Marine Microbial Ecology: Ocean Color, Nitrogen Cycling, and Prochlorococcus

What is a scientific model?

A simplified abstract representation of a real system used to explain, understand, or predict it.

Why are mathematical models useful?

They explore systems or processes that are hard to manipulate directly.

What is an empirical model?

A fitted relationship based on observed data; it may predict without explaining mechanisms.

What is a mechanistic model?

A model built from hypothesized processes and interactions that cause the observed pattern.

What can satellites measure in ocean color models?

Remote-sensing reflectance, including blue-to-green light ratios.

What requires water sampling from a ship?

Chlorophyll-a concentration, measured after pigment extraction.

What does Rrs(lambda) equal?

Water-leaving radiance Lw(lambda) divided by downwelling irradiance Ed(lambda).

What does a low blue/green reflectance ratio suggest?

More chlorophyll and phytoplankton; chlorophyll absorbs blue light.

How are ocean color models calibrated?

Measure reflectance and chlorophyll at the same stations, fit a curve, then invert it for satellite pixels.

Why cannot satellites directly detect all marine microbes?

Many groups such as viruses, bacteria, and zooplankton lack a strong distinctive optical signature.

What three processes are modeled for microbial predators?

Encounter, capture, and transfer.

What is the encounter kernel for a swimming grazer?

Pi times detection radius squared times predator swimming speed; volume swept per unit time.

Why can an accurate prediction still be scientifically limited?

An empirical fit may not explain the underlying biological mechanism.

What is a decomposition hot spot?

A location with elevated microbial activity and enhanced biogeochemical cycling.

Why is carrion different from plant litter?

Carrion has a much lower carbon-to-nitrogen ratio and decomposes rapidly.

What is the approximate C:N ratio of a human body?

8:1.

What is the approximate microbial decomposer C:N demand?

20-30:1.

What happens when microbes decompose high-C:N plant litter?

They often immobilize/scavenge inorganic nitrogen from soil.

What happens when low-C:N carrion decomposes?

Strong net nitrogen mineralization and an ammonium pulse.

Define ammonification.

Conversion of organic nitrogen into inorganic ammonium during decomposition.

Why are extracellular peptidases needed?

Large proteins cannot cross cell membranes; enzymes cleave them into peptides and amino acids.

What cellular step releases NH4+?

Intracellular deamination of amino acids.

Define nitrification.

Oxidation of ammonium to nitrite and then nitrate by nitrifying microbes.

What are AOA and AOB?

Ammonia/ammonium-oxidizing archaea and bacteria.

What are NOB?

Nitrite-oxidizing bacteria such as Nitrobacter and Nitrospira.

What is comammox?

Complete ammonia oxidation to nitrate by some Nitrospira.

How does low oxygen affect nitrification?

It limits oxygen-dependent nitrification.

Define denitrification.

Anaerobic respiratory reduction of nitrate toward gaseous nitrogen products including N2O and N2.

Which conditions favor denitrification?

Low oxygen, available nitrate, and organic carbon.

What is microbial coalescence?

Mixing of host-associated microbes with environmental microbes.

What are anoxic microsites?

Small oxygen-depleted soil zones that can persist even when bulk soil is oxygenated.

What does high NH4+, low NO3-, N2O and Clostridia suggest?

Strong mineralization and oxygen limitation, with altered nitrogen cycling.

What is Prochlorococcus?

The world's most abundant photoautotroph.

What is the euphotic zone depth shown?

Approximately 0-200 meters.

What does forward light scatter indicate in flow cytometry?

Cell size.

What does red fluorescence indicate in flow cytometry?

Chlorophyll.

What are high-light and low-light ecotypes?

Prochlorococcus lineages adapted to different light environments and depths.

What is qPCR used for?

Absolute quantification of Prochlorococcus lineages in environmental samples.

What detection limit is given for qPCR?

Approximately 1 cell per mL.

How many lineages could the qPCR method resolve?

Six.

What is a fundamental niche?

Environmental conditions allowing a lineage to grow based on its physiology.

What is a realized niche?

Conditions and locations where it is observed, shaped by factors such as currents and time lags.

Why can currents affect ecotype distribution?

Water movement transports populations away from the conditions where they grew.

What is HOOH?

Hydrogen peroxide, a reactive oxygen compound harmful to Prochlorococcus.

What does catalase do?

Converts hydrogen peroxide into water and oxygen.

Do the Prochlorococcus strains discussed have catalase?

No; the lecture emphasizes absence of catalase.

How can Alteromonas EZ55 help Prochlorococcus?

Its catalase-positive activity removes environmental hydrogen peroxide, protecting Prochlorococcus.

What is the Black Queen Hypothesis?

Adaptive gene loss can make organisms dependent on shared functions supplied by neighbors.

Why might losing catalase be adaptive?

It saves resources, including nitrogen and iron, when neighboring microbes detoxify peroxide.

What is a key low-nutrient adaptation of Prochlorococcus?

Small cells with high surface-area-to-volume ratio for nutrient scavenging.