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• Habitats are the parts of an ecosystem suited to a particular group of populations
• Examples include soils, air, lakes, oceans, deep sediments (to 2-3 km), and tissues of plants/animals
• Habitats are constrained by temperature, water activity, and pH
• Prokaryotes typically have broader ranges than eukaryotes

Habitat Composition Constraints

• Resources: Carbon (organic, CO2), Nitrogen (organic, inorganic), macronutrients (S, P, K, Mg), micronutrients (Fe, Mn, Co, Cu, Zn, Mn, Ni), electron acceptors (NO3-, SO42-, Fe3+), and inorganic electron donors (H2, H2S, Fe2+, NH4+, NO2)
• Conditions: Temperature (cold to hot), water potential (dry to wet), pH (0 to 14), oxygen (oxic to anoxic), light (bright to dark), and osmotic conditions (freshwater to hypersaline)

Ecological Concepts

• Microbial communities are described by both species richness and species abundance
• Species richness describes the total number of different species
• Species abundance describes the population size of each species

Microbial Guilds

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

Environments and Microenvironments

• A microenvironment is the small part of a local environment that is encountered by a species
• Physicochemical conditions in microenvironments change spatially and temporally
• Resources in natural environments are highly variable
• Many microbes in nature face a feast-or-famine existence
• Growth rates of microbes in nature are below maximum rates defined in the laboratory
• Competition and cooperation occur between microbes in natural systems

Soil Composition

• Inorganic mineral matter at approximately 40% of the volume, and organic matter (~5%)
• Air and water at approximately 50%
• Living organisms
• Water often limits microbial activity in surface soils
• Energy source (organic matter) and inorganic nutrient availability are limiting factors
• The rhizosphere, the area around plant roots, possesses an abundance of sugars, organic matter and microbial life

Soil Horizons (From Top to Bottom)

• O horizon: Undecomposed plant materials

• A horizon: Surface soil high in organic matter, dark in color, tilled for agriculture with many microorganisms, and high microbial activity

• B horizon: Subsoil with minerals and humus, leached from the surface; little organic matter and detectable microbial activity, but lower than in the A horizon

• Diverse microenvironments in soils lead to high microbial diversity

Soil Analysis

• 1. Extract soil microbial community DNA.
• 2. Metagenomic analysis of microbial community 16S rRNA genes.
• An OTU (operational taxonomic unit) defines a 16S rRNA gene sequence that differs from all other sequences by >3%
• Molecular sampling indicates 1000s to 100,000s of different microbial species (OTU's) in most soils
• Microbial diversity varies with soil type and geographical location
• Almost all 16S rRNA genes recovered from soil do NOT match cultured species at >97% identity (or 98.7%)
• There are approximately 13,000 cultured, named species, but about 1 million to 1 trillion uncultured species

Cultivating Bacteria

• Many bacteria are hard to cultivate

Ocean Waters

• Microbial activities are major factors in Earth's carbon balance
• Near-shore marine waters contain higher microbial numbers than the open ocean due to higher nutrient levels
• Chlorophyll distribution can be recorded by satellite

Marine Systems

• Eutrophication influences productivity in surface waters
• Oxygen minimum zones impacts anaerobic respiration
• Cold seeps act as electron donors for chemolithotrophy
• Diverse processes lead to gas hydrate formation

Coastal Oceans

• The coastal ocean is host to bacterial and archaeal diversity
• Most of the primary productivity in the open oceans involves photosynthesis that is conducted by Cyanobacteria
• Prochlorococcus represents >40% of the biomass of marine phototrophs
• The amount accounts for approximately 50% of the net primary production of the ocean

Open Oceans

• "Pelagibacter" is the most abundant marine organoheterotroph, an oligotroph
• Oligotrophs grow best at very low nutrient concentrations
• "Pelagibacter” was known from molecular DNA studies to be the most abundant bacterium, it took decades to finally grow it
• This genus contains proteorhodopsin, a form of rhodopsin allowing cells to use light energy to drive ATP synthesis

