L20 - Environmental Microbiology Flashcards

A set of vocabulary flashcards covering the key concepts and terms from the lecture on environmental microbiology, including ecological levels, biogeochemical cycles, and soil/marine microbiology.

Microbial Ecology

The study of microbes in their natural habitats.

Applied microbiology

The study of the practical uses of microbes in food processing, industrial production, and biotechnology.

Ecosystem

A collection of organisms together with its surrounding physical and chemical factors.

Biosphere

All physical locations on earth that support life.

Hydrosphere

The water portion of the biosphere.

Lithosphere

The soil portion of the biosphere.

Atmosphere

The air.

Biomes

Particular climactic regions characterized by a dominant plant form, temperature, and precipitation.

Communities

Clustered associations of mixed organisms that live together at the same place and time.

Populations

Groups of organisms of the same kind.

Habitat

The physical location and environment to which an organism is adapted.

Microenvironment

The particular qualities of oxygen, light, and nutrient content suitable for a particular microbe.

Niche

Overall roll that a species or population serves in a community.

Consumers

Organisms that feed on other living organisms and obtain energy from bonds present in the organic substrates they contain.

Primary consumers

Grazers or herbivores.

Secondary consumers

Carnivores which feed on primary consumers.

Tertiary consumers

Organisms that feed on secondary consumers.

Decomposers

Primarily microbes inhabiting soil and water that break down and absorb the organic matter of dead organisms.

Mineralization

The process of reducing organic matter into inorganic minerals and gases.

Bioremediation

The process of breaking down most man-made compounds not naturally found in the earth.

Biogeochemical cycling

The movement of elements between the abiotic environment and the biotic environment to maintain a necessary balance of nutrients.

Methanogens

Methane producers that live in anaerobic ecosystems; they produce a greenhouse gas that can trap nearly $20$ times more heat than $CO_2$.

Nitrogen Fixation

The conversion of $N_2$ gas to ammonia by bacteria in root nodules.

Ammonification

The decomposition of organic matter by Clostridium and Proteus to produce $NH_4^+$.

Nitrification

A process where Nitrosomonas, Nitrospira, and Nitrosocossus oxidize $NH_3$ to $NO_2^-$, followed by Nitrobacter, Nitrosospira, and Nitrosococcus oxidizing $NO_2^-$ to $NO_3^-$.

Denitrication

The conversion of $NO_3^-$ through intermediate steps to atmospheric nitrogen ($N_2$), carried out by genera such as Bacillus, Pseudomonas, Spirillum, and Thiobacillus.

Thiobacilli

Gram-negative motile rods that extract energy by oxidizing elemental sulfur ($S$), sulfides ($H_2S$), and thiosulfate ($S_2O_3$).

Phosphorus Cycle

The cycle of phosphorus as $PO_4$ between abiotic and biotic environments, primarily utilizing phosphate rock (fluorapatite) as an organic reservoir.

Metagenomics

The sampling of all the genes in a habitat through environmental DNA extraction and Next Generation Sequencing.

Rhizosphere

The zone of soil surrounding the roots of plants containing associated bacteria, fungi, and protozoa.

Oligotrophic

Nutrient-deficient aquatic ecosystems where organisms like Hyphomicrobium and Caulobacter capture miniscule amounts of hydrocarbons.

Eutrophication

The addition of excess nutrients to aquatic ecosystems causing heavy surface growth of cyanobacteria and algae, leading to oxygen depletion and massive die-offs of aerobes.

Red tides

Harmful algal blooms (HABs) that produce toxins, such as potent muscle toxins, which are concentrated by shellfish through filtration feeding.