Ch. 23 Major Microbial Habitats and Diversity
What does the pie chart show on pg. 681?
-General composition of soil microbial communities based on pooled 16S rRNA sequence data taken from several soils
Why are biofilms antibiotic resistance?
-Grow slowly -Extracellular Matrix prevents penetration of antimicrobial substances -Different patterns of gene expression
Acylated Homoserine Lactones
-Intercellular Signaling Molecule for P. aeruginosa -Signals to adjacent P. aeruginosa cells that population is enlarging -AHL then controls the expression of genes that contribute to biofilm formation
What happens to BOD when oxygen levels decrease? What happens when there is a spike of organic matter
-It increases -Bacterial numbers increase and oxygen levels decrease
Biochemical Oxygen Demand
-Microbial oxygen consuming capacity of a body of water
What is the "gold standard" for identifying and describing new species for the phylogenetic species concept?
-New species arises if 16s rRNA gene sequence differs by more than 3% from any named strain -New genus arises if gene sequence differs by more than 5%
Are soil particles homogenous in oxygen content? If not, describe the distribution of oxygen in a soil particle
-No -Outer edges contain most oxygen -Center has no oxygen
Prochlorococcus accounts for what percentage of biomass for marine phototrophs and what percentage of net primary production?
-Over 40% of biomass of marine phototrophs -About 50% of net primary production
What types of bacteria are in microbial mats?
-Phototrophic and/or chemolithotrophic
What are the factors that cause feast or famine existence for microbes?
-Physiochemical conditions can change rapidly -Resources in natural environments are highly variable -Microbial interactions (cooperation and competition) affect resource availibility
Where can microbial mats grow?
Aquatic environments, hypersaline solar evaporation basins
Why are ocean microbial activities major factors in Earth's carbon balance?
Because oceans are enormous, the collective carbon dioxide sequestration and oxygen production from oxygenic photosynthesis
How many viruses are there in the ocean per liter?
100 billion
What are two important ecosystem functions marine viruses do?
-Facilitate genetic exchange between prokaryotic cells -Allows lysogeny: viruse genome integrates with cell genome
What are the most abundant and versatile phototrophic microbial mat builders?
-Filamentous Cyanobacteria -Oxygenic Phototrophs
What is the operational definition of the phylogenetic species concept?
-97% or greater 16S rRNA gene sequence identity -70% or greater genomic DNA-DNA hybridization
Why are surfaces important for microbial habitats?
-Allows microbes to adsorb nutrients from surface -Microbes can attach to surfaces to take advantage of a favorable habitat -Offers protection from predation and physiochemical disturbances
For a soil particle, which microorganisms thrive on the outer part of the particle? Middle? Center?
-Anaerobic Organisms: Center -Microaerophiles (aerobes requiring little oxygen): Middle -Obligate aerobes: Outer
Microbes can cooperate metabolically. Why do some microbes cooperate with each other?
-Anoxic Carbon Cycling -Organisms that carry out complementary metabolisms
What can marine viruses affect?
-Bacteria and Archeal diversity -Population Structure -Nutrient Regimes
What happens when a biofilms is present in submerged surfaces?
-Biofilm growth is usually more extensive and become anoxic -Opens up new niches for colonization by obligate anaerobes or facultative aerobes
What are the steps to biofilm formation?
-Cells attach together then grow and communicate with other cells on a surface -Biofilm specific genes are expressed, proteins are made that synthesize intercellular signaling molecules to initiate matrix formation
What are microcolonies? Where do they develop?
-Clusters of a few cells that develop from a single colonizing cell -Any natural or artificial surface (ex. tree roots and microscope slides)
What is the phylogenetic species concept?
-Defines prokaryotic species as a group of strains that cluster together and are distinct of other groups of strains based on multiple gene cladistics analyses
What structures allow cells to attach to each other to form a biofilm?
-Protein Appendages -Cell Surface Proteins -Polysaccharides
The outcome of microbial competition is dependent on what factors?