Marine Environments

• The Deepwater Horizon oil spill was the largest marine oil spill ever
• Oil released as a plume at great depths caused a bloom of hydrocarbon-degrading Gammaproteobacteria, Colwellia, and Cycloclasticus
• Early growth of hydrocarbon-degrading bacteria reduced the environmental impact

Deep Sea

• 75% of all ocean water is the deep sea, lying primarily between 1,000 and 6,000 m depths

• Organisms in the deep sea deal with low temperature, high pressure, low nutrient levels, and an absence of light energy

Planktonic vs. Attached Bacteria

• Microbes can be planktonic (floating freely) or attached to surfaces
• Biofilms are bacterial cell assemblages adhered to surfaces and enclosed in an adhesive polysaccharide matrix

Biofilms

• Formation starts with cell attachment to a surface
• Biofilm formation is followed by the expression of biofilm-specific genes
• Genes encode proteins initiating matrix formation
• Quorum sensing is critical in the development and maintenance of a biofilm
• Major quorum sensing molecules are acylated homoserine lactones
• The matrix is typically a mixture of polysaccharides

Properties of Biofilms

• Self-defense: Biofilms resist phagocytosis and penetration of toxins (e.g., antibiotics)
• Nutrient trapping: Nutrients can be trapped for microbial growth while preventing cell detachment in a flowing system
• Provide for close association: Biofilms allow bacterial cells to live in close association, therefore facilitating cross-feeding and symbioses

Biofilm Impact

• Biofilms are implicated in periodontal disease, cystic fibrosis, tuberculosis, Legionnaires' disease, and Staphylococcus infections
• Biofilm formation is a problem with medical implants like catheters and artificial joints
• Biofilms can slow the flow of liquids through pipelines and accelerate corrosion and the damages are in the billions of dollars per year
• There are few effective antibiofilm agents are available

Microbial Mats

• Microbial mats are very thick biofilms built by phototrophic and/or chemolithotrophic bacteria
• Phototrophic mats have existed for over 3.5 billion years (stromatolites)
• Often occur in systems with low predation/grazing, like extreme ecosystems

Extremophiles

• Extremophiles prefer conditions outside the limits of what is normal

Environmental Stresses

• Stresses: Temperature, pH, pressure, water activity/[salt], oxygen concentration, 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"

Cardinal Temperatures

• Microbes have distinct cardinal temperatures for growth
• These include minimum, optimum, and maximum

Temperature Classes

• Psychrophiles have an optimum below 15°C
• Mesophiles have an optimum between 15-45°C
• Thermophiles have an optimum between 45-80°C
• Hyperthermophiles have an optimum above 80°C

Thermophilic Habitats

• Compost and decaying organic matter, the deep biosphere (30°C increase for every 1 km depth), geothermal systems (hot springs and mud pools etc), undersea vents

Hyperthermophiles

• Archaea are the champions

• There are also hyperthermophilic Bacteria

• No Eukarya grow above 62°C

• Methanopyrus kandlerii grows at 122°C

• Separate processes have different temperature maxima

• Photosynthesis stops at 73°C

• Hydrothermal vents consist of thermophiles and hyperthermophiles

• Chemolithotrophic prokaryotes utilize inorganic materials from the vents (S, H2S, H2, Fe2+, Mn2+, etc.)

• Supports thriving animal and microbial communities

Microbial Life at High Temperatures

• High temperature increases reaction rates and growth rates to a point as well as having negative effects
• Problems:
  • Proteins denature
  • DNA/RNA denature
  • Membranes become too fluid
• Solutions
  • Stronger bonds stabilizing proteins
  • Increased DNA/RNA stability (GC content, reverse gyrase)
  • Decreased membrane fluidity (tetra-ethers)
• Thermophilic enzymes and proteins function optimally at high temperatures.
• Critical amino acid substitutions in a few locations lead to more heat-tolerant folds
• An increased number of ionic bonds between basic and acidic amino acids assists with resisting protein unfolding
• Hydrophobic interiors
• The production of solutes (e.g., di-inositol phosphate, diglycerol phosphate) helps stabilize proteins
• Smaller, more spherical proteins with less quaternary structure can withstand higher temperatures

DNA/RNA stability

• Positive supercoiling of DNA occurs via reverse gyrase
• RNA exhibits higher G=C content