Aquatic Ecology Exam 2

Lectures 5-9

How are fish kills caused in Polymictic tropical floodplain lakes

-Heavy rains lower surface temperatures

of epilimnion:

-Surface waters sink and displace anoxic, hydrogen sulfide-rich

water from the hypolimnion

epilimnion

the uppermost, warmest, and least dense layer of water in a thermally stratified lake, sea, or reservoir

hypolimnion

the dense, bottom-most layer of water in a thermally stratified lake

What is more dense: salt water or freshwater?

-Salt water

-heavier than fresh water and so sinks to the bottom

Salt Wedge estuary

where

freshwater flow is strong enough to overcome tidal mixing

Fjord-type estuary

here there are deep pockets for salt water to accumulate

salt wedge estuary ex

Hudson, Mississippi, Amazon, Columbia

Fjord-type estuary ex

Alaska, Norway, Argentina/Chile

Heat Capacity(cp)

the amount of heat required to change a body's temperature by a given amount, expressed in units of joules per unit weight per Kelvin

heat capacity of liquid water

cp = 4.1855 [J/(g·K)] (15 °C, 101.325 kPa)

How many calories are required to raise 1g of water by 1C

-1 calorie

-1 ‘large’ (nutritional) Calorie (note the uppercase C

= 1000 calories or 1 kcal

What does having high heat capacity mean?

-MUCH solar energy is required to raise the temperature of water.

-Water is buffered against large temperature fluctuations, especially large volumes of water

Why is light important to aquatic organisms?

1. Light is required for photosynthesis

2. Light is needed for animals that use light as a sensory cue (eyes, light sensors)

3. Light HEATS water

Macrophytes

plants big enough to be seen as individuals - rooted and unrooted

i.e plantae

Algae

photoautotrophic protista

Phytoplankton

Algae in open water column

Periphyton

Algae growing on surfaces

cyanobacteria

Photosynthetic bacteria with oxygen synthesis

complex eyes: benefits

-Prey detection

-Predator detection

-Sexual Selection

-Mimicry

-etc

animals with simple eyes

Negative phototaxis – allows diurnal vertical migrations

- into surface waters at night

Euglena

-a genus of single-celled eukaryotic microorganisms that share characteristics of both plants and animals

-Protista with photoreceptive pigment spots

Why is light heating water important?

-high latitude lakes are colder than low latitude (tropical) lakes

-stratification of lakes

Origins of electromagnetic radiation

-Extrasolar: stars, neutron stars, black holes, pulsars, quasars etc.

-Most UV, visible and IR light from Sun

light transmission in water

-can be reflected from water surface

-can penetrate water surface and scatter

Total light penetration

the maximum depth to which solar radiation or visible light can travel before it is completely absorbed and scattered by water molecules, dissolved matter, and suspended particles, leaving total darkness

White water total light penetration

Extreme particulate content

Blackwater total light penetration

High DOC but low particulate content

Clearwater Total light penetration

Low particulate and DOC content

Absorption of total light - Oligotrophic

-nutrient poor = less plankton + detritus

- LESS ABSORPTION OF LIGHT

True or False: Scattering and reflectance by particulates in the water affect ALL light frequencies about the same

True. Blue, green, and red areas of the visible light spectrum are equally affected

Frequency-dependent light penetration in Transparent water

-Water absorbs long-wavelength light more than Short-wavelength light.

-Thus, red light is attenuated very rapidly as it passes through clear water.

Transparent Water

free of particulates, organisms, dissolved organic compounds

Why is open-ocean water blue?

Water that is mostly free of sediment, organisms and dissolved organic compounds is intrinsically blue because blue light penetrates and illuminates much more of the water column.

Consequence 1 of open ocean waters being blue

In dimly-lit waters being red is equivalent to being black

Red coloration

-common in deep water fish that rise to nearer surface at dusk. This phenomenon is rare in freshwater fish:

-freshwater fish that are red usually use it for sexual signaling or for crypsis

Phycoerythrin

an ‘accessory photosynthetic pigment’ in plastids

plastids

organelles where photosynthesis occurs – they include chloroplasts

why are red seaweeds red?

-Phycoerythrin works in conjunction with chlorophyll and belongs to a class of red pigments called: phycobiliproteins

-Phycobiliproteins reflect red light and absorb blue + green light

-This increases photosynthetic efficient at depth where (in transparent water) there is little red light. Also, highly effective in low-light conditions

Which habitats can cryptophytes live in?

freshwater, brackish, marine

Are cryptophytes toxic or non-toxic?

non-toxic

What is the ecological role of cryptophytes?

important food source for diverse predators

Where is the greatest diversity of cryptophyte genera found?

marine habitats

Where do the densest cryptophyte populations often develop in freshwater lakes?

In deep-water layers

What allows cryptophytes to photosynthesize in low-light conditions

Biliprotein light-harvesting complexes that help cryptophytes capture light energy in low-light conditions.

