Environmental Microbiology - Exam 2

Nitrogen Cycle

process by which nitrogen moves through atmospheric, terrestrial, and marine ecosystems

Nitrogen Reservoirs

Largest: N2 Gas

Smallest: Earth’s crust

Nitrogen Fixation

the conversion of atmospheric N2 gas to ammonia, energy intensive, 2/3 of all fixed nitrogen is performed by microbes

Ammonification

release of ammonia from dead or decaying cells \n Reverse process of assimilation \n Also called mineralization

Ammonium Assimilation

Two possible pathways: \n • High concentrations \n • Ammonium is reversibly incorporated into glutamate (amino acid) \n • Lower concentrations \n • Energy-dependent pathway involving the enzymes glutamine \n synthase and glutamate synthase \n • Most common pathway in soil and aquatic environments where \n NH4+ concentrations are generally low.

Assimilation

incorporation into cellular biomass

Mineralization

release from cellular biomass

Nitrification

Oxidation of ammonium to nitrate

Predominantly aerobic, chemoautotrophic

2 Step process:

Oxidizes NH4+ to NO2- (Nitrosomonas)

Oxidizes NO2- to NO3- (Nitrobacter)

Anammox 

Anaerobic ammonium oxidation

Uses nitrite as the terminal electron acceptor

Produces Nitrogen gas

NH4+ + NO2- → N2 + NO3-

Responsible for 30 to 50% of N loss in oceans

Assimilatory nitrate reduction

Reduction of NO3 to NH4 to incorporate into \n biomass

\n Dissimilatory nitrate reduction to ammonium (DNRA)

oxidation of organics

Denitrification

Reduction of NO3 to N2

nitrate reductase

NO3 to NO2

nitrite reductase

NO2 to NO

nitric oxide reductase

NO to N2O

nitrous oxide reductase

N2O to N2

Sulfur Cycle

Not usually a limiting nutrient but still important!

Comprises 1% of bacterial biomass

Component of amino acids, coenzymes, hormones, and vitamins

Cycled between oxidized state (sulfate) and reduced state (sulfide)

Sulfur Reservoirs

Largest reservoir is the Earth’s crust

Released through volcanic activity

Human influences: fossil fuels, strip mining

Oceans are most significant reservoir of sulfate

Assimilatory Sulfate Reduction (ASR

Sulfur taken into the cell as SO42- and reduced to sulfide to incorporate into cells

Sulfate is most abundant form

Sulfide is toxic to cells

Sulfur mineralization

Release of sulfur from organic molecules

Serine sulfhydrylase: Removes sulfide from cysteine Cysteine sulfhydrylase: Removes sulfide and ammonia from cysteine

Chemoautotrophic sulfur oxidation

Sulfide oxidized to sulfur

Deposited in granules

H2S + 1/2O2 → S0 + H2O

Energy used to fix CO2

Microaerophilic

Some chemoautotrophs can oxidize elemental sulfur to sulfate

Photoautotrophic Sulfur Oxidation

green and purple sulfur bacteria

Fix C with light energy

But oxidize H2S to S0 instead of H2O to O2

Small contribution to primary production BUT important to the sulfur cycle

Remove sulfide

What are the three types of sulfur reduction?

Assimilate sulfate into cells

Sulfur respiration

Dissimilatory sulfate reduction

Assimilate sulfate into cells

both aerobic and anaerobic

Sulfur Respiration

Sulfur (S0) used as terminal electron acceptor

Anaerobic

Not important environmentally

Dissimilatory sulfate reduction

Sulfate as terminal electron acceptor

Produces sulfide

Marine phototrophs in the spring

surface water bloom of eukaryotic algae, actinobacteria and Alphaproteobacteria

Marine phototrophs in the summer

stratification patterns feature *Pelagibacteria,* Gammaproteobacteria

Marine phototrophs in deep stable community

*Pelagibacteria,* Deltaproteobacteria*,* Chloroflexi*, Fibrobacter*

What are some other important phototrophs?

*Prasinophyceae - eukaryote,* Some of the smallest known eukaryotic cells, 1 chloroplast and 1 mitochondrion per cell

*Ostreococcus-* 0.8 um diameter, equivalent size of *Pro*, but 7x the genome size

*Micromonas -* Swims toward light, Tolerates wide range of temperatures

*Bathycoccus -* Nonmotile

What are the three types of planktonic microbes?

phytoplankton: primary producers

zooplankton: larger heterotrophic bacteria

bacterioplankton: microbial populations

Planktonic Food Web

50% of global primary production is aquatic

What is the planktonic food web dependent upon?

inorganic nutrient availability

water temperature

turbidity

What is the viral shunt?

mechanism that prevents organic matter from moving up trophic levels by turning it into dissolved organic material

What is the microbial loop?

trophic pathway where dissolved organic carbon is returned to higher trophic levels via its incorporation into bacterial biomass

Where can heterotrophs be found in lake ecosystems?

