NPZ Models of Plankton Dynamics: Their Construction, Coupling to Physics, and Application

Nutrient-phytoplankton-zooplankton (NPZ) models have been in use in oceanography for at least three decades, and are still a common research tool. Given the discoveries of the last two decades, particularly concerning the role of bacteria in the plankton, there are questions as to whether NPZ models can still be supported as a useful tool in planktonic research. Here I review the construction of NPZ models, and some of the physical platforms they have been coupled to. I then discuss the applications of NPZ-physical models, and conclude that they still constitute an important and viable research tool, provided that the questions being explored are clearly stated. This revised version was published online in August 2006 with corrections to the Cover Date.     

δC of low-molecular-weight organic acids generated by the hydrous pyrolysis of oil-prone source rocks

Low-molecular-weight (LMW) aqueous organic acids were generated from six oil-prone source rocks under hydrous-pyrolysis conditions. Differences in total organic carbon-normalized acid generation are a function of the initial thermal maturity of the source rock and the oxygen content of the kerogen (OI). Carbon-isotope analyses were used to identify potential generation mechanisms and other chemical reactions that might influence the occurrence of LMW organic acids. The generated LMW acids display increasing ¹³C content as a function of decreasing molecular weight and increasing thermal maturity. The magnitudes of observed isotope fractionations are source-rock dependent. These data are consistent with δ¹³C values of organic acids presented in a field study of the San Joaquin Basin and likely reflect the contributions from alkyl-carbons and carboxyl-carbons with distinct δ¹³C values. The data do not support any particular organic acid generation mechanism. The isotopic trends observed as a function of molecular weight, thermal maturity, and rock type are not supported by either generation mechanisms or destructive decarboxylation. It is therefore proposed that organic acids experience isotopic fractionation during generation consistent with a primary kinetic isotope effect and subsequently undergo an exchange reaction between the carboxyl carbon and dissolved inorganic carbon that significantly influences the carbon isotope composition observed for the entire molecule. Although generation and decarboxylation may influence the δ¹³C values of organic acids, in the hydrous pyrolysis system described, the nondestructive, pH-dependent exchange of carboxyl carbon with inorganic carbon appears to be the most important reaction mechanism controlling the δ¹³C values of the organic acids.     

On the role of soil moisture in daytime evolution of temperatures

This paper explores the relationship between temperature, evaporation and soil moisture using a planetary boundary layer (PBL) model. It focuses on illustrating and quantifying the effect of soil moisture on the evolution of daytime temperatures. A simple convective PBL model coupled with the Penman–Monteith (PM) equation is used to estimate evapotranspiration. Following calibration and sensitivity analysis, the model was used to simulate the relative impact of dry and wet soil moisture conditions on daytime temperatures by changing the surface resistance parameter in the PM equation. It was found that the maximum temperature that can be reached during a day is constrained by the amount of soil moisture and the available net radiation, confirming previously published results. Higher temperatures can be reached with greater net radiation and dry soil moisture conditions. Copyright © 2012 John Wiley & Sons, Ltd.     

Multi-scale permeability estimation for a tropical catchment

Physically based and spatially distributed modelling of catchment hydrology involves the estimation of block or whole-hillslope permeabilities. Invariably these estimates are derived by calibration against rainfall–runoff response. Rarely are these estimates rigorously compared with parameter measurements made at the small scale. This study uses a parametrically simple model, TOPMODEL, and an uncertainty framework to derive permeability at the catchment scale. The utility of expert knowledge of the internal catchment dynamics (i.e. extent of saturated area) in constraining parameter uncertainty is demonstrated. Model-derived estimates are then compared with core-based measurements of permeability appropriately up-scaled. The observed differences between the permeability estimates derived by the two methods might be attributed to the role of intermediate scale features (natural soil pipes). An alternative method of determining block permeabilities at the intermediate or hillslope scale is described. This method uses pulse-wave tests and explicitly incorporates the resultant effects of phenomena such as soil piping and kinematic wave migration. The study aims to highlight issues associated with parameterizing or validating distributed models, rather than to provide a definitive solution. The fact that the permeability distribution within the Borneo study catchment is comparatively simple, assists the comparisons. The field data were collected in terrain covered by equatorial rainforest. Combined field measurement and modelling programmes are rare within such environments. © 1998 John Wiley & Sons, Ltd.     

