Microbial Ecology: Structure, Function, and Symbiosis in Ecosystems and Hosts

Study Guide - Smart Notes

Tailored notes based on your materials, expanded with key definitions, examples, and context.

Microbial Ecology

Introduction to Microbial Communities

Microbial communities are fundamental to Earth's biosphere, shaping the environment for plants and animals and recycling organic material. Microbes also influence geological processes below the surface, such as shaping crustal rock.

Microbial communities are groups of microorganisms living and interacting in a shared environment.
They play essential roles in nutrient cycling, organic matter decomposition, and ecosystem stability.
Examples: Microbes recycle organic material in aquatic environments and shape crustal rock in terrestrial habitats.

Microbes in Ecosystems

Microbes are ubiquitous, found in every habitable environment and filling every potential ecological niche. Their ability to thrive in diverse environments is determined by their genome and environmental factors.

Assimilation: The process by which organisms acquire elements (e.g., carbon, nitrogen) to build into cellular structures.
Dissimilation: The breakdown of organic nutrients into inorganic minerals, releasing energy.
Biomass: The total mass of living organisms in a given area.
All organisms participate in the food web to obtain energy and materials for biomass.
Trophic levels: Hierarchical levels in a food web, representing stages of consumption (e.g., producers, consumers, decomposers).

Food Web Structure

Primary producers: Absorb energy from outside the ecosystem (e.g., sunlight) and assimilate minerals into biomass.
Consumers: Include grazers and predators that feed on producers or other consumers.
Decomposers: Consume bodies of dead organisms, recycling nutrients.

Food Web Component	Role
Primary Producers	Energy absorption, biomass formation
Grazers	Consume producers
Predators	Consume grazers and other predators
Decomposers	Recycle dead biomass

Habitat Differences

Marine ecosystems: Producers are phototrophic bacteria (CO2 fixation), consumers are protists and viruses.
Terrestrial ecosystems: Producers are plants, consumers are herbivores.

Microbial Symbiosis

Symbiosis refers to the intimate association between a microbe and another species. These relationships can be mutualistic, parasitic, or commensal.

Mutualism: Both partners benefit (e.g., lichens, rhizobia-legume interactions).
Parasitism: One partner benefits at the expense of the other (e.g., plant pathogens).
Commensalism: One partner benefits, the other is unaffected.

Examples of Mutualism

Lichens: Symbiosis between a fungus and a photosynthetic partner (alga or cyanobacterium).
Rhizobium: Bacteria inside leguminous plants fix atmospheric nitrogen.
Mixotricha paradoxa: Ciliate in termite guts with bacterial endosymbionts for cellulose digestion.
Mycorrhizae: Fungi associated with plant roots, aiding nutrient absorption.

Lichens

Fungal partner provides shelter, water, and minerals.
Photosynthetic partner (algae/cyanobacteria) generates organic carbon and fixes atmospheric nitrogen.
Pioneer biota for colonizing soil-less surfaces.

Rhizobia/Legume Interactions

Specific signal exchange initiates nodulation.
Rhizobia enter root cortical cells via infection threads and differentiate into bacteroids (irregular shapes, no cell wall).
Bacteroids remain in symbiosomes, supplying fixed nitrogen; plant leghemoglobin sequesters excess oxygen.
Major source of available nitrogen in the biosphere.

Mixotricha paradoxa

Digestive symbiont of termites; large ciliate with bacterial endosymbionts for cellulose digestion.
Has four types of surface bacteria: two spirochetes and two anchor bacteria.

Plant Pathogens and Parasitism

Pathogenic microbes can colonize plants, causing effects from minimal to devastating. Fungi are the most common plant pathogens, but viruses and bacteria also infect plants.

Agrobacterium: Induces plant galls via Ti plasmid, causing tumor growth.
Fungi: Grow haustorium into plant cells, absorbing nutrients without breaking the plasma membrane.
Fungal diseases: Examples include anthracnose and Dutch elm disease.
Virus infection: Example is tulip mosaic virus.

Marine Microbiology

The open ocean (pelagic zone) is divided into distinct regions, each with unique microbial communities.

Neuston (~10 μm): Air-water interface, highest microbe concentration.
Euphotic zone (100–200 m): Receives light, supports phototrophs.
Aphotic zone: Below light reach, supports heterotrophs and lithotrophs.
Benthos: Ocean floor and sediment, includes thermal vent communities.

