Untitled

• Microbial ecosystems are parts of ecosystems suited to particular groups of populations.
• Examples of microbial ecosystems include soils, air, lakes, oceans, deep sediments (2-3 km), and tissues of plants/animals.
• Microbial ecosystems are constrained by temperature, water activity and pH.
• Prokaryotes have broader ecosystem ranges than eukaryotes.

Constraints on Habitat Composition

• Resources like carbon (organic, CO2) and nitrogen (organic, inorganic) affect habitat composition.
• Macronutrients (S, P, K, Mg) and micronutrients (Fe, Mn, Co, Cu, Zn, Mn, Ni) affect habitat composition.
• Electron acceptors (O2, NO3-, SO42-, Fe3+) and electron donors (H2, H2S, Fe2+, NH4+, NO2) affect habitat composition.
• Conditions like temperature (cold to hot), water potential (dry to wet), pH (0-14) affect habitat composition.
• Oxygen levels (oxic to anoxic), light (bright to dark), and osmotic conditions (freshwater to hypersaline) affect the composition of habitats.

Ecological Concepts

• Microbial communities can be described by species richness, i.e. the number of different species present.
• Microbial communities can also be described by species abundance which is population size of each species in an ecosystem.

Guilds

• Guilds are metabolically related microbial populations.
• Guilds perform key steps in biogeochemical cycles.

Environments and Microenvironments

• A microenvironment is the small part of a local environment encountered by a given species.
• Physicochemical conditions in a microenvironment rapidly change spatially and temporally.
• Resources vary greatly in natural environments, leading to feast-or-famine conditions for many microbes.
• Microbial growth rates in nature are usually below maximum rates defined in the laboratory.
• Competition and cooperation occur between microbes in natural systems.

Soil Composition

• Soils are composed of inorganic mineral matter (~40% of soil volume).
• Soils are composed of organic matter (~5%).
• Soils are composed of air and water (~50%).
• Soils are composed of living organisms.
• Water availability limits microbial activity in surface soils.
• Energy source (organic matter) and inorganic nutrient availability are important limiting factors.
• The rhizosphere, the area around plant roots where plants secrete sugars and other compounds, is rich in organic matter and microbial life.

Soil Horizons

• The O horizon is the layer of undecomposed plant materials.
• The A horizon is surface soil, high in organic matter, dark colored, tilled for agriculture, many plants and microorganisms, and has high microbial activity.
• The B horizon is subsoil, contains minerals and humus, and is leached from the soil surface, has low organic matter, microbial activity is detectable but lower than A horizon.
• There are diverse microenvironments in soils and microbial diversity is very high.

Analyzing Soil Bacteria

• Isolate DNA then amplify the 16S gene by PCR.
• Run on agarose gel and check for correct size.
• Sequence, then align sequences to generate a tree.
• An operational taxonomic unit (OTU) is defined as a 16S rRNA gene sequence that differs from all other sequences by >3%.
• Molecular sampling indicates 1000s-100,000s of different microbial species (OTUs) live in most soils.
• Microbial diversity varies with soil type and geographical location.
• Most 16S rRNA genes recovered from environments like soil do NOT match cultured species at >97% identity (or 98.7%).
• There are about 13,000 cultured, named species, but an estimated 1 million to 1 trillion uncultured species.
• The "great plate count anomaly" refers to why so many bacteria are hard to cultivate.

Coastal and Open Ocean Waters

• Due to the size of the oceans, microbial activities are major factors in Earth's carbon balance.
• Near-shore marine waters have higher microbial numbers than the open ocean due to higher nutrient levels.
• Most of the primary productivity in the open oceans is due to photosynthesis by Cyanobacteria.
• Over 40% of biomass of marine phototrophs is Prochlorococcus.
• About 50% of the net primary production of the ocean is Prochlorococcus.
• The most abundant marine organoheterotroph is "Pelagibacter," an oligotroph.
• An oligotroph is an organism that grows best at very low nutrient concentrations.
• Pelagibacter was known from molecular DNA studies to be the most abundant bacterium in the ocean; it took decades to finally grow a strain, and remains unvalidated as a species.
• Pelagibacter contains proteorhodopsin, which allows cells to use light energy to drive ATP synthesis.
• The Deepwater Horizon oil spill was the largest marine oil spill ever.
• The Deepwater Horizon oil spill released oil as a plume at great depths.
• Blooms of hydrocarbon-degrading Gammaproteobacteria, Colwellia, and Cycloclasticus occurred due to the Deepwater Horizon oil spill.
• The growth of hydrocarbon-degrading bacteria reduced the environmental impact of the Deepwater Horizon oil spill.
• More than 75% of all ocean water is deep sea, lying primarily between 1,000 and 6,000 m depths.
• Deep sea organisms deal with low temperature, high pressure, low nutrient levels, and absence of light energy (many lithotrophs!)

