. The outline of the bay can be seen in the upper right corner of each panel. Upwelling is evident in both contours in the bay and along the coast northward. Images by Yafang Su.

The processes determining the spatial distribution of phytoplankton properties have been investigated with a series of meso-scale surveys and with satellite measurements of sea surface temperature. We have access to satellite measurements of ocean color so that physical-biological coupling studies can be expanded beyond our limited meso-scale surveys. With the new research vessel, the WESTERN FLYER, we hope to extend our studies into the California Current and the oligotrophic sub-tropical gyre beyond.

Basin Scale Oceanography

The influence of the large-scale oceanic and atmospheric circulation on the basin-wide distribution of phytoplankton properties has been investigated on extensive cruises through-out the global ocean. The cruises have provided not only a wealth of information on the physical and chemical processes controlling the large-scale distribution but have also provided a platform to test instrumentation for continuous monitoring of surface properties. Questions that we hope to address with the data set include: 1) Are there distinct biogeochemical provinces in the ocean? 2) what are the characteristic bio-optical and food-web signatures of these provinces or ecosystems? 3) what are the physical, chemical and biological processes responsible for the characteristic signatures? and 4) can we quantify the role of phytoplankton in the near-surface carbon and nitrogen cycles?

Partially as a result of our involvement with the large-scale expeditions we have deployed systems and sensors on a few of the moorings of the TOGA-TAO array in the equatorial Pacific. The equatorial Pacific is a region of significant variability in the physical and chemical environment. In sharp contrast the biological variability is not as notable. The biological variability may be linked to variations in atmospheric processes, primarily the deposition of iron-rich dust from the continents. Iron limitation of phytoplankton in the equatorial Pacific has been demonstrated quite clearly using small scale fertilization experiments.

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Last updated: Aug. 19, 2014

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