Advanced studies in biological Oceanography

Ecophysiology (aut-ecology): individual organisms

Population Ecology: population(s)

Community Ecology: entire ecosystem including matter and energy fluxes

Biogeochemistry: the entire earth as ecosystem incl. marine chemistry, geology, sedimentology

By the way of asexual reproduction every individual can produce offspring whilst through sexual reproduction only females can produce eggs and produce offspring

Age distribution: individuals of age x are called cohort e.g. in age distribution of cod

Size distribution: individuals of a certain size make up asizegroup

General observation: many small/young ones, few large/old individuals

Mortality accumulates with age/size class

sometimes mortality rates are highest at young age (e.g. sea turtle and humboldt squid)

Refers to major life-history trade off: either population growth rate (r) or standing biomass (K) can be maximized.

High r, low K: diatoms

low r, high K: kelp

Iteroparity: several reproductive events throughout the livetime of the species (majority of invertebrates, macroalgae, marine vertebrates)

Semelparity: only one reproductive event, then death, terminal investment (some salmon, cephalopods, often >20% weight gains

• impossible to maximize fecundity, longevity, growth, survival

• There are always trade offs that constrain allocation to either function

Periodic: Low parental care, many offspring, mature late (yellow surgeonfish)

Equilibrium: High parental care, few offspring, mature late (sleeper shark)

Opportunistic: Low parental care, few offspring, mature early (Jewetts dwarfgoby)

Network of local populations that are interconected by migration and gene flow

• ballast water of ships

• fouling

• aquaculture

• aquaria trade

fundamental niche: environmental factors that an organism can tolerate -> grpwth/survival determined by abiotic factors

realized niche: including biotic factors like competition and predation -> growth survival determined by abiotic factors and biological interactions

Logistic growth introduces a capacity term (K) that resembles the carrying capacity of the target population in the particular environment

Concept of biocoenosis -> co-occurring species at a location (habitat), which are interacting with one another

-> focus of studies in community ecology is mostly structure/composition and species interactions

-> ecosystem ecology -> energy and matter fluxes

• competition (mythilus and limpets)

• predation (sharks and seals)

• mutualism (clown fish and anemone,coral polyp and endosymbiontic dinoflagellates)

• parsitism (crustaceans living in fish gills/on the skin/Cyanophages infecting synechococcus)

• commensalism (barnacles living on crabs/pilot fish and reef sharks)

-> resources:

• nutrients (plants)

• food (animals)

• settlement space (benthic)

A keystone species is a predatory species that keeps an herbivor from decimating dominating plant species.

e.g. seastars in rocky intertidals

• opportunists can reach higher growth rates than gleaners at the same resource concentrations

• gleaners reach R* quicker than opportunists (R* = resource concentartion level above which net growth is possible)

-> trade off: either reach high maximal growth rates or live in low resource environments

Intraspecific interactions, as individuals of the same species have very similar resource demands

-> sticklebacks with different feeding behavior have different gill rakers, when species with different gill rakers are living together length divides into two extremes (long and short), when in in solitude gill rakers are roughly the same for all

n-dimensional hyperspace with as many dimensions n as there are factors/resources

Many different species live and coexist in a uniform environment

interference competition: direct fighting over resources/territory

apparent competition: indirect competition as two species serve as prey for a predator

Competition is alleviated

The most abundant (primary) producer in an ecosystem e.g. kelp, seagrass, corals, oyster

kelp s eaten by sea urchin

sea urchin is eaten by sea otter

sea otter is eaten by orca (an human)

-> when sea otter population declined due to intense predation sea urchin population grew and decimated kelp (foundational species)

-> hunting ban on sea otter

-> didn’t help because humans intensified cod fishing thereby taking important food source from orca

-> orca intensified predation on sea otter

-> sea otter population declined

-> sea urchin population increased

-> kelp decimated

TA: no effect, CO2 is not a proton donor/acceptor

DIC: increase as pCO2 is part of DIC

pCO2: increase

pH: decrease, CO2 + H2O -> HCO3- + H+

[HCO3-]: increase (for now)

[CO32-]: decrease, CO2 + H2O + CO32- -> 2HCO3-

TA: slight increase, formation of POM

DIC: slight decrease, CO2 is taken up

pCO2: slight decrease, CO2 is taken up

pH: slight increase, CO2 is taken up

[HCO3-]: slight decrease, HCO3- is taken up

[CO32-]: slight increase, pH shifts due to uptake of CO2

(for resoiration it is the exact opposite)

important reactions:

CO2 + H2O -> CH2O + O2

HCO3- + H2O -> CH2O + OH- + O2

CH2O + O2 -> CO2 + H2O

H+ + NO3- + H2O -> NH3 + 2O2

NH4+ -> NH3 + H+

TA: decrease

DIC: decrease

pCO2: slight increase

pH: slight decrease

[HCO3-]: slight decrease

[CO32-]: slight decrease

(for CaCO3 it is the exact opposite)

important reactions:

Ca2+ + 2HCO3- -> CaCO3 + CO2 + H2O

CaCO3 + CO2 + H2O -> Ca2+ + 2HCO3-

106CO2 + 16NO3- + HPO42- + 18H+ + 122H2O

->

(CH2O)106 + (NH3)16 + H3PO4+ 138O2

Primary production ->

Respiration <-

DOM = all OM that passes through a GF/F filter (pore size: 0.7/0.45/0.2µm)

