2012 Bio Ocean

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tritiated thymidine method

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An isotope dilution analysis used to calculate growth rates. In the tritiated thymidine method, the assumption is often made that there is virtually no thymidine present in seawater ( i.e., assumes no isotope dilution).
Or: tritiated thymidine is incorporated into DNA to estimate bacterial growth rates in aquatic environments

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Subsurface chlorophyll maximum SSCM

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maximum concentration of chlorophyll in ocean; often found at a depth between the seasonal pycnocline and permanent halocline

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specific growth rate

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(e.g., 1/N dN/dt) with dimensions of t^-1

increase in cell mass over time

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shade acclimation

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photoautrophs adaption to low light intensity. Two types:

Chlorella-type adaptation: organisms increase their cellular Chl a content with decreasing light with little difference in photosyntheticrates at adapted light intensity between high- and low-light adapted cells)

Cyclotella type adaptation: cellular Chl a content remains unchanged, and only the light-saturated photosynthetic rate varies.

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reverse-diel vertical migration

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migration pattern of phytoplankton. down at night, up during the day.

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Redfield ratio

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The elemental composition (by atoms, not weight!) of O:C:N:P in phytoplankton, and hence, the ratio of long-term nutrient demand and oxygen use during decomposition. The ratio also describes the ratio of C:N:P concentration in oceanic deep water, believed to be controlled by the regeneration of phytoplanktonic nutrients.

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Chemostat

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A culture vessel and pump system designed to maintain steady-state concentrations of most chemical
and biological variables. The dilution rate (D=pumping rate/vessel volume) sets the specific growth rate
of the phytoplankton.

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aerobic respiration

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an energy yielding metabolic process in which either organic compounds or reduced inorganic compounds serve as electron donors, and molecular oxygen is the ultimate electron acceptor.

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anaerobic respiration

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an energy yielding metabolic process that uses an oxidized inorganic compound other than oxygen as the ultimate electron receptor for respiration. The compounds that can so act are sulfates, nitrates, nitrites, and carbonates

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Assimilation number

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a synonym for Pmax in equations relating to photosynthetic rate to light intensity. It is expressed as the rate of photosynthetic carbon assimilation per weight of chlorophyll-specific production.

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assimilatory nitrate reduction

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Nitrate is reduced only for the building of biomolecules (e.g. proteins). Can result in the formation of NO2- .

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autotrophy

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plants and bacteria that utilize CO2 as their sole carbon source.

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heterotrophy

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organisms that depend on external organic matter for maintenance and growth

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BACI

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“Before-After Control-Impact Design.” A type of survey design described by Green (1979) as an optimal impact design.

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biodiversity

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Broad definition: the collection of genomes, species, and ecosystems occurring in a geographically defined region.
Hubbell: species richness and relative abundance in space and time.

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bioirrigation

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movement of porewater and porewater constituents by animal activities

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bioturbation

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movement of sediment particles by animal

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Db: Bioturbation depth

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The depth of sediment mixing due to animal activities

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C:Chl a ratio

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Carbon to Chlorophyll a ratio. Used to convert Chlorophyll a concentrations to estimate amount of carbon. A typical value is 30 but may be >300.
Expressed as: gC
cChl a

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chemolithotrophs

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bacterium living off inorganic compounds: a bacterium that obtains its energy from inorganic compounds containing iron, nitrogen, or sulfur, and not from living on decaying organisms

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chemostat

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a method of growing microbes (autotrophs or heterotrophs) in which the culture vessel volume is held constant while new growth medium is added at a constant rate.

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community

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Mills: groups of potentially interacting populations that occur in a given area and are separable from other such groups by ecological survey
Hubbell: a group of trophically similar, sympatric species that actually or potentially compete in a local area for the same or similar resources.

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compensation depth

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the depth at which the gross primary production equals respiration i.e. the depth at which net primary production is zero.

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compensation light intensity

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the light level at which respiration rate=gross photosynthetic rate

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critical depth

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the depth above which the depth-integrated daily gross primary production equals respiration i.e. the depth above which integrated net primary production equals zero.

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exploitative competition

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resource depletion caused by one organism affects the fitness of another organism

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interference competition

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one organism limits its competitor’s access to the shared resource

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Connell & Slatyer's succession models

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facilitation: early species modify the environment to increase the odds of later species colonizing

inhibition: early species reduce the probability of later species colonizing the area

tolerance: early species neither inhibit nor facilitate the recruitment of later succession species

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conveyor-belt feeder

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a subsurface deposit feeder that feeds at depth and defecates at the sediment surface. This is an example of non-local mixing. Example: the sea cucumber

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denitrification (dissimilatory nitrate reduction)

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utilization of nitrite or nitrate as a terminal electron acceptor for anaerobic respiration and its conversion to gaseous N2O and N2 by heterotrophic, generally facultative, anaerobic bacteria.