Physical dynamics controlling variability in nearshore fecal pollution: Fecal indicator bacteria as passive particles

We present results from a 5-h field program (HB06) that took place at California’s Huntington State Beach. We assessed the importance of physical dynamics in controlling fecal indicator bacteria (FIB) concentrations during HB06 using an individual based model including alongshore advection and cross-shore variable horizontal diffusion. The model was parameterized with physical (waves and currents) and bacterial (Escherichia coli and Enterococcus) observations made during HB06. The model captured surfzone FIB dynamics well (average surfzone model skill: 0.84 {E. coli} and 0.52 {Enterococcus}), but fell short of capturing offshore FIB dynamics. Our analyses support the hypothesis that surfzone FIB variability during HB06 was a consequence of southward advection and diffusion of a patch of FIB originating north of the study area. Offshore FIB may have originated from a different, southern, source. Mortality may account for some of the offshore variability not explained by the physical model.     

Reservoir geochemistry of South Pass 61 Field, Gulf of Mexico: compositional heterogeneities reflecting filling history and biodegradation

Cluster analysis of GC data for gasoline and mid-range hydrocarbon ratios from fifty-one South Pass 61 Field oils reveals geochemically similar oil clusters corresponding to geographically coherent groups. Insight into the groupings is obtained from examination of indicators of geochemical processes, e.g., anaerobic biodegradation, aerobic biodegradation and extensive remigration of light ends. Six duplicate samples collected in 1986 and 1992 as well as replicate runs on a single sample showed excellent analytical reproducibility.Subtle but consistent differences in both gasoline and oil-range hydrocarbon maturity indicators are observed between the east, west, and far west flanks of the field, suggesting filling of different segments of the reservoir from different kitchens at slightly different stages of thermal maturity or with slightly different chemical character. The west flank of the salt dome was charged with slightly more thermally mature petroleum than the east flank. The stratigraphically oldest and deepest sand on the far west flank has received the most mature petroleum. Different fluid contacts and GORs are observed in different sands and different fault blocks. The stacked pay geometry of the field and widespread faulting have led to considerable remigration of gas and condensate as observed in other fields in the Gulf of Mexico (Thompson, 1987).Biodegradation varies in severity with depth and reservoir zone, but is frequently overprinted by remigration of light end hydrocarbons. Anaerobic biodegradation by sulfate-reducing bacteria is probably the cause of light to moderate alteration in intermediate depth Pliocene sands which are hydraulically connected to the salt dome (with dissolution of anhydrite from the salt dome providing the sulfate). Widespread late pyrite formation in reservoir sandstones is inferred to represent the ultimate sink for reduced sulfur from sulfate reduction during oil biodegradation. Co-produced water compositions suggest no oxygenated freshwater infusion.     

Flat laminated microbial mat communities

Flat laminated microbial mats are complex microbial ecosystems that inhabit a wide range of environments (e.g., caves, iron springs, thermal springs and pools, salt marshes, hypersaline ponds and lagoons, methane and petroleum seeps, sea mounts, deep sea vents, arctic dry valleys). Their community structure is defined by physical (e.g., light quantity and quality, temperature, density and pressure) and chemical (e.g., oxygen, oxidation/reduction potential, salinity, pH, available electron acceptors and donors, chemical species) parameters as well as species interactions. The main primary producers may be photoautotrophs (e.g., cyanobacteria, purple phototrophs, green phototrophs) or chemolithoautophs (e.g., colorless sulfur oxidizing bacteria). Anaerobic phototrophy may predominate in organic rich environments that support high rates of respiration. These communities are dynamic systems exhibiting both spatial and temporal heterogeneity. They are characterized by steep gradients with microenvironments on the submillimeter scale. Diel oscillations in the physical-chemical profile (e.g., oxygen, hydrogen sulfide, pH) and species distribution are typical for phototroph-dominated communities. Flat laminated microbial mats are often sites of robust biogeochemical cycling. In addition to well-established modes of metabolism for phototrophy (oxygenic and non-oxygenic), respiration (both aerobic and anaerobic), and fermentation, novel energetic pathways have been discovered (e.g., nitrate reduction couple to the oxidation of ammonia, sulfur, or arsenite). The application of culture-independent techniques (e.g., 16S rRNA clonal libraries, metagenomics), continue to expand our understanding of species composition and metabolic functions of these complex ecosystems.