POM = all OM that stays on such a filter

-> DOM combines DOC, DON and DOP

labile (LDOC): minutes - days

semi-labile (SLDOC): weeks - months

semi-refractory (SRDOC): years - centuries

refractory (RDOC): centures - millenia

Sources:

• direct exudation (uptake of excess C)

• viral lysis

• POM degradation

Sinks:

• bacterial consumption/degradation

• aggregation

TEP = transparent exopolymer particles

increases the stickiness of particles

• all organic C which passes through a GF/F filter with 0.7µm

• 90% of DOM is chemically uncharactericed

• DOC is the primary source in the microbial loop

• most of the DOM is old (>100 years) and refractory

• Surface ocean DOC concentrations can vary (70-100 µmol/L), deep ocean conc. are rather stable (40-50 µmol/L)

1:1 up to 15:1

• Diploid organisms

• Sexual Reproduction

• Random Mating with respect to genotype

• Random union of gametes

• Discrete, non-overlapping generations

• Very large populations

• No migration

• No population structure

• No natural selection

• Two alleles

• Identical allele frequences in both sexes

HWE is disturbed by:

• Inbreeding

• Assortative mating

• Migration

• Natural selection

• Population structure

Fixation Index (F):

proportion by which heterozygosity is reduced or increasedrelative to the heterozygosity of a population at HW-equilibrium wiith the same allele frequencies

Typical values are around zero (a little bit higher)

Any location in the genome: gene, single base pair, microsatelite

The variants at a locus (polymorphic when more than one)

Set of alleles possessed by an indvidual (at one locus or several loci)

an organisms observable attribute (morphological, developmental, biochemical, physiological, behavioral)

N_AA: 3

N_aa: 2

N_Aa: 4

f_AA = 3/9 = 0.33

f_aa = 2/9 = 0.22

f_Aa= 4/9 = 0.44

f_Genotype = N_Genotype/N_All

f_A = p = 2N_AA + NAa / 2N = fAA + f_Aa / 2

f_a = q = 1-p

f_A = 0.33 + 0.44 / 2 = 0.55

f_a = 0.22 + 0.44 /2 = 0.44

• Mating strategies

• Dispersal

• Self fertilization

• Mate choice

• It describes the dynamics of genetic variation within a population over time

• It makes several assumptions:

  • Finite population size

  • Non-overlapping generations

  • Random mating

  • Equal fitness

  • No mutation

• helps to understand how genetic diversity changes in anpopulation under different conditions e.g. population size, migration and selection

The number of individuals that would produce the same amount of drift as the observed population

In contrast to the census size

Influenced by:

• change in population size

• Variance in reproductive success (common in marine species)

• Uneven breeding sex ratios (the less frequent sex can be seen as an allelic bottle neck)

-> Mutation

• Drift decreases variability

• Mutation increases variability

Typically 10^-7 - 10^-9

• Most common way to measure population subdivision

• The degree to which random mating (HW) xpectatioins for the frequencies of heterozygotes are not met

• values closer to 0 point towards low levels of subdivision ehile values vloser to 1 point towards higher levels of subdivision

Populations aren’t real, species are commonly continuously distributed

• The non-random association of alleles at two or more loci

• Two homologous chromosomes in diploids(except in the gamets which are haploid)

• Each chromosome has two dentical sister chromatides

• Recombination:

  • Chromosomes exchange short segments

  • happens in the germline during meiosis

• Breaks down with physical distance

20% of maintanance cost reductioin can lead to 100% biomass increase after 10 years

• Release protons into the mitochondrial matrix without ATP production (induced proton leak)

  • to generate heat (brown adipose tissue)

  • to avoid accumulation of oxygen radicals that harm molecules in the cell

• Proton leaks are costly -> substrate is oxidized but no ATP is produced

Fight agains entropy!

• Creating an ordered environment through integuments and epithelia

• However, membranes are not 100% tight, there always is some leakage and transport proteins have to restore order

In order to sustain and regulate crucial parameters in blood or cytosol marine organisms use feedback loops

e.g. body temperature

• Enzymatic reactions are often very sensitive to pH changes (e.g. phosphofructokinase duriing glycolysis)

• to keep homeostasis in changing salinity you need to use ATP

  • Sodium proton exchange (uses Na gradient provided by Na-K-ATPase)

  • Sodium Potassium ATPase (uses ATP)

• Tools to better understand energy fluxes within organisms

• incorporated energy loss during trophic transfer and their variation related to assimilation efficiency (10-80%), physical activity, as well as somatic and reproductive maintainance costs

Energy needed to keep organisms/gonad tissue alive

Through the gills:

• V-H+-ATPase (proton pump)

• Enzyme is located in vesicles that can be transferred into plasma membrane

• soluble adenylyl cyclase (sAC) produces intracellular messenger cAMP (using ATP) -> is induced by HCO3-

• CO2 is transported from the blood into the cell adn converted intoHCO3- by carbonic anhydrase

• The higher the [HCO3-] the higher the sAC activity

• disffusion. most dissolved substances diffuse at speeds of 50µm/s

• typical eukaryotic cells are about 10-20µm in diameter

• compartimentalization of substances

• bufferiing of ATP concnetratioins vi phospagen systems

Proteinbiosynthesis and ion regulation (exceed 50-60% of total energy demand

Not all protein synthesized is retained as growth. The recycling and replacement of damged/ poor quality proteins relative to the amount of protein synthesized gives you the efficiency of protein retention

