Module 4: Microbial Ecosystems (Oceanic and Soil Environs.) Flashcards
What percentage of Earth is covered by water?
70%
What percentage of oceanic biomass is microbes?
> 98% of oceanic biomass consists of microbes (viruses, bacteria, archaea, eukarya)
What is the salt concentration of ocean waters?
35g of salt / L of water
= 3.5% salt!
What is the composition of oceanic water salt?
~2/3 of the oceanic salt is composed of Na+ and Cl- ions
The rest consists of small amounts of the following ions:
1) Mg2+
2) Ca2+
3) K+
4) SO4-
5) HCO3-
Ocean water is _______ for the most part which means that _______ can occur
Ocean water is largely OXIC which means that aerobic respiration can occur
What is a common characteristic of oceanic waters?
Oligotrophic conditions
–> Low concentration of Nitrogne, Phosphorus, and Iron
Oceanic water is low in…
this makes it characterized as….
Concentration of:
1) Nitrogen (N)
2) Phosphorus (P)
3) Iron (Fe)
OLIGOTROPHIC
Oligotrophs
Organisms that utilize nutrients at very low concentrations
What has been found to decrease the oxygen content of ocean waters?
(generally)
An increase in nutrient concentration!
–> Causes greater growth of heterotrophs == greater aerobic respiration == greater O2 consumption!
What are the divisions of the ocean (and their depths)?
1) Surface Zone (0-200m)
2) Dark Mid-Water Zone (200-4,000m)
3) Deep Sea Zone (>4,000m)
What are the characterizing features of the ocean zones?
1) Surface zone = Light can penetrate!
2) Dark Mid-Water Zone = Constant temp of around 2-3C (No light)
3) Deep Sea Zone = Very high pressure
What is the typical ocean seafloor depth?
How does this compare to the deepest know spot (what is this)?
Typical Seafloor Depth = 3,500m
Deepest Spot = Mariana Trench @ 11,000m
How are microorganisms distributed throughout the ocean?
NOT uniformly!
–> As depth increases, microbial abundance decreases
BUT: As depth increases, the PROPORTION of archaea increases!!!
For most of the ocean’s volume, there is a greater # of ________ compared to ___________
Greater # of ARCHAEAL cells than BACTERIAL cells
The surface zone of the ocean is home to:
Photosynthetic microbes, mainly PHYTOPLANKTON
(And some zooplankton)
Phytoplankton
Photosynthetic microorganisms (aquatic)
What is example of phytoplankton?
Cyanobacteria such as:
–> Prochlorococcus
–> Synecoccus
What is the significance of phytoplankton?
Responsible for oxygenating the ocean waters AND support all other life in the oceans! (Original “source” of energy)
What are the main primary producers within oceans?
Phytoplankton
Main primary producers in oceans vs soil:
Oceans = Photosynthetic microbes
Soil = Plants
Zooplankton
Non-photosynthetic consumer microorganisms
–> Feed on primary producer phytoplanktons!
In the dark mid-water zone, ___________ is not possible BUT __________ exist here
Photosynthesis is not possible (no light)
BUT zooplankton live here!
Where do zooplankton get food from in zones below the surface zone?
From organic materials released from viral lysis of phytoplankton that drift down into lower zones
Viral Lysis of Phytoplankton
(What gets released?)
Bacteriophages and other viruses that target phytoplankton invade these photosynthetic cells, reproduce like crazy inside them, and lyse the photosynthetic cells
–> Results in the release of organic materials such as frags. of:
1) PM
2) DNA
3) Protein
4) and Nutrients
The materials released from lysis feed zooplankton in all zones of the oceans
Lysis mainly occurs in the dark mid-water zone!!!!
What amount of primary producer product reach the seafloor?
~1% of primary producer products reach the seafloor
What happens to primary producer products that reach the seafloor?
Create a rich seafloor sediment
Because they don’t really biodegrade due to:
1) Very low temperature at the seafloor
2) Anoxic conditions at the seafloor
What is the rich seafloor sediment used for?
Used by humans as a source of gas and oil
What is the pressure like at the seafloor compared to sea level?
1000x greater pressure
What lives in the deep-sea zone?
Piezophiles (barophiles)
Piezophiles
Organisms that can withstand high pressure and often require it for survival and growth
What effect does high pressure have on the PM?