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diazotrophy

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bacteria and archaea that can fix atmospheric nitrogen and convert it to a more usable form such as ammonia. They are therefore able to grow without an external source of fixed nitrogen.

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diel vertical migration

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a commonly observed pattern of migration of zooplankton: up at night, down during the day. Opposite for phytoplankton.

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Diversity indices

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describe the number of species in a local area and their relative abundances
alpha indices: Fisher's log-series: Gini-Simpson, Hubbell's theta, Pielou’s J’,
Sanders-Hurlbert E(Sn): a diversity index sensitive to richness and evenness. The “expected number of species.” INSERT EQUATION HERE

Shannon’s H: a diversity index sensitive to richness and evenness. INSERT EQUATION HERE

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Droop, Michaelis-Menten & Ivlev functions to couple nutrients-phytoplankton and zooplankton

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a two-parameter equation describing the relationship between specific growth rate, the cell quota, and the minimum cell quota. It is the rate of an enzyme reaction as a function of external substrate concentration.

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Ekman depth

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depth of frictional influence determined largely by the balance of friction and Coriolis forces. At Ekman depth, water velocity is exactly opposite that of the surface water direction.

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Ekman spiral

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the clockwise spiral (in the Northern hemisphere) of water velocity with increasing depth.

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Ekman mass transport

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the depth-integrated flow resulting from the Ekman spiral. The net transport is 90 degrees to the right of wind direction in the Northern hemisphere.

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El Niño & ENSO

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a period when upwelled water is warmer than usual due to deepened sea-surface isopycnals.

El Niño Southern Oscillation: an oceanic scale phenomenon which is characterized by weakened easterly winds and deeper isopycnal surfaces on the Eastern boundaries of oceans and at the equatorial divergence. They are associated with increased rainfall on the West Coast and droughts inland.

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euphotic zone

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the top layer of water in an ocean or lake which sunlight can penetrate and in which photosynthesis can occur

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exponential growth equation:

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expresses rate of exponential growth of a species, often as doublings per day. INSERT EQUATION HERE.

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fermentation

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the energy-yielding anaerobic metabolic breakdown of a nutrient molecule, such as glucose, without net oxidation. Fermentation yields lactate, acetic acid, ethanal, or some other simple product.

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food caching

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storage or hoarding of food for later eating during times of limited food availability.

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functional group

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all organisms which use and affect their environment in approximately similar ways

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guild

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a group of species that exploit the same class of environmental resources in a similar way. This term groups species, without regard to taxonomic positions, that overlap significantly in their niche requirements

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Goldberg-Koide equation

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model for bioturbation that models local mixing. A form of advection-diffusion equation used to model movement of sediment constituents such as radioisotope activities.

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gross primary production

net primary production

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production by autotrophs before respiratory costs

gross production by autotrophs minus respiration

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hydrogenotrophy

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the conversion of hydrogen to other compounds for use in metabolism

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intermediate disturbance hypothesis

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increasing predation or disturbance leads to enhanced species diversity by freeing limiting resources for competitively inferior species.

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kairomone

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a chemical that is pertinent to the biology of an organism (organism 1)and that when it contacts an individual of another species (organism 2) evokes in the receiver a behavioral or physiologic response that is adaptively favorable to organism 2 but not to organism 1.

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keystone predation

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A species whose presence and role within an ecosystem has a disproportionate effect on other organisms within the system. A keystone species is often a dominant predator whose removal allows a prey population to explode and often decreases overall diversity.

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Lasker’s stable ocean hypothesis:

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one of several hypotheses within larval fish ecology that attempts to explain recruitment variability.
“When tranquil ocean conditions occur in upwelling systems, the water column becomes stratified in layers that concentrate larvae and plankton, which increases successful larval feeding, which increases larval recruitment and contributes to year class strength.”

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Liebig’s law of the minimum

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maximum population size, yield, or growth rate is controlled by a single, limiting factor. i.e. growth is controlled by one nutrient at a time

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non-local mixing

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benthic animal activities that displace particles distances greater than the scale over which the concentration of a tracer changes substantially

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Lotka-Volterra competition model

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a paired, six-parameter equation that describe competition between pairs of species. INSERT EQUATION HERE
(r, K, interspecific competition coefficient {alpha}) Lotka-Euler equation and net replacement rate (Ro)

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macrofauna

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those benthic organisms whose typical adult cross-section is larger than 1 mm.

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meiofauna

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a subset of benthic fauna which is operationally defined as those organisms whose typical size allows them to be retained on a 63-i m mesh sieve but pass through a 500-i m (1 mm) mesh sieve.