-> cephalopods: up to 90%

-> teleosts: up to 40%

That also leads to different energy expanditure of protein synthesis

-> cephalopods: 35-51%

-> teleosts: 24-42%

• Abiotic stress e.g. increased pCO2

• most energy used in protein synthesis and ion transport

• protein turnover rate increases with higher stress, body protein content stays the same

• Change in rate of function. (e.g. enzyme activiity, metabolic rate) over 10°C increase in temperature

• typical values. are between 2 and 3 (e.g. 2-3 times higher metabolic rate)

• used as a rough proxy for responses to temperature (makes things comparable)

-> Arrhenius equation (exponental increase)

• Acclimatization: natural, multi-factorial: light, temperature, biotic factors

• Acclimation: artficial: one fcator, i.e. temperature)

• Phenotypic plasticity (physiological features of a given genotype can be flexible, can be regulated in response to outside stimul such as abiotic stress)

• Adaptatioin (different genotypes can evolve, e.g. with mutatioins in DNA that produce a fitness advantage)

-> within a day! (diel thermal cycles)

• expression of different genes

• high mobility group proteins help stabilize other proteins during heat stress (chaperone function)

• Membranes need to be in fluid state

• low temperature amkes membranes stiff, high ttemp. more fluid

• membrane disruption may be a major cause of heat death

• normal fluidity is enabled by homeoviscous adaptation

• a higher degree of unsaturation makes membranes more fluid

• enzymes that catalyze changes in fatty acid composition = desaturases

• very important: delta^9-desaturase incorporates first double bond into stearic/ palmitic acid

• gene expression and protein biosynthesis

• enzyme activities (enzymes can be turned on/off)

• ultrastructural modificatioins: membranes, mitochondria, muscle fibres

• heart and metabolic rates

The acceleration of naturally occuring evolutionary processes to enhance certain traits (climate resilience related)

-> domestication of animals and plants

-> Crisper/Cas genome editing

• mutatoins that happen by chance -> evolutoin

• change in nucleotide sequence that potentially bring advantage

• if advantageous it will increase its frequency in a population

• survival of the fittest; bring about local adaptatioin

• fittest in the sense: the best adapted to teh current environmental pressures

• fittest meaning the one producing the most offspring

• or select ourself

• so in respect to AE - we want to take advantage of sites that already select for higher coral resilience e.g. in terms of thermal tolerance

• conflicting selection pressures

• the movement of alleles from one population to another

• source of genetic diversity

• it matters - in assisted migration, if you want to migrate within their natural range

• so in respect to AE - we ideally want to make sure to have populations conected to spread novel adapted genotypes between populations

• stochastic event

• cause random fluctuations in allele frequencies

• leads to the loss of genetic diversity e.g. bottleneck effect

• can overwhelm natural selection, in particular in small populations

• we can hardly infere and only overcome by a large population size

• ttype of genetic drift

• when a few individuals are geographically isolated and establish a new population

• can result in low genetic or genotypic diversity

• often captive populatioins or nurseries come from a limiited number of founding individuals

• also relevant for AE

• increases homzygosity

• when homozygosity increases lethal alleles may be expressed

• reach a dip in fertility/biological fitness = inbreeding depression

• however, e.g. highly inbred plants often do not show inbreeding depressioin n a later life stage

• not known for corals, if it has inbreeding depressioin, even if we see high inbreeding values and we do not know whether it has a fertility effect

• can be within (very distant population) or between species

• more fit: hybrid vigor

• less fit: outbreeding depression - you bring genes together that do not work well; often observed in the second or third generations

• no indication in corals, but hard to test

1. Induce acclimatization

   • Pre-condition > generations of natural stocks to various environmental conditions

2. Modification of microbial symbiont communities

   • Inoculate early coral life stages with stress tolerant microbial symbionts

3. Selective breeding

   • Select stocks using ambient environment, genetic markers or species ID; Cross Stocks

4. Evolution of Symbiodinium

   • Mutagenesis and selection through experimental evolution; inoculate coral early life stages

Silicification

Building material: Silicium Si4+, iin water as silicic acid, Si(OH)4

Product: Opal, amorphus silica, biogenic siilica (BSi), SiO2*nH2O

Reaction: Si(OH)4 + Si(OH)4 <—> (OH)3Si-O-Si(OH)3 + H2O

Calcificatoin

Bulding material: Calcium, Ca2+ and carbonate, CO32-

Product: Calcium carbonate, CaCO3, aragonite, calcite, high-Mg calcite

Reactions: Ca2+ + CO32- <—> CaCO3

Ca2+ + 2HCO3- <—> CaCO3 + H2O + CO2

By weathering of carbonates and silicates:

CO2 + H2O + CaCO3 -> Ca2+ + 2HCO3

2CO2 + 3H2O + MgSiO3 -> Mg2+ + 2HCO3 + H4SiO4

Global ocean silicification:

240 x 10^12mol Si/yr = 240 Tmol/yr

Global ocean export:

120 x 10^12 mol Si/yr = 120 Tmol/yr

95% are made up by diatoms

• Diatoms

• Silico flagellates

• Radiolaria

• Silicifying sponges

• A parent cell divides and passes down its hypo- and epitheca

• for each a new hypotheca is formed

• thus one doughter cell has the same size of the parent cell while the other one is smaller

• at a certain size limit the smaller cell goes into sexual reproduction

• Hypotheca (smaller) and Epitheca (larger)

Surface

• Most of the ocean has small amounts (0-15µmol)

• Higher concentratoins in Arctic (20-40µmol) and Southern Ocean (up to 75µmol)

