Lec20A Ch24 Environmental micro

Microbial Ecology: Study of microbes in their natural habitats.
Applied Microbiology: Focus on practical uses of microbes in various sectors (food processing, industrial production, biotechnology).
Ecosystem: Collection of organisms and their surrounding physical and chemical factors.

Biosphere: All physical locations on Earth supporting life.
Hydrosphere: Water component of the ecosystem.
Lithosphere: Soil component.
Atmosphere: Air surrounding the Earth.
Biomes: Climactic regions characterized by dominant plant forms, temperature, and precipitation.
- Communities: Groups of different organisms living together.
- Populations: Groups of the same species living in the same area.
Habitat: Physical location and environment to which an organism is adapted
- Microenvironment: Specific environmental factors affecting particular microbes (oxygen, light, nutrients).
- Niche: Role of a species or population within a community.

Consumers: Organisms that feed on others for energy.
- Primary Consumers: Grazers/herbivores.
- Secondary Consumers: Carnivores feeding on primary consumers.
- Tertiary Consumers: Organisms feeding on secondary consumers.

Decomposers: Primarily microbes that break down and absorb organic matter from dead organisms.
Active at all levels of the food pyramid.
Mineralization: Breakdown of organic matter into inorganic minerals and gases.
Bioremediation: Ability to break down man-made compounds not found in nature.

All elements originate from nonliving reservoirs (atmosphere, lithosphere, hydrosphere).
Element Cycling: Interaction between abiotic and biotic environments, maintaining nutrient balance.
Recycling maintains a necessary balance of nutrients in the biosphere so that they do not build up or become unavailable
Complex cycles involve primary producers, consumers, and decomposers.
All organisms participate in the recycling, but only certain categories of microorganisms have the metabolic pathways for converting inorganic compounds from one nutritional form to another

Carbon: Fundamental atom in biomolecules; significant component of weight in biomass.
Exists in mineral states and as organic reservoirs in organisms.
Methane gas plays a secondary part in the carbon cycle
Methanogens: methane producers that live in anaerobic ecosystems
More potent greenhouse gas than CO2
Ruminant animals contribute to 20% of global methane production.

Nitrogen Fixation: Conversion of N2 to ammonia by bacteria (e.g. in root nodules).
Ammonification: Decomposition leads to NH4+ from organic matter (e.g. by Clostridium).
Nitrification: Conversion of NH3 to NO2- (carried out by organisms like Nitrosomonas) and then to NO3- (through Nitrobacter).
Denitrification: Process by which NO3- is converted back to atmospheric nitrogen by various bacteria (e.g. Bacillus, Pseudomonas).

Similar to carbon cycle in terms of origin (sedimentary deposits).
Transformations involving elemental sulfur, hydrogen sulfide, and sulfate occur via bacteria.
Thiobacilli: Bacteria that oxidize sulfur compounds for energy and thrive in specific environments.
- gram-negative motile rods
- flourish in mud, sewage, bogs, mining drainage, and brackish springs

Phosphorus: Essential for DNA, RNA, and ATP.
Cycles as phosphate (PO4) between biological and abiotic environments.
Chief organic reservoir is phosphate rock, which contains fluorapatite
Major reservoir is phosphate rock, released naturally by bacterial sulfuric acid ( created by Thiobacillus) that dissolves phosphate rock

Soil: A dynamic ecosystem with interactions between geological, chemical, and biological factors.
- Antibiotic-producing microbes are prevalent.
- Porous nature of the soil provides numerous microhabitats
- that support diverse microbial communities, including bacteria, fungi, and archaea, all of which play crucial roles in nutrient cycling and soil health.
  - Antibiotic-producing and antibiotic-degrading microbes are present in the soil
  - Porous nature of the soil provides numerous microhabitats
Microhabitats: Various conditions (aerobic, anaerobic) support different microorganisms.

Metagenomics: Technique sampling all genes in a habitat starting from environmental samples.
Involves extraction of DNA and Next Generation Sequencing.
Related fields include metatranscriptomics and metaproteomics.
Synthesis of genes of interest for expression and further study
Also metatranscriptomics and metaproteomics

High microbe count in moist loam soil (up to 10 billion in a gram).
Rhizosphere: The soil zone around plant roots, populated with various microbes influencing plant health.
- contains associated bacteria, fungi, and protozoa
- Plants interact w/ microbes in a synergistic fashion

Sampling deep below the surface (up to 2 miles) reveals ancient microorganisms.
- Bacteria found 500 meters below the seafloor in clay deposited 86 million years ao
Discovery of new metabolic capabilities in subsurface microbes may inform theories on the origin of life.

Oceans present extreme conditions (salinity, pressure); support diverse microbial life.
Early expeditions revealed vast genetic diversity and new proteins.
- 6 million new genes
- Thousands of new proteins
Recent sampling
- 12 x more diversity than previously thought
Estimates indicate 10 million of viruses per ml in marine samples, predominantly bacteriophages.

Red Tides: Result from environmental factors enhancing algal growth, creating toxic effects.
Algae can produce muscle toxins that accumulate in shellfish, impacting humans and marine life.

Chlamydomonas: Example of a unicellular green alga; notable features include nucleus and chloroplasts.

Oligotrophic environments: Nutrient-poor ecosystems with specialized microbes like Hyphomicrobium and Caulobacter
- These capture miniscule amounts of hydrobacrbons in these environments
Eutrophication:
Excess nutrient addition leads to cyanobacteria blooms, depleting oxygen and causing die-offs in aerobic species.
Common nutrient sources implicated in algal blooms often stem from agricultural runoff.
Aerobic heterotrophs deplete oxygen further by decomposing organic matter
- cause massive die-offs of strict aerobes