-Rates of nutrient uptake -Inherent metabolic rates -Growth rates
Why do near-shore marine water contain higher microbial numbers than an open ocean?
-There are higher nutrient levels -Due to terrestrial inputs, retention of nutrients, and upwelling of nutrient-rich waters
What are the three types of symbioses that microbes establish?
1. Parasitism 2. Mutualism 3. Commensalism
Give three reasons why microbes grow very slowly?
1. Resources and growth conditions are suboptimal 2. The distribution of nutrients throughout the habitat is not uniform 3. Microbes grow in mixed populations rather than in pure culture
Why do bacteria form biofilms?
1. Self-defense that increase survival 2. Allows cells to remain in a favorable niche 3. Allow for bacterial cells to live in close association with each other 4. "Default" mode of growth
Different 16s rRNA gene surveys from the soil tell us what two things?
1. Undisturbed, unpolluted soils support very high prokaryotic diversity 2. Perturbations in soil trigger measurable shifts in community composition--->favoring competitive species-----> decrease in prokaryotic diversity
Microbes account for what percentage of all of Earth's biomass?
50%
Ecosystem
A dynamic complex of plant, animal, and microbial communities and their non-living surroundings, which interact as a functional unit; contains different habitats
Population
A group of microorganisms of the same species that reside in the same place at the same time, often descended from a single cell
What is contained in the adhesive matrix of a biofilm?
A mixture of polysaccharides , nucleic acids, proteins,
Habitat
A part of the ecosystem best suited for one or few populations -Also a space that supports a viable population of a specific type of organism
What do phylogenetic species have in common?
A recent common ancestor
Lake Taihu in China has high species richness or abundance?
Abundance-there is a huge bloom of only cyanobacterium Microcystis.
What are P. aeruginosa's major signaling molecules?
Acyl Homoserine Lactones
Where can you find P. aeruginosa forming a biofilm?
Artificial surfaces (hospitals)
What types of viruses are the most abundant in the ocean?
Bacteriophages
Mutualism
Both species benefit
How does a P.aeruginosa community form?
By intra and interspecies signaling
How does P. aeruginosa develop and maintain its biofilm?
By quorum sensing (intracellular sensing)
What are the two ways to express microbial diversity?
By species richness or species abundance
What is the role of c-di-GMP in biofilm formation?
Chemical second messenger that switches bacterial cells from planktonic growth to biofilm growth
Microcolonies
Clusters of a few colonies that develop from a single colonizing cell
Community
Consists of populations of one species living in association with populations of one or more other species
Which types of marine viruses have the largest gene pool, virions, and genomes?
Cyanophage in Algal Blooms
Where do iron-oxidizing bacteria form biofilms?
Rocks that have iron-rich water passing on them
Oligtrophic
Environment that is dilute in nutrients
Prime Niche
For each organism there exists at least one niche in which that organism is most successful
Ecological Theory
For every organism three exists at least one niche, the prime niche, where it will be the most successful
What does BOD determination tell you?
Gives the measure of the organic material in the water that can be oxidized by microorganisms present in the water
Where can cyanobacterial microbial mats grow?
Hot springs and thermal regions
Biogeochemistry
Interdisciplinary between biology, geology, and chemistry. It is the cycling elements in microorganisms, particularly C,N,S, and Fe between chemical forms
From the same graph, which group makes up the largest phylotype? Which is the second largest? Which is the smallest?
Largest: Proteobacteria Second: Unclassified Smallest: Archaea
What is a natural surface for biofilm formation (tree)?
Leaf
What is the role of cyanobacterial microbial mats?
Mediate all key nutrient cycles in ecosystems
Species Composition
Membership. the specific species present (or the type of species present)
Guilds
Metabolically similar microbial populations that exploit the same resources in a similar way
How do microorganisms store energy for periods of nutrient deprivation?