Is red freshwater cyanobacteria toxic or non toxic

often toxic

Planktothrix rubescens

-Temperate latitude lakes: most of the year – live at depth – often at a thermocline between warm epilimnion and colder hypolimnion

-Photosynthesize at depth: often come to surface in fall as waters undergo turnover following surface cooling.

Frequency-dependent penetration: Water rich in phytoplankton

-PHYTOPLANKTON (various protists+ cyanobacteria) and

MACROPHYTES all have chlorophyll a and b and have

oxygenic photosynthesis

-absorbs mostly blue and red so reflects mostly green

Frequency-dependent penetration: Water with high DOC concentration

-Humic compounds (aka tannins or ‘tannic acid’ absorb mostly green and blue light, reflecting red light, and leaving red light to penetrate further

-yields the distinctive reddish coloration of blackwaters-

What domain do viruses belong to?

Viruses do not belong to the 3 domains of life : but a domain ACYTOTA has been suggested (“without cells”)

Viruses

-Non cellular, simple genomes

-Very small (20 – 300) nm (nm = 10-9 m)

-Viruses are DNA or RNA sequences surrounded by a protein shell (capsid) and/or a membranous envelope studded with glycoproteins)

3 defining properties of living organisms

1) Growth

2) Metabolism

3) Heredity via the copying of genetic material and evolution by

natural selection and other mechanisms

Is a virus alive?

-Viruses are not living organisms sensu stricto.

-They are mobile, obligate intracellular parasites of cellular organisms and probably appeared soon after the first cellular life

Do viruses have heredity?

yes, and they are subject to evolution by natural selection (although their genetic material can only be replicated using host resources)

Do viruses have genes?

viral nucleic acids do have genes that code for proteins – for capsid formation and proteins (glycoproteins) that bind to chemicals of their hosts, as well as some enzymes

Do viruses grow?

Viruses do not grow (they are assembled in their final state using host resources) and they do not have metabolism

Phylogenetic reconstructions are hindered by:

1. Lack of fossil record

2. Morphology limited to protein shell/envelope/glycoproteins

3. Viruses exhibit recombination in a manner very different to prokaryotes/eukaryotes

True or False: phylogenies based on DNA or RNA sequence can be readily built?

True

International Committee on Taxonomy of Viruses (ICTV)

hierarchical taxonomy, with Order, Family, Subfamily, Genus, Species

-provides precise standards for describing a viral species.

-But these standards correspond only LOOSELY to those applied to sexually reproducing eukaryotes

True or False: there likely to be a LOT of viral species, most of which are unknown and undescribed

True

viruses in the 1960’s-1980’s

-thought to be present in very low to negligible concentrations in unpolluted freshwaters and sea water

-important ecologically ONLY as pathogens of aquatic animals and plants

electron microscopy

imaging technique that uses a beam of accelerated electrons instead of visible light to examine specimens at the micro- and nanoscale

Virus discovery in 1989

-used electron microscopy, found that 1000 to 10,000,000 times more viruses than previously recorded

-Highest concentrations in a eutrophic lake

-Abundances rise and fall seasonally with nutrient levels

bacteriophages

viruses that infect bacterial cells and cause lysis

how do bacteriophages harm bacteria?

-They spread through populations of bacteria in freshwater and marine environments via the lysogenic cycle, and they can cause massive depletion of bacterial cell numbers via the lytic cycle.

-Bacteriophages are predators of bacteria

How do bacteriophages help bacteria?

-by facilitating transfer of bacterial DNA among bacterial cells – a process called transduction. This form of genetic recombination is important for bacteria to maintain genetic diversity

Transduction

-Transfer of DNA from one bacterium to another via bacteriophages (viral transfer). This facilitates genetic recombination in bacteria

-How does it work? Bacteriophages sometimes carry random bits of

bacterial chromosome following lysis

True or false: DNA sequences indicate that the vast majority of the viral sequences in the ocean are bacteriophages

true, “hundreds of thousands” of species in the oceans

Global Ocean Sampling Expedition

Venter’s entry into metagenomics inspired by voyage of the Beagle

Goal to evaluate the biodiversity of microorganisms in the world’s oceans using a metagenomic approach

Global Ocean Sampling Expedition Methods

1. 2003 – 2005: Sail around the sea in a sailing boat for 2 years (Craig Venter’s hobby) 32,000 nautical miles, 23 countries

2. Filter buckets of seawater. Dry and send to lab.

3. 2005 – 2006: Use shotgun sequencing techniques to evaluate the diversity of nucleic acid in sea water samples

Shotgun sequencing

-developed in 1970’s

-Total DNA in sea water from many sources, amplify by cloning techniques

-Break DNA up into small random sequences

-Look for overlapping segments (contigs)

-Reassemble with high-power computers

-Find diversity of sequences = estimate of species diversity

Global Ocean Sampling Expedition Results

-Dataset of 6.3 billion base pairs of DNA

-91% of DNA sequences not in known databases

-tens of thousands of bacterial genomes – mostly un described

-hundreds of thousands of un described viral “species”

viral biomass abundance

-Viral genomes 26x more common than prokaryotes

-5% of prokaryotes infected with viruses (mostly phages) at a given time

Traditional view

Heterotrophic bacterial density limited by food availability -MOST are decomposers of dead organic matter

Some bacteria predated by protists – especially nannoflagellate

Emerging Vuew

The paradigm shift in the early 2000s:

Bacteriophages regulate bacterial abundance and diversity in the oceans and Freshwaters of the world (in addition to above processes)

Ecological relevance of unexpectedly high bacteriophage density in seas and freshwaters

-Cycles of viral/host abundance resembling Lotka-Volterra models

driven primarily by phage immunity in bacteria

-phages can act like keystone species

what are the 3 ways bacterial genetic recombination occurs?