High pressure decreases fluidity of PM
How do piezophiles combat the effects of pressure on their PM?
They have PM with high concentration of polyunsaturated fatty acids to increase fluidity
Compared to other microbial cells, how abundant are viruses in the oceans?
of viral particles is >10x the number of bacterial + archaeal cells combined
What is the importance of viruses within the oceans?
They provide marine ecosystems with nutrients (via phyoplankton lysis!)
What types of viruses are most abundant in the surface zone?
Bacteriophages of cyanobacteria
Dead Zones
Areas of oceans without enough oxygen to support marine animal life
Where are dead zones mainly observed?
Coastal areas
(where rivers and other waterways feed into the oceans)
How many dead zones have been documented?
> 400 dead zones around the world
Process of Dead Zone Formation:
1) Farms use synthetic fertilizers
2) Nutrient rich runoff from farms enters waterways (like rivers)
3) Rivers become nutrient rich and carry this water into the ocean
3) Excess nutrients increases proliferation of phytoplankton = increased O2
4) Increased O2 and nutrient concentration causes increased heterotrophic growth
5) Increased heterotrophic growth = more aerobic respiration = decrease in oxygen content of water
6) Anoxic areas are created; heterotrophic microbes and zooplankton in this region die
–> Some escape to areas of higher oxygen content, doing the same process over again and growing the dead zone
Dead zones aren’t really _______, they contain __________
Dead zones aren’t really DEAD, they contain communities of microorganisms (that are anaerobic)
Dilution to Extinction
A technique that produces very dilute solutions from environmental microbial samples in which each dilution contains 1 to a few cells that can be grown to produce pure culture
With what organisms is dilution to extinction most helpful?
In cultivating oligotrophs (especially marine ones)
What are the problems with culturing oligotrophs?
1) Many cannot withstand high concentrations of carbon and nutrients
2) Low metabolism = low biomass production (do not proliferate enough to form visible colonies in traditional culture methods)
3) Competition: If oligotrophs are in solution with other microbes that can more efficiently handle a > amount of nutrients, the oligotrophs will get outcompeted!
What are the issues with current techniques for culturing marine microbes?
Commercially available marine growth media contains element profiles similar to sea water (salt levels)
BUT: these media contain levels of carbon, nitrogen, phosphorus, and iron that is much higher than what’s naturally found in sea water
(will not work for many oligotrophs!)
What is the problem with marine growth media?
Do NOT accurately replicate conditions of growth in natural sea habitat
Dilution to Extinction Process:
1) Sea water is sampled
2) Microscope is used to count number of cells in the sample
3) Series of serial dilutions are conducted into which the original sample is divided amongst various tubes
–> # of dilutions is calculated based on # of cells counted to achieve dilutions that have around 1 cell per tube
4) Tubes are left to grow
5) The tubes that display growth are subcultured into a larger volume of autoclaved sea water (NO GROWTH MEDIUM)
6) Left to grow
7) If growth occurs, cells can be harvested using centrifugation
Terrestrial Ecosystems are divided into
Biomes
Biomes
Categories of terrestrial ecosystems based on vegetation characteristics
What factors distinguish biomes?
1) Temperature
2) Precipitation
(determines what vegetation can/can’t grow)
What are the primary producers in terrestrial ecosystems?
Photoautotrophic plants
Plants provide nutrients to the soil via:
1) Microbial decomposition (of the plants themselves)
2) Photosynthesis derived plant root EXUDATES
Why is soil health important?
It is a key determinant in the functioning of terrestrial ecosystems
Soil
A relatively thin band over the terrestrial surface of earth
What is soil made of?
Decomposed plant and animal matter that combines with abiotic materials (minerals) and nutrients excreted by plant roots (root exudates)
Root excretions encourage…
the growth of diverse soil microbial communities
–> Especially ammoniafiers and denitrifiers
Horizons
Layers of soil with distinct characteristics
–> How the soil is categorized into layers
What are the horizons of soil from top to bottom?
1) O-Horizon
2) A-Horizon (topsoil)
3) B-Horizon (subsoil)
4) C-Horizon
(BEDROCK)
O-Horizon
Organic matter on surface of the soil
A-Horizon
The topsoil; Uppermost layer of soil
–> Has a greater concentration of organic material than other layers (due to proximity to roots)
B-Horizon
The subsoil; Contains some organic material but less than the top soil
C-Horizon
Deepest soil layer (above the bedrock) composed mainly of inorganic matter
How does microbial abundance change with soil depth?
