Lecture 21 Microbial Ecology

Question 1

What are the foundations of microbial ecology?

Answer 1

• Symbioses: “relationships among organisms in an ecosystem”…
• Populations: assemblages of similar organisms
• Communites: mixtures of different populations
• Ecosystems: self-reguatling biological communities and their physical environment

Question 2

What are some of the physical associations in microbial interactions?

[MCB Ecology]

Answer 2

• Ectosymbiont: organism located on surface of another organism (usually larger)
• Consortium: physical contact between dissimilar organisms of similar size
• Endosymbiotic: organism located within another organism
• Ecto/endosymbiosis: organism lives both on inside and outside of another organism.

Question 3

What is mutualism? Give an example.

Answer 3

• Some receiprocal benefit to both partners
• Often with some degree of obligation
  
  • Mutualist and host are metabolically dependent on each other
• e.g. protozoan-termite relationship
  
  • Termite provides food for protozoan
  • Protozoan digests cellulose in wood particles, providing nutrients for termite
• e.g., zooxanthellae-marine invertebrate interactions
  
  • Zooxanthellae: algae harbored by marine invertebrates such as reef-building corals
    
    • Provide organic carbon
  • Coral has pigments that protect algae from UV radiation

Question 4

Describe the sulfide-based mutualisms.

Answer 4

Reduced chemicals including sulfide are released as seawater penetrates the fratured basaltic ocean floor, is heated, and returns as vent fluid to the ocean, creating environments for growth of the tube worms and their procaryotic mutualists.

Question 5

What is the rumen ecosystem?

Answer 5

• Ruminants: animals that have stomach divided into four compartments and chew a cud.
• Rumen: one of compartments
  
  • Contains large, diverse population of microbes

Question 6

What are lichens?

Answer 6

Lichens are composite organisms consisting of a fungus and a photosynthetic partner growing together in a symbiotic relationship

• Association only occurs when organisms are nutritionally deprived
• Mycobiont: fungal partner
  
  • Provides water, minerals, sheltered environment and firm substratum for growth
• Phycobiont: alga or cyanobacterium
  
  • Provides organic carbon and oxygen

Question 7

Define cooperation in the microbial ecology sense.

Answer 7

• Both organisms benefit
• Nonobligatory syntrophic relationship: growth of one organism depends on or is improved by growth factors, nutrients, or substrates provided by another organisms growing nearby.
  
  • Also called crossfeeding or satellite phenomenon

Question 8

Define commensalism in the microbial ecology sense.

Answer 8

• One organism benefits and the other is neither harmed nor helped
• Commensal: organism that benefits
• Can also invoke modification of environment by one organism, making it more suited for another organism
• E.g. nitrification (NH3-> NO2-> NO3). Nitrosomonas carries out first step. Nitrobacter carries out second step

Question 9

Give some examples of microbial commensalism.

Answer 9

• Microbial succession during spoilage of milk
  
  • Fermentative bacteria produce acids that promote growth of acid tolerant species
• Formation of biofilms
  
  • Initial colonizer makes it possible for other microorganisms to attach
• Skin or surface microbes on plants or animals
  
  • Host plant or animal releases volatile, soluble, and particulate organic molecules

Question 10

Define predation in the microbial ecology sense.

Answer 10

• One organism gains and the other is harmed.
• Predator engulfs or attacks prey
  
  • Prey can be larger or smaller than predator
  • Prey is killed

Question 11

What are some microbial predators?

Answer 11

• Predatory bacteria
• Ciliates prey on bacteria
• Protozoa-trapping fungi
• Nematode-trapping fungi

Question 12

Define parasitism in the microbial ecology sense.

Answer 12

• One organism gains (parasite) and the other is harmed (host)
• Difficult to distinguish from predation
• Can be used as a biological control
  
  • Viruses
  • Parasitic fungi

Question 13

Define ammensalism in the microbial ecology sense.

Answer 13

• Negative impact of one organism on another based on release of a specific compound
• E.g.,
  
  • Antibiotic production by fungi and bacteria
  • Bacteriocin production by bacteria
  • Production of antibacterial peptides by insects and mammals
  • Production of organic acids during fementation

Question 14

Define competition in the microbial ecology sense.

