Soil Ecology - Exam 2

Module 9 - 13

Enzymes

Proteins that catalyze biochemical reactions by lowering activation energy and increasing the speed of chemical reactions in cells. It binds to specfic substrates in active site of proteins

Catalase

A common enzyme that breaks down peroxide into water & oxygen - it protects organisms from oxidative damage 2H2O2 → O2 + 2H20

Peroxidases - Intracellular or Extracellular

oxidative stress response and lignin degradation (blank cell walls)

Chitinases - Intracellular or Extracellular?

degradation of chitin polymers (fungal cell walls)

Cellulases - Intracellular or Extracellular?

degradation of cellulose polymers (plant cell walls)

Amylases - Intracellular or Extracellular?

degradation of starch polymers (C cycling)

Proteases - Intracellular or Extracellular?

degradation of protein (C and N cycling)

Phosphates - Intracellular or Extracellular?

removes inorganic P from organic substrates

What does enzyme activity in soil indicate?

change in soil structure and chemistry

Cellular Functions of Extracellular Enzymes:

• solubilize/breakdown large polymers

• detoxify the environment

• reduce/oxidize insoluble minerals/metals

What traits make soil fungi so effective at secreting extracellular enzymes?

Fungi are filamentous, can create a large surface area to search for food and secretes enzymes

Why do fungi act as good extracellular enzymes?

They are primary degraders of plant cell wall material using hydrolases, oxidases, laccases, peroxidases, and phenol oxidases. They also perform phosphorus mineralization, which is when the fungi release enzymes to collect phosphate groups from organic compounds which they then turn into something useful for plants to grow

Methods to measure general microbial activity and specific enzyme activity in soils - know limitations of each method

1. Soil Respiration - measures the rate of carbon dioxide released from the soil as microbes break down organic matter. Limitations: cannot distinguish the difference between microbial respiration and root respiration; heavily fluctuates with immediate changes in soil moisture & temperature rather than remaining stable

2. Dehydrogenase Activity Assays - dehydrogenase acts as an intracellular marker of intact, viable oxidative metabolism. Limitations: do not function outside a cell, highly sensitive to air drying and storage

Microbial Ecology

The study of interactions of microorganisms with each other and their environment

Population

All the organisms belonging to a single species with the potential to interact. The spatial scale of a population depends upon the size, mobility, and reach of the species

Community

All the organisms living in one habitat; includes both populations or subpopulations of various species

Community Structure

The numbers and types of organisms present

Neutralism

A type of interaction where organisms occupy the same habitat but are neutral to each other, neither organism benefits nor is harmed by the actions of the other organism in the community

Commensalism

Describes an interaction where organisms occupy the same habitat but at no cost or benefit to another species - very common

Examples of Commensalism

1. Oxygen utilization by aerobes in surface areas can benefit obligate anaerobes (symbiotic relationship) - obligate anaerobes gain a critical survival advantage, given access to new resources, habitats, & protection against oxygen toxicity (+) whereas aerobes are completely unaffected (0)

2. Degradation of complex organic matter - specialized microbes secrete extracellular enzymes that break down complex polymers to produce byproducts that are simple nutrients to the surrounding environment (+). In contrast, neighboring microbes that lack the degrading gene will take the free simplified nutrients (0)

3. Production and release of metabolic byproduct - the first organism creates and releases byproducts naturally (0), while the consumer uses the waste products as a primary source of nutrients, energy, or environmental modification; think of it as a free meal (+)

4. Toxin Inactivation/Detoxification - one organism breaks down environmental toxins/ metabolic waste products (0); the second organism now has a safe, habitable environment (+)

Auxotroph

An organism that has a nutrient deficit and is unable to synthesize one or more vitamins, growth factors, amino acids, nucleotides, etc. Organisms must obtain the missing compound from its environment.

Prototroph

An organism that can make all intermediates and end-products necessary for growth and metabolism from the basic building blocks

Mutualism

Interactions that benefit both organisms involved

What are 2 types of Mutualism and examples?

1. Proto-cooperation: a temporary mutualistic association where both partners benefit

ex. cross-feeding nutrients: species A produces an amino acid that species B takes up and uses. Species B produces biotin, which is taken up and used by species A. Both partners benefit when needed, but a species can easily be replaced with another that does the same function

1. Symbiotic mutualism: an obligatory, non-transitory, mutually beneficial interaction

ex. Mycorrhizal fungi and plant roots: The plant performs photosynthesis and supplies fungi with Carbon, energy-rich sugars, and nitrogen. While the fungi provide a large network that extends far beyond the root, increasing the surface area for plants to absorb water, phosphorus, nitrogen, and other essential minerals

Competition

rivalry over a limiting factor or resource

Interspecies Competition

complex interactions with neighboring organisms from a different species; includes many trophic levels

Intraspecies Competition

competition between parents and progeny in the same species - leads to variation in phenotype and abilities within a population

Carrying Capactiy

the maximum population of a particular species that a given habitat can support over a given period of time

Common Competitive Strategies

1. High growth rate

2. Efficient use of nutrients

3. Metabolic diversity - switches to other metabolisms/pathways with less competition

4. Motility - leaves one habitat to colonize a new one

5. Amensalism

Oligotrophs

Organisms that are able to sense and acquire resources that are scarce and highly dilute (low in concentration) and use them more efficiently; slower to metabolize & grow, but can grow at nutrient concentrations that would not be accessible to other organisms

Copiotrophs

Organisms that have high nutrient requirements both to sense, acquire, and utilize those nutrients; usually grow faster when nutrients are abundant; however do not grow well when nutrients are scarce

Amensalism

a type of antagonistic interaction between organisms - one organism is harmed/destroyed while the other is completely unaffected (no benefit)

ex. pH change, antibiotic production, siderophore (iron cage)

What are biotic and abiotic factors that influence the soil bacteria communities?