Deep Ocean

• increase with the THC (Ocean conveyor belt)

  • Low in North Atlantic, high in North Pacific

Dissoluton of biogenic silica is slow compared to remineralization of organic matter -> SiO2 shows more curvature

Opal export is high in areas of high surface layer silicic acid concentrations -> Southern Ocean

• Opal accumulatioin in sedments is a functoin of export fluxes and dissolution

• Atlantc: low to moderate fluxes, high dissolutioin rates due to low deep water Si(OH)4

• Pacific: Low to high fluxes, lower dissolution rates due to high deep water (Si(OH)4

• Southern Ocean: high fluxes, high deep water Si(OH)4 allow for opal preservation

• Species richness (number of species, abundance is not taken into account)

• Diversity indices

  • Simpson/Shannon-Wiener Index (Combination of species richness and contribution of species)

  • Pielou’s Evenness (Disttributioin of species)

Simpson:

• Robust for small sample szes

• Less sensittive to species richness

• Heavily weighted towards the most abundant species iin the sample

Shannon -Wiener:

• Sensitve to small sample sizes and speciies richness

Local diversity: Alpha diversity

Regional diversity: Gamma diversity

Differenc ebetween local patches: Beta diversity

-> alpha + beta = gamma

Regional diversity:

• Immigratioin

• Species sorting/ Speciation

• Extinction

Local diversity:

• Random extinction

• Local species interactions

• Competition

• Consumption/Predation

• Emigration

• Dispersal from Regional diversity

S increases with increasing extinction rates and decreases with increasing immigration rates

• The point of resource availability where you start having net growth

• When two species compete the one wiith the lower R* usually wins

• Coexistance is only possible through resource partitioining (species having lowest R*for different resources)

Dispersal can mediate competive exclusioin and enhance diversity as local habitats are not closed but connected by dispersal

Four perspectives of species coexistance through dispersal

1. species sorting: species coexist regionally along environmental gradients

2. mass effects: soecies coexist locally by source-sink dynamics

3. patch dynamics: species coexist via a competition-colonization trade-off (better competitors are inferior colonizers and vice versa) -> also relates to the intermediate disturbance hypothesis (max. diversity at medium disturbance)

4. neutral perspective: species are assumed being ecologically similar and coexist by pure stochasticity

• Land/sea use change

• Direct exploitation

• Climate change

• Pollution

• Invasive alien species

(mostly in this order of magnitude from most to least intense)

Ecosystem functions: resource capture, biomass production, decomposition, nutrient recycling)

-> increases with biological diversity (variation in genes, species, functional traits)

Complementary effect:

• Species are limited by different resources -> stable coexistance

• Niche partitioning because each species has lowest R* for a different resource

• Complementarity in resource use

Selection effect:

• Species are limited by the same resource -> Best competitor (with lowest R*) regulates ecosystem functioning

• Competitive exclusion

Above the threshhold of 40% species lost, diversity is equally important than environmental factors for the functioning of ecosystems

Ultimately it is the given set of coexisting species and traits that process. the available resources into the realized productivity which, among others, we consider as ecosystem functioning

-> the lving together of differently named organisms (de Bary, 1879)

————> Infectivity

Coexistence <————-

• deep sea hydrothermal vents

• coral reefs

Phototrophy

Anaerobic respiration

Lithotrophy

-> can enhance/complement the aerobic respiration and fermentation of animalm metabolism

• Trophosome tissue in Riftia pachyptila at hydrothermal vents (16% of animals net weight is bacteria, 10^10-10^11/g cell density)

• Extensive digestive tubules of sea slugs

• Gland of Deshayes in wood-boring bivalves

• Greatly expanded extracellular matrix of high microbial abundance sponges (microbes contribute up to one third of the animals biomass)

• Corals and Zooxanthellae (Sybiodinium sp.)

• Symbionts provide CO2 to the coral host

• Nitrogen-assimilation (recycling of ammonia)

• Carbon-assimilation (“symbiotic heterotrophy”)

• Chemical defenses

• Defense against foreign DNA

• <0.1mm

• BNacteria & Archeae ~ prokaryotes; no nucleus, no organelle

• Eukaryotes: have nucleus and cell organelles (mitochondrium, chloroplast)

• comprise the three domains of life: bacteria. archeae, eukarya

• absence of light

• high pressures. ~1atm/10m

• toxic chemistry (e.g. hydrogen sulfide)

• temperature extremes (0-400°C)

• high inorganic nutrient concentrations

• energy limitation (photo vs. chemosynthetic)

• ~75% of prokaryotic biomass

1. Epipelagic: surface - 200m

2. Mesopelagic: 200-1000m (dim light); water-mass residence times ~ decades

3. Bathypelagic: 1000-4000m; water-mass residence times ~ centuries

4. Abyssopelagic > 4000m

   

• DOM from Plankton

• Bacteria and Archeae break it down into rDOM

• Viruses kill microbes and thereby release DOM (viral shunt)

• >1mg of DOM per litre of seawater

• DOM pool also contains nitrogen, phosphorus, rion

• observable DOM lifetime of 16.000 yrs

• Microbial loopconverts up to 40 Pg C/yr

• small fraction escapes immediate utilization - decomposes slowly and is transported by currentsacross the globe for 1000s of years

• DOM is diversified through enzymatic reactions

• freshly produced DOM is composed of polysaccharides, proteins, lipids, metabolic intermediates and DNA