Neuston layer

Thermocline

Upper layer of the benthos (bottom)

What is GOS?

Global Ocean Sampling

Expedition where they sailed all over the world collecting samples in order to assess genetic diversity in marine microbial communities and their role in nature.

What are the major components of soil?

Inorganic mineral material (40%)

Organic matter (5%)

Air and water (50%)

Microbes and macro-organisms (5%)

Why is *Trichodesmium* important in the open ocean? What is unique about its physiology?

important for sustaining marine life via release of nitrogen and carbon

It has the ability to fix nitrogen during the day without heterocysts.

Why is the genus *Pelagibacter* important?

Most cells in marine environments are Pelagibacter

Total population size of 2.4 x 1028 cells

What are the different layers of a freshwater system?

* Littoral Zone
* Limnetic Zone
* Profundal Zone
* Benthic Zone

Littoral Zone

* top, near-shore layer of a lake
* shallow
* plenty of sunlight and nutrients
* supports wide variety of plants and animals

Limnetic Zone

* lake’s sunlit surface layer
* where most photosynthesis takes place
* supports phytoplankton and zooplankton, along with freshwater fish

Profundal Zone

* lake’s deep, open-water layer
* too dark for photosynthesis
* water is cooler and contains less dissolved oxygen
* supports fish adapted to these cooler waters

Benthic Zone

* soil and soil organisms that live at the bottom of a lake
* inhabited mostly by decomposers and other organisms that feed on dead and decaying material
* can withstand a low-oxygen environment.

What drives stratification in lakes?

Stratification is driven by temperature or salinity.

What is the thermocline?

middle layer characterized by a steady drop in water temperature, that prevents water mixing between the epilimnion and hypolimnion. Where this layer begins is dependent on the how far down into the water the sun’s rays reach

What is the Epilimnion?

less dense layer of warmer water, that is readily mixed by wind. Oxygen producing plants and algae typically live in this zone

What is the Hypolimnion?

This is the bottom, denser layer of cold water. Low light levels in the hypolimnion prevent growth of aquatic plants and algae.

polymictic mixing pattern

Mix several times per year

amictic mixing pattern

never mixes

monomictic mixing pattern

mixes once per year

Dimitic mixing pattern

mixes 2x per year

Why of all the Great Lakes is Lake Erie the most susceptible to harmful algal blooms?

Because of all the runoff pollution

Ocean Depth

Average Depth: 4000 m

Deepest: 11,000 m

Sediment thickness ranges from 0 m to 2000 m

The Photic Zone

0 - 200 m

majority of primary prodution

nutrient (N, Fe, P) limitation

The Mesopelagic Zone

200 - 1000 m

Only \~20% of Photic Zone 1° Prod. Transfers

The Bathypelagic Zone

1000 - 4000m

no sunlight penetration

5% of Photic Zone 1° Prod. Transfers \n Pressure reaches 5,850 lbs/sq. inch

The Abyssopelagic Zone

4,000 to 6,000 \n 75% of ocean floor

The Hadalpelagic Zone

6000 - 11000 m

4 successful manned dives

Why are marine phototrophs important?

They generate energy and reduce carbon dioxide, providing the system with organic substrates and oxygen.

What limits the growth of marine phototrophs in the ocean?

•Inorganic nutrients (P, N, Fe)

•Temperatures

What is the most abundant marine phototroph and how do scientists differentiate between the different “types?”

The most abundant marine phototroph is Prochlorococcus. Scientists differentiate between different ecotypes by temperature tolerance and what inorganic nutrients they use

What are high light ecotypes?

•Dominant in upper layer of stratified waters

•Found all over the world

What are low light ecotypes?

•Dominant in lower layer of stratified waters

What is a Whale Fall?

Whale carcass sinks to ocean floor (acts as a large carbon source)

What are the stages of a whale fall?

Mobile Scavenger Stage

Enrichment opportunist stage

Chemoautotrophic stage

Chemoautotrophic Stage

•Large and diverse assemblage lives in sulphides released from microbial breakdown of oil in bones

•Can last for decades

enrichment opportunist stage

•Sediments around the carcass colonized by invertebrates

•DENSE

mobile scavenger stage

•Deep sea scavengers remove soft tissue

•4 mos. to 1.5 years

How does soil formation happen?

1. Algae, lichens, mosses on exposed rock
2. Chemoorganotrophs produce CO2
3. Carbonic acid dissolves rock
4. Plant excretions promote microbial growth in rhizosphere
5. Decaying plants contribute to organic material
6. Soil profile forms

Where do we find hyperthermophilic bacteria?