1. Transduction

2. Transformation

3. Conjugation pilli and exchange of plasmid and chromosomal DNA

viruses contribute to 1 and 2

Transformation

uptake of free fragments of DNA (often floating around due to viral lysis)

recombination

provides variation that allows organisms to respond to changes in the environment, via natural selection

Freshwater viromes

Diverse viral communities in open water and sediments of: lowland lakes, alpine lakes, water-filled tree holes, forest streams, hot springs etc. etc.

Freshwater viral communities

Higher densities than marine viral communities

- But seem to exert less effect on bacterial communities (for unknown reasons)

- Bacteriophage/bacterial dynamics in freshwaters may be more important in freshwater sediment than in open freshwaters

- Viruses in freshwater that infect and kill phytoplankton (mostly small protists) are more important in freshwaters than in the sea

In sea and freshwater Cyanophages are often abundant bc

-cyanophages attack cyanobacteria and can regulate cyanobacterial blooms thereby regulating a dominant component of primary production

-25% of photosynthetic activity in oceans due to the cyanobacterial genus Synechococcus.

-cyanophages also control over dominance of some cyanobacteria

True or false: Many viruses infect freshwater animals and

plants

True

phages

-most abundant “organisms” on earth

-100 million more bacteria in waters of the planet than stars in the universe & 1000 x more viruses than bacteria

Cyanobacteria oxygenic photosynthesis

-only ones among prokaryotes

-water is the 1st electron donor in redox reactions on the thylakoid membrane

-Using aerobic respiration, sugar converted to pyruvate (later released as ATP via cellular respiration). These reactions also occur within the same membranes

True or false: Photosynthesis involves light-driven redox reactions

in thylakoid membrane

-true

-Here reactions occur on chlorophyll and light-harvesting/shunting accessory pigments such as carotenoids and phycobiliproteins

Cyanobacteria: thylakoid

concentric layers adjacent to the cell membrane

Eukaryotic photoautotrophs: thylakoid

-inside chloroplast

-Chloroplasts and other plastids (e.g.l eucoplasts and chromoplasts) in algae and plants contain their own DNA and derive from ancient endosymbiosis of cyanobacteria into eukaryotic cells

Purple and Green sulfur bacteria

Non-oxygenic photosynthesis. Anaerobic respiration. Occur on the surface of H2S-rich mud

Purple

bacteriochlorophyll + carotenoids and other accessory photosynthetic pigments

Green

mainly bacteriochlorophyll

what do Non-oxygenic photoautotrophic bacteria use?

-bacterioclorophyll, not chlorophyll

Most efficient in low-light systems, shallow water, or light from marine hydrothermal vents

do Bacteriochlorophylls absorb at higher wavelengths or lower rates in the infrared

much higher

Green non-sulfur bacteria

-Some found around deep sea hydrothermal vents

- They use the dim glow of the vents as (infrared) light to photosynthesize!

- Some are closely related to mitochondria

Cyanobacteria: the “blue green algae”

NOT TRUE ALGAE!! (which are protists):

- But very similar chlorophyll to that seen in chloroplasts of eukaryotes

-Many species form part of the PHYTOPLANKTON (photosynthetic organisms in open water) and PERIPHYTON (photosynthetic organisms growing on underwater structures)

How do cyanobacteria support life

Cyanobacteria support 20-30% of all photosynthesis on earth

ecological importance of cyanobacteria

1. Important part of the trophic level supporting zooplankton

2. Compete with eukaryotic phytoplankton (algae) for nutrients and light

3. Can cause oxygen supersaturation

4. Populations mainly regulated by nutrient availability, light availability and by cyanophages

Terrestrial cyanobacteria

Form film on rocks, soil. - many can fix nitrogen

cyanobacteria photosynthetic pigments

-Have Chlorophyll A (primary pigment)

-Some have Chlorophyll B (accessory pigment)

-Some have other chlorophylls

-All have carotenoids (function as accessory

pigments, and for UV protection)

What do accessory pigments do?

Harvest light and pass it to chlorophyll A

Complementary chromatic adaptation in cyanobacteria

-In blue-green light: photosynthetic apparatus: accumulate phycoerythrin.

-In red light: accumulate more phycocyanin (a greenish phycobiloprotein)

-LOOK GREEN (in ‘normal’ light) after bathed in red light for a while

-LOOK RED (in ‘normal’ light) after bathed in green light for a while