Metabolism provides a basis for using first principles of physics, chemistry, and biology to link the biology of individual organisms to the ecology of populations, communities, and ecosystems. Metabolic rate, the rate at which organisms take up, transform, and expend energy and materials, is the most fundamental biological rate. We have developed a quantitative theory for how metabolic rate varies with body size and temperature. Metabolic theory predicts how metabolic rate, by setting the rates of resource uptake from the environment and resource allocation to survival, growth, and reproduction, controls ecological processes at all levels of organization from individuals to the biosphere. Examples include: (1) life history attributes, including devel- opment rate, mortality rate, age at maturity, life span, and population growth rate; (2) population interactions, including carrying capacity, rates of competition and predation, and patterns of species diversity; and (3) ecosystem processes, including rates of biomass production and respiration and patterns of trophic dynamics. Data compiled from the ecological literature strongly support the theoretical predictions. Even- tually, metabolic theory may provide a conceptual foundation for much of ecology, just as genetic theory provides a foundation for much of evolutionary biology.

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Toward a metabolic theory of ecology

This review shows that thermodynamic and kinetic constraints largely prevent large-scale methanogenesis in the open ocean water column. One example of open-ocean methanogenesis involves anoxic digestive tracts and fecal pellet microenvironments; methane released during fecal pellet disaggregation results in the mixed-layer methane maximum. However, the bulk of the methane in the ocean is added by coastal runoff, seeps, hydrothermal vents, decomposing hydrates, and mud volcanoes. Since methane is present in the open ocean at nanomolar concentrations, and since the flux to the atmosphere is small, the ultimate fate of ocean methane additions must be oxidation within the ocean. As indicated in the Introduction and highlighted in Table 3, sources of methane to the ocean water column are poorly quantified. There are only a small number of direct water column methane oxidation rates, so sinks are also poorly quantified. We know that methane oxidation rates are sensitive to ambient methane concentrations, but we have no information on reaction kinetics and only one report of the effect of pressure on methane oxidation. Our perspective on methane sources and the extent of methane oxidation has been changed dramatically by new techniques involving gene probes, determination of isotopically depleted biomarkers, and recent 14C-CH4 measurements showing that methane geochemistry in anoxic basins is dominated by seeps providing fossil methane. The role of anaerobic oxidation of methane has changed from a controversial curiosity to a major sink in anoxic basins and sediments. © 2007 American Chemical Society.

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Oceanic methane biogeochemistry.

Few of us may ever live on the seaor under it, but all of us are mak-ing increasing use of it either as asource of food and other materi-als, or as a dump. As our demandsupon the ocean increase, so doesour need to understand the oceanas an ecosystem. Basic to the un-derstanding of any ecosystem isknowledge of its food web, throughwhich energy and materials flow.(Pomeroy 1974, p. 499)

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Viruses and Nutrient Cycles in the Sea Viruses play critical roles in the structure and function of aquatic food webs

Predation in aquatic microbial food webs is dominated by phagotrophic protists, yet these microorganisms are still understudied compared to bacteria and phytoplankton. In pelagic ecosystems, predaceous protists are ubiquitous, range in size from 2 µm flagellates to >100 µm ciliates and dinoflagellates, and exhibit a wide array of feeding strategies. Their trophic states run the gamut from strictly phagotrophic, to mixotrophic: partly autotrophic and partly phagotrophic, to primarily autotrophic but capable of phagotrophy. Protists are a major source of mortality for both heterotrophic and autotrophic bacteria. They compete with herbivorous meso- and macro-zooplankton for all size classes of phytoplankton. Protist grazing may affect the rate of organic sinking flux from the euphotic zone. Protist excretions are an important source of remineralized nutrients, and of colloidal and dissolved trace metals such as iron, in aquatic systems. Work on predation by protists is being facilitated by methodological advances, e.g., molecular genetic analysis of protistan diversity and application of flow cytometry to study population growth and feeding rates. Examples of new research areas are studies of impact of protistan predation on the community structure of prey assemblages and of chemical communication between predator and prey in microbial food webs.

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Significance of predation by protists in aquatic microbial food webs.

Publisher Summary This chapter explores that the pelagic food chain is mainly linear and short, and there is a relatively close coupling between the primary production and the production of (pelagic) fish in the oceans. It has been realized that pico- and nano-sized phytoplankton (e.g. cyanobacteria) and heterotrophic micro-organisms (heterotrophic bacteria, heterotrophic nanoflagellates and ciliates) play a much larger quantitative role in production and mineralization, respectively, of the phytoplankton than formerly believed. Moreover, as microbial food webs are typically long and primarily based upon regenerated phytoplankton production, microbial production contributes insignificantly to fish production in the oceans. This chapter illustrates the significance of net-phytoplankton blooms to the fisheries production in the ocean, first of all blooms associated with larger-scale physical processes, such as the major upwelling regions and the vernal temperature stratification in temperate waters.