Example: Riftia Tube Worms

Found near deep-sea hydrothermal vents.
Symbiosis with endosymbiotic bacteria for nutrient acquisition.

Wastewater Treatment

Wastewater treatment reduces organic matter and human pathogens before water is returned to the environment.

Preliminary treatment: Removal of solid debris.
Primary treatment: Fine screens and sedimentation tanks remove insoluble particles.
Secondary treatment: Microbial decomposition of organic content.
Tertiary (advanced) treatment: Chemical applications (e.g., chlorination) to eliminate pathogens.

Measuring the Unculturable

Many marine prokaryotes are uncultured due to unknown culture requirements. Metagenomics allows characterization by sequencing community DNA.

Metagenomics: Sequencing of all DNA from a microbial community to identify species and functional genes.
Revealed ~25,000 different microbial species per liter of seawater.

Measuring Planktonic Communities

Counting organisms via DNA content (fluorescence microscopy with DAPI dye).
Measuring biomass (chemical assays of protein).
Carbon fixation measured by incorporation of radiolabeled .

Metagenomics Process

Step	Description
Sequence-based metagenomics	Identify genes and metabolic pathways; compare communities
Function-based metagenomics	Screen for functions of interest (e.g., antibiotic production)

Animal Microbial Communities

Animals host diverse microbial communities, especially in digestive systems. These microbes are essential for digestion and nutrient absorption.

Thousands of microbial species in gut and stomach.
Cellulose digestion in termites and ruminants (e.g., cattle, sheep).
Rumen: Largest digestive chamber in ruminants, critical for cellulose breakdown.

Coral Symbiosis

Mutualistic Zooxanthellae (algal symbionts, mostly dinoflagellates) in coral.
Coral responsible for reef formation and coastal shelf ecosystems.
Coral bleaching: Loss or expulsion of algal symbionts, often due to global warming.

Human Microbiome

Humans harbor trillions of microorganisms, forming the microbiome. Each body site has a distinct microbial community, which plays vital roles in health and disease.

Humans have over 1,000 species of bacteria; ratio of human to bacterial cells is about 1:1.
Microbiome functions include vitamin production, immune system development, digestion, and pathogen exclusion.
Microbiome composition varies between individuals but is metabolically similar.

Studying the Microbiome

Historical studies began with Antonie van Leeuwenhoek's observations.
Modern methods include 16S rRNA gene sequencing and metagenomic 'shotgun' sequencing.
16S rRNA sequencing identifies bacterial taxonomy; metagenomics reveals functional potential.

Microbiome Acquisition and Dynamics

Infants are colonized by maternal and environmental microbes at birth.
Human milk contains oligosaccharides that support beneficial gut bacteria and modulate the immune system.
Families share similar microbiomes due to close contact.

Human Microbiome Project

Large-scale study to characterize human microbiome diversity and function.
Sequenced thousands of bacterial isolates from hundreds of individuals.

Lifestyle and Microbiome

Diet, travel, and genetics can alter the microbiome.
Obesity and leanness in mice linked to differences in gut microbiome composition.
Dieting can shift microbiome composition toward that of lean individuals.

Microbiota Fecal Transplantation (FMT)

FMT restores healthy microbiome by transferring fecal material from a healthy donor to a patient.
Used to treat recurrent Clostridioides difficile infections; success rate ~80.5%.
Antibiotics are administered before FMT to clear pathogenic bacteria.

Key Terms

Microbiome: The collective genomes of microorganisms in a particular environment.
Metagenomics: The study of genetic material recovered directly from environmental samples.
Symbiosis: Interaction between two different organisms living in close physical association.
16S rRNA gene sequencing: A method for identifying and classifying bacteria based on the sequence of the 16S ribosomal RNA gene.

Equations

Carbon fixation measurement:

Summary Table: Microbial Roles in Ecosystems

Role	Example
Primary Producer	Phytoplankton, plants
Consumer	Grazers, predators, protists
Decomposer	Fungi, bacteria
Symbiont	Rhizobia, Zooxanthellae
Pathogen	Agrobacterium, fungi, viruses

Additional info: Expanded explanations and context added for clarity and completeness, including definitions, examples, and summary tables.