Microbial abundance is greatest towards the surface and decreases as you go deeper down
–> Due to greatest presence of organic material towards the surface
Soil Taxonomy
A set of 26 soil classifications based upon physical soil characteristics
Soil Textural Classes
12 classes of soil determined by texture of the soil (proportion of clay to silt to sand)
What determine soil texture?
The proportion of particle sizes of minerals within the soil
–> Categorized by relative amounts of clay, sand, and silt
What is soil texture important for?
1) Water retention
2) Concentration of microbial communities
How does soil texture relate to microbial abundance?
Increase in particle size has been correlated to decreased microbial ABUNDANCE
BUT increased microbial DIVERSITY (possibly due to greater spatial segregation between microbial communities)
What is soil aggregation?
The tendency of soil to form clumps
–> Degree of clumping is dependent upon binding agents in the soil
What are the main binding agents of soil?
1) Substances from microbial cells
2) HUMIC material (Products of incomplete plant breakdown)
Humic Material
Products of incomplete plant breakdown
Do microbes tend to disperse through soil or stay close together?
Microbes tend to be found in biofilms within or near soil pores (which enables for access to air, water, nutrients, etc.)
Organic compounds in soil are mainly from and consisting of…
Mainly from PLANT MATTER DECOMPOSITION
–> Soluble components (sugars and AAs) (readily metabolized by most organisms)
–> Lignocellulose molecules (not readily metabolized, must be digested by extracellular enzymes first)
Lignocellulose molecules
Complex macromolecules made up of
1) cellulose
2) hemicellulose
3) lignin
What enzymes break down lignocellulose?
Cellulose –> broken down by cellulASE
Hemicellulose –> Broken down by hemicellulASE
Lignin –> Quite resistant to breakdown and so it typically remains in the soil (acting as a humic material!)
Rhizosphere
Region of the soil immediately surrounding the plant roots
What is the rhizosphere characterized by?
1) High conc. of organic carbon
2) High abundance of microbes
What produces the high concentration of organic carbon in the rhizosphere?
1) Plant root exudates
2) Sloughing off of plant root cap cells
What do plant root exudates consist of mainly?
1) Sugars
2) Sugar Alcohols
3) Organic Acids
Explain the rhizosphere symbiosis: What do plants provide microbes?
Plants provide microbes with a ton of nutrients and carbon sources
Explain the rhizosphere symbiosis: What do microbes provide plants (4)?
Some microbes produce and provide the following:
1) Phytohormones ==> stimulate plant growth
2) Antibiotics agents ==> Protect plant from pathogens
3) Nitrogen source ==> Nitrogen fixation turns N2 into a usable form of nitrogen for plants
4) Solubilize phosphate ==> Allows plant to uptake phosphorus!
Xenobiotics
Chemicals NOT naturally found in or produced by organisms
Most xenobiotics are…
1) Carcinogenic
2) Mutagenic
3) Toxic
4) Teratogenic (affect fetal development)
Most concerning and predominant xenobiotics:
1) PAHs ==> Polycyclic Aromatic Hydrocarbons
2) PCBs ==> Polychlorinated biphenyls
3) TCE ==> Trichloroethylene
4) TNT ==> 2,4,6-trinitrotoluene
(PAH is petroleum-derived)
Limitations of natural biodegration
1) Limited by O2 availability
2) SLOW
Why is O2 availability important for biodegration?
The best degrading enzymes typically need O2
Biostimulation
Addition of O2 of limiting nutrients to areas of contamination
–> Purpose is to increase metabolic activity of microorganisms that degrade organic wastes or pollutants
Bioaugmentation
Introduction of microorganisms known to degrade certain contaminants to a contaminated area
Co-Metabolism
Addition of natural substrates to a contaminated environment to induce degradation pathways with a broad substrate range!
–> Mainly used for areas contaminated with xenobiotics that have no current degradation pathways
Co-metabolism example
Adding methane (CH4) to areas contaminated by TCE
–> Microorganisms that metabolize methane become stimulated and actually begin producing metabolic enzymes that ALSO degrade TCE!