Turbulence, Phytoplankton Cell Size, and the Structure of Pelagic Food Webs

A new extension of digestion theory and re-interpretation of published empirical evidence suggest that the principal pathway of dissolved organic carbon (DOC) from phytoplankton to bacteria is through the byproducts of animal ingestion and digestion rather than via excretion of DOC directly from intact phytoplankton. Simple model calculations reveal that for a substance with diffusion coefficient equalling 10−5 cm2 s−1, excess (over ambient) concentrations of solute in a fecal pellet of typical size (diam. ⩽ 1 mm) are lost rapidly; ⩾ 50% of any excess is diffused out of the pellet within 5 min—even in a stagnant water column and without particle sinking. Reasons for rapid loss and its insensitivity to fluid dynamic conditions are small size of the pelletal reservoir and the sharp concentration gradient between pelletal and ambient concentrations upon pellet release. As a consequence, most solutes initially contained in fecal pellets of zooplankton generally will remain in the 10–100 m thick water layer within which the pellets initially are deposited. Focus on animal-caused organic release over these very short time scales may help to resolve some of the growing paradoxes of DOC standing stocks and fluxes in the upper ocean.

Closing the microbial loop: dissolved carbon pathway to heterotrophic bacteria from incomplete ingestion, digestion and absorption in animals

Chemical-reactor theory recognizes three ideal reactor types: batch reactors, which are filled with reactants, continuously stirred during the reaction, and then emptied of products after a given reaction period; plug-flow reactors (PFR's), in which reactants continuously enter and products continuously exit with no mixing along the flow path; and continuous-flow, stirred-tank reactors (CSTR's), in which reactants continuously enter and products continuously leave a stirred vessel. Performance equations for these reactors, together with kinetic models for simple enzymatic catalysis and microbially mediated (autocatalytic) digestive fermentation, reveal necessary functional relationships among initial concentrations of the limiting food component, gut volume, throughput time or gut holding time, and digestive reaction kinetics. We use these models to suggest optimization constraints for digestion, analogous to those of optimal foraging theory. Two general predictions are possible. To sustain the greatest d...

Modeling animal guts as chemical reactors

of energy and nutrient gain. According to the principles of dynamic programming, a method for formulating and solving optimization problems (Bellman 1957), the entire process is optimized only if digestion follows an optimal path constrained by the food items actually ingested. An animal feeding on a variety of foods should thus exhibit the flexibility to adjust digestion with respect to that range of food types. Conversely, the net rate of gain to an animal lacking such flexibility will be maximized over a restricted set of food types, making it a dietary specialist. To test these general predictions and to formulate more specific ones, we must identify the operating variables for each stage. Many foraging theories exist (e.g., Charnov 1976, Orians and Pearson 1979, Pyke 1984, Schoener 1971), but there are only rudiments of an optimal digestion theory (Milton 1981, Sibly 1981, Taghon 1981, Troyer 1984). Without such a theory, studies of digestive systems (e.g. gut anatomy, histology, or enzymology) tend to be static, piecemeal, and most often nonpredic-

Chemical Reactor Analysis and Optimal DigestionAn optimal digestion theory can be readily derived from basic principles of chemical reactor analysis and design

https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.1991.36.1.0147

Chlorophyll a degradation by Calanus pacificus: Dependence on ingestion rate and digestive acclimation to food resources

We analyze gut architectures of 42 species of marine polychaetes in terms of their anatomically distinct compartments, and quantify differences among guts in terms of ratios of body volume to gut volume, relative compartmental volumes, total gut aspect ratios and compartmental aspect ratios. We use multivariate techniques to classify these polychaetes into 4 groups: carnivores with tubular guts; deposit feeders with tubular guts; deposit feeders with 3 gut compartments; and deposit feeders with 4 or 5 gut compartments. Tubular guts, morphological expressions of plug flow, are common among deposit feeders and may allow relatively rapid ingestion rates and short throughput times. Median gut volume per unit of body volume in deposit feeders (31%) is twice that of carnivores (15%) and ranges up to 83% in one deep-sea species. Deep-sea deposit feeders tend to have relatively larger and longer guts than closely-related nearshore and shelf species. Guts of a number of deep-sea deposit feeders and nearshore and shelf deposit feeders from muddy environments are relatively longer and narrower as body size increases, suggesting that digestive diffusion limitations may be important. Gut volume scales as (body volume)1 while ingestion rate scales as (body volume)0.7. If diet and the chemical kinetics of digestion do not change appreciably, throughput time and thus the extent of digestion of given dietary components therefore must increase as a deposit feeder grows. Digestive processing constrainst may be most important in juveniles of species (especially those species with plug-flow guts) that are deposit feeders as adults.

Deborah L. Penry

Papers

Closing the microbial loop: dissolved carbon pathway to heterotrophic bacteria from incomplete ingestion, digestion and absorption in animals

Modeling animal guts as chemical reactors

Chemical Reactor Analysis and Optimal DigestionAn optimal digestion theory can be readily derived from basic principles of chemical reactor analysis and design

Chlorophyll a degradation by Calanus pacificus: Dependence on ingestion rate and digestive acclimation to food resources

Gut architecture, digestive constraints and feeding ecology of deposit-feeding and carnivorous polychaetes