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microphytobenthos

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small, unicellular sediment-associated photoautotrophs (dominated by pennate diatoms)

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new production

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that fraction of production which can be coupled to nutrient inputs outside the system of interest. Operationally, new production is often coupled to nitrogen uptake.

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niche (at least 2 meanings)

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Elton: the function performed by a species in a community
Hutchinson: a set of points, each one of which defines a possible set of environmental values permitting a species to live

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oligotrophic

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area or water with low fertility; area of low nutrient loading

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ordination

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a large variety of multivariate statistical procedures for analyzing a multidimensional swarm of data points in such a way that when this swarm is projected onto a two-space, any intrinsic pattern the swarm possesses becomes apparent.

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P vs. I [P vs. E] curves

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photosynthetic rate (ordinate) vs. light intensity (abscissa)

The initial slope, á, is controlled by the light
reactions of photosynthesis and the asymptote, or assimilation number is controlled by the dark reactions. The P vs. I curve is often modeled with the 2-parameter Jassby-Platt equation.

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PAR

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photosynthetically available radiation. The quantity of light in those wavelengths that can be utilized for photosynthesis (400 to 700 nm)

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PDO

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Pacific Decadal Oscillation.

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photoinhibition

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the decline in photosynthetic rate at high light intensities.

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photorespiration

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the light-dependent loss of CO2 and incorporation of O2 into organic compounds resulting from the oxygenase activity of RuBPCO.

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photosynthetic quotient

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the ratio of evolved O2 to CO2 incorporation (by atoms or moles).

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Redfield ratio

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The elemental composition of O:C:N:P in phytoplankton and, hence, the oxygen use during decomposition, It also describes the ratio of C:N:P in oceanic deep water.

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Light attenuation coefficient for PAR (kpar) and optical depth

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1 optical depth = 1/k, where k=the light attenuation coefficient for PAR (Photosynthetically available radiation)

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Light-dark bottle O2 method

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compares the rate of change in O2 bottles held in light (net effects of production and respiration) with those in dark (respiration only) to calculate primary production by difference

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Gaues`s competitive exclusion principle

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states that two species competing for the same resources cannot coexist if other ecological factors are constant

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Exponential growth equation

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dN/dt=μN where μ=specific growth rate

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La Nina

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oscillation event where the usual pressure gradient from the region of high atmospheric pressure in the Southeast Pacific ocean to a region of low pressure in Indonesia becomes higher than average.

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primary vs. secondary production

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primary production is by autotrophs

secondary production: all animal and heterotrophic bacterial production. Earlier, secondary production was restricted to herbivores, and carnivores represented the tertiary production. Note that animal production usually comprises growth of survivors and of those which died between dates of collection and should include sexual products (reproduction).

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Lotka-Euler equation

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The discrete-stage form for calculating r, the instantaneous rate of population increase

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dilution method

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A method of estimating specific growth rate of phytoplankton as well as grazing rates. By slowly adding filtered (plankton-free) seawater to a water sample, you reduce the density of prey, reducing the incidence of predator-prey interactions and thus % prey consumed, allowing population growth rates to increase to their maximal (near exponential) levels.

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in situ florescence

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A method of estimating phytoplankton productivity proposed by lorenzen 1966 whereby water is pumped through a fluoremeter (which measures fluorescence yield). Based on the known nearly linear relationship between fluorescence and chl a, one can then estimate chlorophyll concentration.

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Pearson & Rosenberg SAB diagrams

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Pearson & Rosenberg showed that species, abundance and biomass (SAB) parameters in benthic communities change predictably over a gradient of disturbance over time and space. The overall trend is the replacement of small, opportunistic, shallow-feeding species (e.g.
capitella) with larger, deeper-feeding organisms (e.g conveyor belt feeders) as enrichment/pollution
decreases. Also increasing depth of the redox potential discontinuity (RPD).

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in situ vs simulated in situ incubation

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Alternative ways of conducting O2 or C14 based incubation- estimates of production in incubation bottles. In situ incubations, are conducted in the field with
incubation bottles suspended in the water column, and are the preferred method. Simulated in-situ incubation use controlled lighting conditions outside of the water column to simulate light quality at depth.

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funnel feeder

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a type of deposit feeder. often live in U or J shaped burrows with a funnel extending to the surface. examples are pectinarid and arenicolid polychaetes.

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Lag layer

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since few deposit feeder ingest pellets, the residence time of pellets should be very short. Pellets would be quickly subducted to the zone beneath the zone of deposit feeding to form a lag layer. this quick subduction is due to the selective ingestion of fine particles by deposit feeders.