In high temperature environments (>80C)

How do their adaptations to living in high heat environments differ from the other hyperthermophiles we have discussed this semester?

•Production of chaperonins

•Increased number of disulfide bridges

•Increased interactions among aromatic peptides

•Increased hydrogen bonding among peptides

•DNA gyrase

What is White Nose Syndrome?

Disease caused by Pseudogymnoascus destructans.

Causes abnormal active behavior, leads to loss of fat, wing damage, death

How does the organism infect/kill the host?

* Infects bats during winter hibernation


* invades and ingests the skin of hibernating bats, including their wings.

What are possible treatments for WNS?

•Cooling the hibernacula

•Probiotics (Bacterial and Fungal)

How does primary production occur in cave systems?

•As gases: CO2, N2, aromatic hydrocarbons

•Hydrocarbons from soils that percolate down via surface water

•Reduced metal ions derived from the cave rock (Mn II and Fe II, etc)

Why would NASA be interested in funding cave microbiology?

Because cave microbiology may give insight as to terrestrial life on other planets.

When researchers set out to make a drill to reach an under-ice briny lake that had been closed off for up to 2 million years, what were the important considerations they had to make to ensure they were preserving the pristine ecosystem?

* Only drills downward- will get trapped when ice behind refreezes
* Can’t penetrate dust or dirt due to friction issues

Why is Blood Falls red?

The lake is highly saline and rich in iron, when the iron in the water reacts with oxygen it gets it’s red color.

How is Antarctica considered a desert when it’s covered in ice?

Low rainfall

What are the McMurdo Dry Valleys and why are they important for Antarctic science?

Snow free valleys in Antarctica, only permanent ice covered lakes on earth,

Leads to reduced mixing, light penetration, gas exchange, sediment deposition.

Considered to be the closest thing to terrestrial life on mars which could give insight into extraterrestrial life

What is the role of cyanobacteria in Antarctic/Arctic ecosystems?

•Nitrogen cycling

•Carbon fixation

•Toxin production

Be able to give an example of a bacterium isolated from an extreme cold environment.

*Psychromonas antarcticus*

*Desulfotalea psychrophila*

*Thiomicrospira arctica* - sulfur oxidizer, Chemolithoautotroph, isolated off coast of Svalbard, important role in primary production (new organic C without sunlight)

*Thiomicrospira arctica* 

* sulfur oxidizer
* Chemolithoautotroph
* isolated off coast of Svalbard
* important role in primary production (new organic C without sunlight)

*Desulfotalea psychrophila*

* *isolated from sediments samples in Svalbard*
* *chemoorganotroph*

*Psychromonas antarcticus*

* *aerotolerant*
* *isolated from high salt pond*

What is watermelon snow? What organism is responsible for the phenomenon?

Watermelon snow is green alga that can grow in the snow, it gets it’s name from the red pigment it has.

*Chlamydomonas nivalis is responsible*

What are some physiological adaptations microbes employ to survive extreme cold conditions? 

enzyme adaptations, cytoplasmic membrane adaptations, and cold shock proteins

What are examples of enzyme adaptations for surviving in extreme cold temps?

•α-helices vs. β-sheets

•Polar vs. hydrophobic amino acids

•Fewer weak bonds

What are examples of cytoplasmic membrane adaptations for surviving in extreme cold temps?

Higher unsaturated and short-chain fatty acid content

What are examples of cold shock protein adaptations for surviving in extreme cold temps?

•Cryoprotectants- antifreeze proteins or solutes (glycerol)

•Cold shock proteins- bind to mRNA to lead to translation

What a psychrophile?

maximum temperature for growth at 20 degrees C or below and are restricted to permanently cold habitats.

What is a psychrotroph?

maximum temperature for growth above 20 degrees C, widespread in natural environments

What are the conditions in the atmosphere that impact microbial growth?

Relative humidity, temperature, radiation, oxygen

What organism is known to be able to withstand high levels of radiation without mutating? How can it do this?

*Deinococcus radiodurans*

Its genome structure (2 chromosomes, 2 plasmids) could be the reason why it can withstand radiation, has multiple gene copies on each.

What are the 4 phases of *Streptomyces* growth?

1. Spores germinate into vegetative hyphae
2. Grow as filaments- growth is at the tip
3. **Sporophores** form
4. **Sporophores** give rise to **conidia**

What are the metabolites that *Streptomyces* produce?

Antibiotics

How do bacteria and acintomycetes differ? Do they differ? 

Acintomycetes are a type of bacteria but are unique enough to be their own group.

They are generally one to two orders of magnitude smaller than the total bacterial population

What are the different microbial life forms that make up soil communities? Understand how they break down in terms of abundance and role in soil communities.

Bacteria, Actinomycetes, Fungi, Algae, and Protozoa