• deep-sea DOM has high level of molecular diversity, universal structural composition around the globe, low molecular mass (<1000Da)

• minor fraction of DOM compounds is known

• <20.000 molecular farmulae have been identified with FTICR-MS

  

mesopelagic ~ 25%

bathypelagic ~ 7%

of the mean prokaryotic abundance of the epipelagic zone

mesopelagic ~ 18%

bathypelagic ~ 2%

of the mean prokaryotic productivity of the epipelagic zone

-> abundance and productiivity decrease with depth

• photoautotrophs

• aerobic anoxygenic phototrophs

• heterotrophs

• mixotrophs

• chemolithoautotrophs

optimal growth rates > 10 MPa (Tolerate pressures as high as 100 MPa

• likely originated from psychrophiles

• mostly bacteria (5 genera)

• first example of piezophiles archaeon in 2009

PA

• taxonomically & functionally diistinct from FA

• larger

• higher uptake and exoenzyme production rates

• copiotrophic lifestyle

• motility genes

• oxygenic, and aerobic anoxygenic photosynthesis, nitrogen fixation, proteorhodopsin based photoheterotrophy, heterotrophy,…

• seasonality in microbial community composition

• free enzyme strategy

FL

• smaller

• non-motile

• temperature & depth drive community composition

• oligotrophs dominate FA community

• heterotrophy, mixotrophy, chemoautotrophy

• attached enzyme strategy

• important players in microbial loop

chemo litho auto trophs

• inorganic carbon fixation

• Calvin cycle, RuBisCo

• nitrogen metabolism

• methane/ammonia-monooxygenase A (FL)

• sulfur metabolism

• methane metabolism

• hydrogen metabolism (PA)

• Co-oxidation (cox) (FL)

• unicellular

• no nucleus

• no complex endomembrane system

• circular genomes

• highly diverse with respect to morphology

• typical size 0.7-4µm

• max. 100µm

• min. 100-300µm

• mydrophobic anschor associated with the lipid membrane

• linked to pseudomurein or methanochondroitin (peptidogycan-like polymere)

1. TACK

2. DPANN

3. Asgard

Six out of 27 proposed archaeal phyla have cultured representatives

Asgard:

• closest to eukaryotes

• conatin eukaryotic sgnature proteins

TACK:

• chemolithotroph

• protein and cellulose degradation

• CO2 fixation

• methanogenesis

DPANN:

• limited genomic and molecular capabilities -> rely on interactions

• Ammonia oxidizing archeae can use cyanate/urea/NH3 and convert them into NO2- (40% of nitrificaton)

• Nitrite oxidizing bacteria use the NO2- and convert it in to NO3- (1% of nitrification and high mortality rate)

• efficient nitrite oxidizers have

1. Nitrification is a prominent biogeochemical process in the dark mesopelagic ocean

2. You get ODZs when anaerobic metabolc processes dominate; anamox and denitrification

• poor ventilation

• high export of OM from productive surface waters -> oxygen consumption through respiratiion

• loss of fixed nitrogen due to denitrification and anammox

Oxygen accumulates as a net balance of simultaneous oxygen production and oxygen consumption by ammonia oxidation

1. uptake of CO2 via photosynthesis

2. export of resulting organic C to the deep sea

3. consists of:

   • Mixing pump

   • Aggregate POC (Gravitational pump)

   • Fecal pellet POC (Gravitational pump)

   • Migrant pump

A) global climate dynamics

B) food security

C) all deep sea life

• 10.2 Pg C/yr export (25% of human CO2 emssions)

  -> we have no idea how much of this is further exported by the BCP

• atmospheric pCO2 would be 230ppm higher without the BCP

• BCP sets the DIC gradient

• BCP has an effect on the oceans oxygen content

  -> 6% change in BCP could explain the oceanic O2 loss

• Single dead phytoplankton cells sink very slowly and contribute little to passive flux

• Marine snow formation via aggregation is a crucial component in flux generation

• Animals contribute to passive flux mainly via fecal pellet fomration, but also as carcasses and via discarded exuviae and feeding structures. These sink “fast” but are more rare then aggregates

Drivers:

• avoidance of optically oriented predators vs. food availability

• organisms target a certain isolumen (depth of a certain light level)

• physiological constraints also important (e.g. hypoxia tolerance)

About 30% od Meso-, Macrozooplankton and Nekton are migrating

The migrating planktonic biomass is 5x the biomass of the human

• Migrations into the mesopelagic (Zooplankton, Nekton) result in the export of carbon and other elements, ontogenetic seasonal migratioins also contribute

• studies estimate that DVM flux is about 1/6 to 1/7 of the gravitational flux

• Local studies find ratios between 0 an 1/1

Attenuation is the reduction of the passive gravitational flux through several processes:

1. microbial activity

2. zooplankton organisms “mining” particles

3. flux feeding

4. particle fragmentatioin (leads to lower sinking speeds)

Phenomena that are larger than individual weather systems or ocean eddies but smakler than global or regional scale

• result from instabilities of the large scale circulation (eddies, filaments

• (Sub)Mesoscale impacts on the biological pump?

  • productivity (PP to fish)

  • export associated with mesoscale features

  • Eddies and the paradox of the plankton

Swirling rotating currents that occur in fluids such as the atmosphere and oceans. They are characterized by circular oor elliptical motion. They form spontaneously through the interactioin of different water masses or the interaction of currents with irregular coastlines or seafloor topography.