Soil pH, Organic carbon quality & quantity, Soil (O2) and redox status

Predators vs. Parasites

Predators = feed on prey, actively hunts/kills them to survive

Parasites = live on/inside a host organism for an extended period of time, feeding off its resources without killing it immediately

Scramble Competition

Deprive another of a resource by depleting that resource first

ex. 2 different species of microbes colonize a new microhabitat in soil, and both use the same energy source, which is initially abundant. Organism A has a slower growth rate than Organism B

Contest Competition

actively harms another competitor by “germ warfare” - production of toxins and antimicrobials

Competitive Exclusion Principle

2 species competing for the same exact limited resources cannot stably coexist at a constant population sizes in the same ecological niche

Mycorrhizae

A symbiotic association between plant roots and fungi - in most terrestrial plant and all woody plants, relatively non selective

What are the important roles of mycorrhizae?

1. Nutrient acquisition

2. Water acquisition

3. Sequestration of heavy metals

4. Defense against plant pathogens

Arbuscular Mycorrhizae (AM)

A very common type of mycorrhizal association, mostly herbaceous and some trees. Limited range in taxa but not in the plant.

Describe arbuscular mycorrhiazae and its location.

It is the place of contact between the plant and fungi. The fungal hyphae penetrates epidermis of root and cortex of plant cell walls, produces spores within or outside the root. *The arbuscules are the site of nutrient exchange

Benefits of arbuscular mycorrhizae.

• enhances uptake of nutrients to plant (inorganic phosphorus and some nitrogen)

• improves plant & and health

• can encourage plant diversity under stressful conditions

• exhibits limited extracellular enzymatic activity - depends upon plant & soil bacteria for carbon, which minimizes metabolic energy waste

Vesicular-Arbuscular Mycorrhizae

Similar to arbuscular mycorrhizae, but they also form vesicles. The vesicles almost completely fill host plant cortical cells and contain lipids and phosphorus (provides storage for both Carbon and Phosporus)

Ectomycorrhizae

Relatively few in plant species; more dominant in trees and some shrubs. They do not penetrate host cells; instead, they wedge between them. They form an extensive hyphal network (Hartig net) and a sheath on the surface or root. Spores produced in specialized structures away from the root (ex. mushrooms, truffles) *Hartig Net = site of nutrient exchange. It also produces more extracellular enzymes

Ectomycorrhizae extracellular enzymatic activity.

• phosphatase - liberate phosphorus from organic matter

• Proteinase - liberates nitrogen & carbon (some sulfur) from proteins

Benefits to the fungal partner.

• fungi are heterotrophs, the plant provides a ready source of carbon, energy, and growth factors

• improves fungal competitiveness with bacteria for shared resources so no competition for food because the plants provide carbon

• fungi are heterotrophs (cannot produce their own food); mycorrhizae can demand 20-40% total fixed carbon produced by the plant

Benefits to the plant partner.

• increases root contact with nutrient pool - AM mainly supply of inorganic P to plants, ECM provide P & N to plant through proteinase & phosphatase

• ECM important in seedlings to help with tree growth

• promotes plant-to-plant communication & resource sharing

• increased tolerance to stress

• protection from plant pathogens

Rhizosphere

the portion of soil under the direct influence of the roots - it is extremely diverse and microbial colonization is patchy along the root

Rhizoplane

the physical surface of the plant root

How does organic carbon affect the rhizosphere?

• causes changes in the physical, chemical, and biological nature of soil

• can account for about 50% of rhizosphere respiration

• high & low molecular weight compounds

High molecular weight organics

• the majority of carbon released from roots

• complex organic matter ex. mucliage & cellulose

• turnover time: days

Mucliage

insoluble high molecular weight polysaccharide-rich material secreted from the root cap and border cells - a large amount of carbon that goes out is found here

Low molecular weight organics

• highly diverse suite of molecules

• turnover time: minutes-hours

• soluble and gaseous compounds like O2

• not easily moved, mostly stays at root - in order to secrete the plant might use a gas to transport

Functions & impact of rhizosphere microbiome on plant

Good

• growth & development, nutrient acquisition, tolerance to abiotic stress, protection against pathogens, physiology/metabolism, immune response

Bad

• plant diseases & food contamination

Beneficial Microbe-Plant interactions

1. Beneficial rhizobacteria provide nutrients - plants need N,P and trace metals (iron): nitrogen fixation, degradation & mineralization of organic matter, production of bacterial siderophores

2. Rhizobacteria support plants under abiotic stresses: flooding, salinity, cool temperatures, low pH, soil contaminants/toxins

3. Provide the first line of defense against plant pathogens: competition for limited resources (food, nutrients, space), parasitism (some beneficial bacteria parsitize pathogens), amensalism

4. Prime plant for systemic resistance response: induce plants to activate cellular defenses to mitigate pathogen attack, establish disease-suppressive soils, induce plant cell wall reinforcements, enhance production of plant defense metabolites

Replication

• capture natural variance: distinguish “true” biological signals from background soil heterogeneity

• avoid pseudo-replication: samples should come from separate, independent experimental units

• budget constraints: need to balance fine-scale detail with statical power