Produce storage polymers. Ex. polysaccharides, polyphosphate, and beta hydroxyalkanoates
Allochthomous Organic Matter
Newly synthesized organic material from sources and organic matter that enters the ecosystem from the outside
Is there a universally accepted concept of species for bacteria and archaea?
No
What happens to nutrients and energy within an ecosystem?
Nutrients and energy are cycled within an ecosystem
What does the biogeochemical cycle provide?
Nutrients for other organisms
What are some factors that make open ocean environments different than freshwater environments?
Ocean Water: -Has saline -Low in nutrients, especially N, P, and Fe (oligotrophic)
Parasitism
One member in the relationship is harmed and the other benefits
Commensalism
One species benefits and the other is neither harmed nor helped
What type of reaction takes place in the biogeochemical cycle?
Oxidation-Reduction Reactions. Element is tightly coupled with transformations in one cycle impacting one or more other cycles
What other diseases/conditions can biofilms contribute to?
Peridontal Disease Kidney Stones TB Legionnaires Disease Staph Infections Infections of implants
Much of the primary productivity in the open oceans is due to photosynthesis by what microorganism?
Prochlorophytes
In the same pie chart, which groups have the highest species richness?
Proteobacteria, Acidobacteria, and Bacteriodetes
What can biofilms do to pipes?
Slow the flow of water and accelerate corrosion of inert surfaces
Give some examples of types of habitats?
Soil, rock, subsurface, coastal, pelagic (open water), ocean bottom, vents
What happens to species diversity if the number of niches increase?
Species diversity increases
What are two ways to measure the diversity of microbial species in a community?
Species richness and Species abundance
What are the sources of energy for ecosystems?
Sunlight, organic carbon, and reduced inorganic substances
What does diffusion determine in small microorganisms?
The availability of resources, whether they can diffuse through
Microbial species abundance and richness are functions of what?
The conditions and the kinds of and the amounts of nutrients available in the habitat
Fundamental Niche
The full range of environmental conditions under which an organism can exist
Microenvironment
The immediate environmental surroundings of a microbial cell or group of cells
Where in the human body can P. aeruginosa grow? What disease can it cause?
The lungs forming cystic fibrosis.
What happens to the number of niches if there is higher diversity in resources and physiochemical conditions?
The number of niches increase
Species Abundance
The proportion of each species in the community
Niche
The specific type and quantity of resources and the physiochemical conditions of a habitat
Where on Earth are microbes usually found?
The surface and subsurface
Species Richness
The total number of different species present, determined by isolating cells and diversity of phylotypes (ribosomal RNA for example)
Biogeochemical Cycle
The transformation of an element that are catalyzed by either biological or chemical agents or both.
In an example of a lake ecosystem, what is happening to CO2, SO4, S^0, and NO3?
They are being reduced fro anaerobic respiration
What is an advantage of biofilms in hospitals?
They are tolerant of antibiotics (resistant) and antimicrobial stressors compared to planktonic forms
What is the growth pattern of microbes in nature?
They grow in spurts, due to intermittent availability of nutrients, usually lower than growth rate in lab
Microbial Mats
Thick microbial accumulations , contains highly complex yet very stable assemblages of phototrophic, autotrophic, and heterotrophic microorganisms
Prochlorophytes
Tiny prokaryotic phototrophs that are phylogenetically related to cyanobacteria
In the same example of the lake ecosystem, where do you find the highest energy yield? Where are methanogens and fermentative bacteria located?
Towards the top of the sediments. Methanogens and fermentative bacteria are located at the bottom of the sediments
What is the function of biofilms?
Trap nutrients for microbial growth and help prevent detachment of cells on dynamic surfaces, such as flowing systems
What are the most abundant microorganisms in the ocean?
Viruses
"Feast-or-Famine" Existence
When a large amount of nutrients enter the ecosystem followed by nutrient deprivation, happens intermittently
Biofilms
When bacterial cells grow on surfaces and form assemblages of bacterial cells attached to a surface and enclosed in an adhesive matrix secreted by cells
Quorum Sensing
intracellular communication