Cyclonic eddies:

• anticklockwise rotation on northern hemisphere, clockwise on southern

• sea-level depression and uplifting of isopycnals

Anticyclonic eddies:

• clockwise rotation on northern hemisphere, anticlockwise on southern

• sea-level rise and downward displacement of isopycnals

-> eddies forming at the eastern boundaries often migrate west (earth moves underneath them)

-> both types can be >2 years old

-> eddies are largest closer to the equator, but “no” eddies between 5°N and 5°S

-> eddies can also form in the wake of islands

• extended streaks of water with different properties compared to surrounding water

• upwelling filaments often form at capes

• can lead to downwelling of upwelled nutrients

Nutrient supply and primary productivity also depend on mesoscale dynamics

• mixing at eddy edges and other fronts

• uplifting of pycnocline/nutricline in cyclones

Cyclones are generally more productive, anticyclones less productiive

Zooplankton and fish might aggregate at fronts

• Frontal subduction at eddy edges and other frontal features can lead to rapid export

• Frontal-subductiion pump could contribute 10% to the Biological Carbon Pump

• Anticyclonic modewater eddies are formed as instabilities of subsurface currents

• They are generally very productive

• Different eddies can host different communities, that might even affect their biogeochemistry

• Competetive exclusion principle -> number of species </=. number of resources

• But, many different phytoplankton species co-exist on large scale

• Two species competing for one resource, in a 2d model

Explanations:

• Resource partitioning (in space and time -> different needs)

• Temporal availability (fluctuations)

• Predation and grazing (selective grazing pressures)

• Interactions with physical environment (mixing, currents, turbulence -> heterogenous habitats

stagnation ≠ stability

wild fish stocks are continuously being exploited

• Fishing mortality (F) must be sustainable (F<F_MSY)

• Stocks (B) have to be of sufficient size (B>B_MSY)

  -> Catching more than what grows back = fishing mortality F too high

  -> Stocks are too small (Spawning stock bomass B)

Fish stocks as well as Fish used to be bigger:

• A catch from 70 years ago was very different

Fishing down the food web means to first exploit the largest fish until yields are not lucerative anymore and then move further down to smaller species

• Only 4.7 out of 82 Mio t of aquaculture production are real marine fish

• fish feed is amde from wild capture fish

There are many more trophic levels in the ocean:

• phytoplankton

• copepods

• small fish

• large fish (this alone can include 2-4 trophic levels)

-> energy loss per trophic level is <90%

-> desired aquaculture fish need to be fed with smaller fish

-> efficient aquacultures have a fish-in/fish-out ratio of 3-5/1

-> omnivorous fish can be fed with entirely plant based protein (e.g. pangasius, carp)

• Wild fish stocks need to be heavily overfished for aquaculture to become profitable

• larvae/juvenile fish need to be taken from the wild

• farming other marine organisms like mussels and algae

• Possible MSY catch from healthy stock can be much higher than todays yields -> but the populatioins need to recover first (e.g. herring after 1977)

• Marine protected areas work

• Regulatoin of amateur fishermen take out

• ideally, fish larvae hatch in synchrony wiith their food (phyto-/zooplankton blooms)

• due to warmer winters, spawning happens earlier, leading to mismatch (phytoplankton is more light than temperature dependent)

• high mortality in herrinng larvae as tehre is no food

• less cod

• less harbour porpoise

• less seals

• less seabirds

• more flatfish/sprat

NIS, non-native, alien or exotic species:

-> species that do not necessary cause any impact

Invasive species:

-> NIS which cause significant ecological, economical or health impact

Ecological:

• disrupt ecosystems

• alter biological diversity

• change key pathways in important biogeochemical cycles

• deteroratiion of ecosystem health

Economical:

• threatening jobs and industries due to increased maintenence cost

• reduced efficiency/yield

Health:

• Transmission of pathogens

Possiibiilty for ecological and evolutionary studies:

• high number of natural experiemnts across space and taxa

Propagule pressures:

• number of individuals of one speciies (population level)

• number of individuals of more species (community level)

Colonization pressure

• number of species (community level)

Pathway: route between the source region of a NIS and its location of release (the route)

Vector: the manner in which species are carried along the pathway (the ship)

Intentional:

• food and games

• garden ornamentation

• biocontrol

Unintentional:

• aquaculture

• planes, ships, trains, trucks

Speed of vectors has increased dramatically (e.g. planes, modern ships)

Number of vectors and pathways increased greatly

• Ship ballast

• deliberate release

• unauthorized introduction

• range extensioin

• ship fouling

• aquaculture

• natural dispersal

• recreational boating

• phytoplankton <20µm is responsible for the majority of primary production in the ocean

• phytoplankton exude organic carbon (PER: 5-75%)

• bacteria preferentially utilize released organic carbon

• bacteria are grazed by nanoflagellates (HNF)

• HNF are grazed by microzooplankton

• Microzooplankton enters the food chain

Link:

• Active biomass, 40-70% of living carbon reservoir

• Production of living biomass from dead biomass (DOM & detritus)

• Diverting biomass to higher trophic level

Sink:

• Bacteria are responsible for most of the respiration (organic C into inorganic C)

• Natural major source of CO2

• 3-4 levels in vascular plant based systems on average

• 5 levels in pelagic, plankton based, much higher max chain length (better food source)

• Size classes

  • trrestrial system sspan fewer size classes -> shorter food chains

  • in terrestrial systems, herbivores can be much smaller tha their food

Microbial loop:

• return DIC to grazing chain, system more closed nature

• mixotrophs: same species at different TL simutaneously, hugher number of possible interactions at base of food web

Jelly food-chain:

• span large size and food range -> complexity

More interactions than predator-prey:

• Influence food web

• Symbiosis

• Phycosphere (exsudates)

• Saprotrophy -> external digestive enzymes -> affect nutrient availability

• Mixotrophy: species can serve as 1ary producers or as herbivores

Hterotrophic nanoflagellates:

• food web in food web

• has been underestimated

• can consist of 5 trophic levels themselves

• predator-prey-size-ratio lower than often assumed -> affects energy transfere between trophic levels

Assumption: predator-prey-size-ratio: 100:1 to 10:1

-> studies show that smaller size ratio can fit more trophic interactions into size range of prevelant species -> longer chains

species feed on different trophic levels/along trophic chains of different lengths -> assumed to stabilize the system (prey switching)

• Generalists can also only feed on 1 trophic level

• Herbivores for instance (physiologically constrained to trophic level 1 as food source)

• herbivores often exactly trophic level 1

• Assumption: supresses intermediate consumers -> are excluded from system -> 1 predominant chain prevails -> discrete trophic levels, short chains, omnivory supressed

• Predator feeds on 2 trophic levels, negatively affects intermediate predator by competition as well as predation

• However: only temporary supression of omnivory in real systems

Plankton ecosystem:

• Pyramid of production (90% loss along trophic level)

  • because: turnover rate ~ body size(/TL) -> high PP

• Annual mean bodymass: XXXXXXX: XXX: XXXXXXX (TL 1-3)

Nekton P = 0.000306 PP^1.653

Highly productive systems: high PP, high total NP

• Nekton at TL3: high overall efficiency (only 3TL spanned in food web)

• Low ecological efficiency between individual levels

• Available energy is sufficient, no high efficiency needed

Oligotrophic systems: low PP, low NP

• Nekton at TL4

• Low overall efficiency, higher efficiency between levels (necessary to maintain higher TL at all)

• Total available energy limited

• Energy has to pass more TL before reaching nekton (becuase microbial loop dominates)

• longest chain, shortest chain

• flow based (relative importance of food sources, most informative)

• Gut content analysis

• stable isotopes (need to know signature of prey)

• qPCR (not biased by differential digestion)

• ususally: more easy seperable prey at higher TL

Energy constraint hypothesis

• Discarded, longer food chains in oligotrophic systems (paradox of richness)

Ecosystem size hypothesis

• Large ecosystems sustai long trophic chains, higher TL-max

• Large systems can sustain large predators, which roam larger volumes to meet their energetic requirements

• Top-Down

Productivity space hypothesis

• Large product of size and productivity -> long chains

• Bottom-Up

• Initial assumption: 15N-enrichment constant along TL

• However, narrowing with increasing TL -> can fit more TL in same range of delta-15N-values -> long time underestimation of number of TL determined by stable isotopes

Terrestrial systems:

• primary producers driven by light, water and nutrient competition (shade competitors, extend root system) -> supporting tissues required

  -> polymers recalcitrant for animals, void of nutrients

  -> shorter chains

Pelagic systems:

• Dilute medium, diffusive nutrient transport

  -> small organisms

• less nutrient limitation _> less competition/protection, more nutritious tissue

• longer chains

• Should be highest in oligotrophic systems, contradicting energy constraint hypothesis

• Prevalence of weak links reduces maximal food chain legth

• Ecological efficiency should be higher than 10% to explain fish production (because more TL than previously assumed)

• Break polymeres into smaller subunity (has to be smaller than 500Da to be taken up by cell)

  -> 1Da = 1/12 of the mass of a free 12C isotope

• Hydrolytic extracellular enzymes cleave large organic molecules outside the cell to make them smaller

  • Ectoenzyme: Any enzyme found outside or on the outer surface of a cell

  • Exoenzyme: Any enzyme secreted by a cell into the extracellular medium

E + [S] <—> [ES] -> E + [P]

Affinity Reaction Velocity

V = Rate of substrate conversion -> Vmax x [S] / Km + [S]

• Acceleratted dissolution of silica from diatom frustules after bacterial degradation of organic surface (proteases)

• Bacteria mediated silicon regeneration my thus critically control diatom productivity and the cycling and fate of silicon and carbon in the ocean

-> Uptake and regeneration of nutrients in the photic zone

Marine bacteria:

• consume both organic (e.g. AA) and inorganic (e.g. NH4+) nitrogen

• regenerate ammonium

• compete with autotrophs for nutrients

• can synthesisze amino acids from both inorganic nitrogen (de novo) and combined amino acids

• Ammonium is released during the process of ammonification (=the catabolic breakdown of amino acids); fuels regenerated primary production

• whether ammonium is taken up or released depends on the C:N ratio of organic matter (C:Ns) and the bacterial growth efficiency

The addition of labile carbon (glucose) reduced phytoplankton biomass as a result of stimulated bacterial competition for mineral nutrients

-> Marine bacteria recycle nitrogen but can also be strong competitors for inorganic nutrients

Marine organic matter

• Dissolved OM (DOM) -> <0.7µm

  • High molecular weight -> >1kDa

  • Low molecular weight -> <1kDa

• Particulate OM (POM) -> >0.7µm

• Sugars and amino acids are the major known components of marine OM

• ~90% of DOM are chemically uncharacterized

• Deep-Sea OM contains less known biochemicals than surface OM

• High-molecular Weight (HMW) compounds contain more known biochemicals than Low-Molecular-Weight (LMW) compounds