Answer 14

• Occurs when two organisms try to acquire or use the same resource
• Two possible outcomes:
  
  • One organism dominates competitive exclusion principal: one population is excluded
  • Two organisms share the resource
    
    • Both survive at lower populaton levels

Question 15

How is symbioses achieved in complex systems?

Answer 15

• Symbiotic interactions do not occur independently
• Each interaction triggers feedback responses in the large biotic community.
• Over time, symbiosis becomes more and more effiicient.

Question 16

Describe nutrient cycling interactions (i.e. Biogeochemical cycling or nutrients)

Answer 16

• Biogeochemical cycling of nutrients involves biological and chemical processes. It often involves oxidation-reduction reactions that change chemical and physical characteristics of nutrients
• All nutrient cycles are linked and have global-level impacts
  *

Question 17

Describe macrobiogeochemistry.

Answer 17

• All biogeochemical cycles are linked, with energy being obtained from light and pairs of reduce and oxidized compounds. The forms that move between microorganisms and multicellular organisms can vary. The broad concept is that all cycles are linked. The biotic components include both lving forms and those that have died/senesced and which are being processed. Flows from lithogenic sources are important for phosphorus. Methane transformations are only microbial.

Question 18

Describe the carbon cycle as it relates to microbial ecology.

Answer 18

Carbon fixation can occur through the activities of photoautotrophic and chemoautotrophic organisms. Methane can be produced from inorganic substrates (CO2 and H2) or from organic matter. Carbon monoxide, produced by sources such as automobiles and industry, is returned to the carbon cycle by CO-oxidizing bacteria.

Question 19

Which factors influence degradation of organic matter?

Answer 19

• Nutrients present in environment
• Abiotic conditions
• Microbial community present

Question 20

What are two types of degradation of organic matter?

Answer 20

• Mineralization: decomposition of organic matter to simpler inorganic compounds (e.g., NH4)
• Immobilization: Incorporation of simple, soluble substances into body of an organism
  
  • Accompanies growth of microorganism on complex substrates that do not provide essential nutrients.

Question 21

What is lignin degradation?

Answer 21

• Lignin or lignen is a complex chemical compound most commonly derived from wood, and an integral part of the secondary cell walls of plants and some algae.
• Biodegradation of lignin by brown rot, soft rot, or white rot fungi leads to destruction of wood on the forest floor and man-made structures such as fences and wooden buildings.
• Only occurs aerobically
  
  • Under anaerobic conditions, lignin accumulates to form peat bogs and muck soiles
• Practical important
  
  • Preservation of wood pilings below the water table (or 10,000 y/o mummies).

Question 22

Describe the sulfur cycle in terms of microbial ecology.

Answer 22

Photosynthetic and chemosynthetic microorganisms contribute to the environmental sulfur cycle. Sulfate and sulfite reductions carried out by Desulfovibrio and related organisms are dissimilatory processes. Sulfate reduction also can occur in assimilatory reactions, resulting in organic sulfur forms. Elemental sulfur reduction to sulfde is carried out by Desulfuromonas, thermophilic archaea, or cyanobacteria in hypersaline sediments. Sulfur oxidation can be carried out by a wide range of aerobic chemotrophs and by aerobic and anaerobic phototrophs.

Question 23

What is nitrogen fixation?

Answer 23

• Reduction of N2 -> organic nitrogen
• Requires an expenditure of energy, source of electrons, and anaerobic environment
• Carried out by aerobes or anaerobes
  
  • Aerobes maintain anaerobic conditions by using physical barriers, O2 scavenging molecules, and high rates of metabolic activity.

Question 24

What is the iron cycle in terms of microbial ecology?

Answer 24

In addition to ferrous ion (Fe2+) oxidation and ferric ion (Fe3+) reduction, magnetite (Fe3O4), a mixed valence iron compound formed by magnetotactic bacteria is important in the iron cycle. Different microbial groups carry out the oxidation of ferrous ion depending on environmental conditions.