Planktonic vs. Attached Bacteria

• Microbes can be planktonic (floating freely) or attached to a surface.
• Biofilms are assemblages of bacterial cells adhered to a surface, enclosed in an adhesive matrix of polysaccharides excreted by the cells.
• Biofilm formation is initiated by attachment of a cell to a surface followed by expression of biofilm-specific genes.
• Genes encode proteins that initiate matrix formation.
• Quorum sensing (sensing and responding to population density) is critical in the development and maintenance of a biofilm.
• The major quorum sensing molecules are acylated homoserine lactones.
• Bacteria form biofilms for self-defense, resisting phagocytosis by immune system cells, and penetration of toxins (e.g., antibiotics).
• Biofilms trap nutrients for microbial growth and prevent detachment of cells in a flowing system.
• Biofilms allow bacterial cells to live in close association with one another, facilitating cross-feeding and symbioses.
• Biofilms have been implicated in several medical and dental conditions, like periodontal disease, cystic fibrosis, tuberculosis, Legionnaires' disease, and Staphylococcus infections.
• Biofilms are a problem with medical implants like catheters and artificial joints.
• Biofilms in industrial settings slow liquid flow through pipelines and accelerate corrosion, causing billions of dollars in damage.
• Very few effective antibiofilm agents are available.
• Microbial mats are very thick biofilms, built by phototrophic and/or chemolithotrophic bacteria.
• Phototrophic mats have existed for over 3.5 billion years (stromatolites)
• Microbial mats often occur in systems with low predation/grazing, e.g. extreme ecosystems

Extremophiles

• Extremophiles prefer conditions outside normal limits.

Environmental Stresses

• Environmental stresses include temperature, pH, pressure, water activity/[salt], oxygen concentration, and radiation.
• Organisms that can grow in different ranges of these parameters are given the suffix -philes.
• Organisms that can survive in different ranges of these parameters are given the suffix -tolerant.
• Enzymes have minimum, optimum, and maximum temperatures.

Temperature Classes

• Psychrophiles have an optimum temperature <15°C.
• Mesophiles have an optimum temperature of 15-45°C.
• Thermophiles have an optimum temperature of 45-80°C.
• Hyperthermophiles have an optimum temperature >80°C.
• Thermophilic habitats include compost, decaying organic matter, the deep biosphere, geothermal systems, hot springs, mud pools, and undersea vents.
• Hyperthermophiles include Archaea, and some Bacteria, but NO Eukarya grow above 62°C.
• Different processes have different temperature maxima, e.g. photosynthesis stops at 73°C.
• Thermophiles and hyperthermophiles thrive in hydrothermal vents.
• Chemolithotrophic prokaryotes in hydrothermal vents utilize inorganic materials, e.g. S, H2S, H2, Fe2+, Mn2+.
• Thriving animal and microbial communities are associated with deep-sea hydrothermal vents.

Microbial Adaptations to High Temperatures

• High temperature increases reaction rates and growth rates to a point, but high temperatures can have negative effects on cells.
• Problems at high temperature include:
  • Proteins denaturing
  • DNA/RNA denaturing
  • Membranes becoming too fluid
• Solutions to these problems:
  • Stronger bonds to stabilize proteins
  • Increase DNA/RNA stability (GC content, reverse gyrase)
  • Decrease membrane fluidity (tetra-ethers!)
• Thermophilic enzymes and proteins function optimally at high temperatures due to thermal stability features.
  • Critical amino acid substitutions in a few locations provide more heat-tolerant folds.
  • Increased number of ionic bonds between basic and acidic amino acids resists unfolding in the aqueous cytoplasm.
  • Highly hydrophobic interiors.
  • Production of solutes (e.g., di-inositol phosphate, diglycerol phosphate) helps stabilize proteins.
  • Smaller, more spherical proteins with less quaternary structure
• Positive supercoiling of DNA occurs via reverse gyrase to provide to DNA/RNA stability at high temperatures.
• Higher G=C content can increase RNA stability.