Fresh DOC is on average younger than deep water DOC

• Deep water DOC is largely very old

• Fresh DOC does not reach the Deep-Sea to a significant degree

BUT: DOC from glaciers is old and bioavailable -> preservation of labile DOC in ice

Bacteria prefere young DOC, but not exclusively

Bacterial growth increased with the addition of freshly produced organic matter, glucose and DFAA(=dissolved free amino acids)

Labile DOC - minutes to days

Semilabile DOC - weeks to months

Semi-Refractory DOC - years to centuries

Refractory DOC - centuries to millennia

• Global ocean inventory: <0.2 GtC

• Labile compunds are present in nM concentrations; e.g. free amino acids, simple surgars

• Although concentrations are low, high fluxes of labile DOM can support a large portion of bacterial growth

• Labile DOC does not accumulate in seawater owing to rapid bacterial tturnover

• Absence/low availability of labile DOC often limits bacterial growth

• Seasonally accumulated surface DOC resistant to surface bacterioplankton

• Removed on timescales of weeks once exported to the mesopelagic

• Dissolved combined neutral sugars (DCNS) enriched in SLDOC

SDOC is more abundant than LDOC (SDOC accumulates)

SDOC can be related to total DOC concentration

Uronic acids (URA) were identified as a major component of combined carbohydrates (CCHOO) (20-40%) -> biomarker

• Global ocea inventroy: 6 Gt C

• Resists rapid bacterial degradation

• Observable in the euphotic zone as the seasonal variability in DOC concentrations

• Largely exported to the upper mesopelagic zone (<500m), where it supports the microbial loop

• Enriched in components of HMW; mainly polysaccharides and polypeptides

• Global ocean inventory: 630 Gt C

• ~40µM refractory DOC in the Ocean

• Important in carbon sequestration

• Radiocarbon ages of 10^2-10^4 years

• chemical composition largely unknown

• Production & removal processes largely unknown

• Microbial utilization leads to the diagenetic transformation of OM

• Labile components are continuously removed

• Larger molecules are enzymatically degraded

A) Increase resilience

-> protect critical habitat areas

-> maintain connectivity/ecosystem functioning

-> Reduce artificial stressors (e.g. fishing)

-> use of ecosystem based management

B) Protect climate refugia (slower changing areas)

-> Climate velocity - speed and direction a species has to move to remain within climate niche

-> Timing of stress - e.g. warming vs. cold water upwelling for coral reefs

-> Current range and present exposure

C) Protect future habitat

-> prioritizing habitats that currently exist and are expected to continue to exist in the future

D) Increase connnectivity (within an MPA network)

-> changes in connectivity are expected (e.g. alterration of circulation and stratification)

-> Both ecological and physical asppects should be taken into account (species transport, movement across life stages)

E) Increase heterogenity

-> protect areas across the full range of climate change impacts, including climate refugia, areas with high climate variability and high exposure areas

F) Reduce other stressors

-> minimize cumulative impacts

G) Other methods

-> dynamic MPAs that can move in space and time

MPAs enhance adjacent fisheries mainly in two ways:

• through increased export of eggs and larvae that eventually augment populations of target species

• through increases in biomass of animals near MPA borders that move into fished areas and are caught as spillover

Indopacific

It is deacreasing

25-40km2 until 2066 if nothing is being done

• Herbivory

• Mussle larval recruitment leading to plant stress and mortality

• Arenicola mounds cause transplant mortality

reduction of harmful bacteria

• thermal sensitivity (80% mortality at 27°C -> heat waves are increasing)

• Breeding of heat tolerant types might be an option

Analysis of a large amount of data representing an entire set of some kind,especially the entire set of molecules, such as proteins, lipids or metabolites in a cell, organ, tissue or organism.

• genomics (genes)

• mRNA (transcriptomics)

• proteins (proteomics)

• metabolites (metabolomics)

• omics refers to a field of study (genomics/proteomics)

• omes adress the objects of study (genome/proteome)

• Goal is the identification and characterization of a mix of mRNA that is present in a specific sample

• The principle is that the abundance of specific mRNA transcripts in a biological sample is a reflection of the expression levels of the corresponding genes

• It is used to associate differences in mRNA mixtures originatiing from different groups of individuals

• In contrast to the genome, the transcriptome is highly variable over time, between cell types and environmental changes

Proteomics provides insight into the role of proteins in a biological system

• A proteome consists of all proteins present in a specific cell type or tissue

• it is highly variable overr time and in between cell types

• it changes in response to changes n the environment

-> expressed proteins and their abundance inform about the function of the cells

Tools:

• Mass spectrometry

• Protein microarrays using capturing agents such as antibodies

Major focuses:

• Identification of proteins and proteins interacting in protein complexes

• Quantification of protein abundances. The abundance of a specific protein is related to its role in cell function

• post translational modfications and environmental interactions impede to predict functions from gene analysis alone

Metaproteomics

1. coverage of the organism depends on the representatiion of that organism in an environmental sample

2. abundance of the protein in the cell

3. methodological factors

The metaproteome informs about the proteins synthesized by a microbial community at the time of sampling

• Calvin-Cycle (Carbon-metabolism) -> represented by RuBisCo-gene (48%)

• very low archaeal representation (surprising considerng the amount of archeae expected in the dark ocean)

• H2-oxidation in O2 deprived areas

• CO-oxidation is an important supplement for heterotrophic MOs in the deep ocean