MICR 4040: Scales

Ecological scale

The level or range at which an ecological pattern or process is studied.

Grain

The smallest unit of observation or measurement, such as a sample, OTU, or ASV.

Extent

The breadth of a study across space or time, such as a geographic range or time span.

Why does scale matter in microbial ecology?

Different scales can reveal different patterns and processes, so conclusions depend on the scale studied.

Microscale

Spatial scale from micrometers to millimeters, where cells, aggregates, and biofilms interact.

Local scale

Spatial scale from centimeters to meters, such as within soil cores or gut compartments.

Landscape scale

Spatial scale across kilometers, where distinct habitats can be compared.

Global scale

Worldwide spatial scale used to study microbial biogeography across places such as oceans and soils.

Short-term temporal scale

Hours to days, when processes such as daily rhythms, bacterial replication, viral infection, or diet shifts can affect communities.

Medium-term temporal scale

Weeks to years, when communities may respond to disturbances and recover, such as after antibiotic treatment.

Long-term temporal scale

Decades to millennia, when processes such as succession and host–microbe coevolution occur.

Phylogenetic scale

The taxonomic level of analysis, from genes and strains to species and broader clades.

Why do phylogenetic scale and taxonomic resolution matter?

Patterns can differ by level: broad clades may share functions, while strain-level differences can affect interactions such as pathogenicity.

OTU

Operational taxonomic unit, a way of grouping microbial sequences for analysis.

ASV

Amplicon sequence variant, a sequence-based unit used to distinguish microbial variants.

Distance–decay relationship

Community similarity tends to decrease as geographic distance increases.

What can drive distance–decay patterns?

Dispersal limitation and environmental filtering.

Taxa–area relationship

The number of taxa observed tends to increase as the sampled area grows.

Why does the taxa–area relationship matter?

It can guide sampling design, conservation, and the search for useful microbial resources.

Microscale assembly in biofilms and flocs

The identity and location of neighboring microbes matter; complementary metabolisms can support cooperation, while antagonistic taxa may become segregated.

Short-term microbiome dynamics

Daily changes in factors such as food intake can shift community composition; bacterial replication and viral infection can occur over hours.

Community response to perturbation

After disturbances such as antibiotics, infections, or pollutants, some communities return toward baseline while others settle into a new stable state.

Microbial succession

Changes in community composition over time as an environment or host develops; for example, the infant gut microbiome changes during early life.

Spatiotemporal pattern

A pattern shaped by both location and time, such as seasonal cycles across regions.

Legacy effect

A past environmental condition that continues to influence a community in the present.

Nestedness

A pattern in which less diverse communities contain subsets of the taxa found in more diverse communities.

Taxa–time relationship

A scaling pattern in which the taxa observed in a community relate to how long it is sampled; longer observation can reveal more taxa.

How do ecological processes vary across scales?

Selection can dominate at the microscale, dispersal limitation can matter regionally, and mutation and speciation shape patterns over long evolutionary times.

Environmental microbiomes

Soil, marine, and natural biofilm communities are shaped by factors such as pH, climate, land use, seasonal change, dispersal, and local interactions.

Host-associated microbiomes

Microbial communities vary across body sites or plant tissues, and they can also change over time through daily rhythms, development, and seasonal succession.

Human microbiome spatial variation

Skin, gut, and mouth communities can differ strongly, even while an individual's microbiome may remain relatively stable over time.