Question 25

What are **magneto-aerotactic** bacteria?

Answer 25

* Transforms extracellular iron to magnetite (Fe3O4) and construct intracellular magnetic compasses * Use magnetic fields to migrate to a position where O2 level is appropriate

Question 26

What do we know about microorganisms and metal toxicity?

Answer 26

Microorganisms can modify toxicity of metals They may also lead to bioaccumulation or -magnification

Question 27

Define **microenvironment**.

Answer 27

* Specific physical location of microorganism * Impacted by fluxes of nutrients and diffusion rates of waste products

Question 28

Define **niche**.

Answer 28

* Function of an organism in a complex system, including place of the organism, resources used in a given location, and time of use

Question 29

Define **biofilms**.

Answer 29

Organized microbial systems consisting of layers of microbial cells associated with surfaces. Formation of biofilms creates microenvironments and niches hospital to different types of microbes

Question 30

Define **microbial mats**.

Answer 30

Thick biofilms having macroscopic dimensions. Often found in aquatic environments.

Question 31

Define **ecosystems**.

Answer 31

* Communties of organisms and their physical and chemical environments that function as self-regulating units.

Question 32

What are the 3 different roles of organisms within ecosystems?

Answer 32

* **Primary production**: synthesis of organic matter from CO2 and other inorganic compounds. * Primary producers: organisms that carry out primary production * **Decomposers**: decompose accumulated organic matter * **Consumers**: use accumulated organic matter as food.

Question 33

What are the various roles of microbes in an ecosystem?

Answer 33

* Primary producers * Decomposers (often carry out mineralization) * Food source for other organisms * Biogeochemical cycling * Change amounts of materials in soluble and gaseous form * Produce inhibitory compounds tha tlimit microbial activity or limit survival and functioning of plants and animals * Impact function of plants and animals through symbiotic interactions.

Question 34

How do microbes move about in ecosystems?

Answer 34

* In soil, transported by windstorms * In rivers containing eroded materials, sewage plant effluents and urban wastes * By plants and animals * Waste products * Dead organisms * Intentional or accidental transport by human acitivity

Question 35

What are the fates of transported microbes?

Answer 35

* Often unable to compete effectively with indigenous organisms * Some survive, but become nonculturable microorganisms * Alive, but unable to be cultured using techniques normally used for that microbe

Question 36

Describe what an **extreme environment** is.

Answer 36

Physical factors are outside normal range for growth of most microorganisms.

Question 37

Define **extremophiles**.

Answer 37

Organisms that survive in extreme environments

Question 38

What are the two goals of microbial ecology?

Answer 38

* Understanding physical structure of community * How microorganisms are physically associated * Understanding constituents of community * Microorganisms in community * Checmical constituents

Question 39

How do we understand the physical structure of a community in microbial ecology?

Answer 39

* Direct observation * Classical staining procedures * Fluorescent stains * Fluorescent molecular probes * Often coupled with molecular techniques * Specific molecular probes

Question 40

How do we understand constituents of a community in microbial ecology?

Answer 40

* Filtration can be used to collet microorganisms from habitat * Volume, dry weight, or chemical content can be measured * Not useful for non-discrete organisms (e.g., filamentous fungi) * Molecular "fingerprinting" techniques identify members of community

Question 41

What stresses microbes?

Answer 41

* Absences of nutrients * External factors (e.g., toxic chemicals, temperature changes)

Question 42

How do we measure microbial responses to stress?

Answer 42

* Cultural techniques * Stressed microorganisms do not grow as well * Viability stains

Question 43

How do we measure microbial activity and turnover?

Answer 43

* Direct chemical measurements of specific processes (e.g. nitrification) * Microarrays to measure gene expression * Stable isotope measurements * Microbial growth rates measure two ways: * Direct micoscopic examination * Incorporation of radiolabeled components (e.g., thymine)

Question 44

How can we measure microbial-microbial interactions?

Answer 44

* Measurement of communication molecules * Measurement of metabolic intermediates and toxic microbial products