Spatial and temporal scales in microbial ecology

A set of vocabulary flashcards covering key concepts from the lecture notes on spatial and temporal scales in microbial ecology.

Grain

Smallest unit of observation in ecology (e.g., sample, OTU, ASV).

Extent

Breadth of the study; geographic range or time span.

OTU

Operational Taxonomic Unit; a taxonomic grouping based on sequence similarity used as a proxy for microbial species.

ASV

Amplicon Sequence Variant; exact sequence variant used for high-resolution microbial profiling.

Microscale

The smallest spatial scale (approximately μm–mm) where cell aggregates and biofilms occur.

Local scale

cm–m scale; e.g., soil cores, gut compartments.

Landscape scale

km scale; different habitats across a landscape.

Global scale

Biogeography across oceans and soils worldwide.

Spatial granularity of sampling

Resolution at which sampling occurs (from μm² to km²), determining what can be identified.

Short-term temporal scale

Hours–days; diurnal rhythms, diet shifts.

Medium-term temporal scale

Weeks–years; perturbations and recovery after antibiotics.

Long-term temporal scale

Decades–millennia; succession and host–microbe coevolution.

Phylogenetic scale

Taxonomic level of analysis (genes, strains, species, higher clades) affecting conclusions.

Taxa–area relationship

Diversity increases with sampled area; microbes follow the same scaling as plants and animals.

Distance–decay relationship

Community similarity decreases with geographic distance; driven by dispersal limitation and environmental filtering.

Dispersal limitation

Constraint on organism movement shaping spatial community structure.

Environmental filtering

Environmental conditions select for taxa with suitable traits.

Functional redundancy

Different taxa performing similar ecological roles; function remains despite taxonomic turnover.

Taxonomic levels (OTU, ASV, genus, species, higher clades)

Conclusions depend on whether OTUs, ASVs, genera, species, or functional guilds are analyzed.

Microscale assemblies

Within biofilms and micro-aggregates; interactions like complementary metabolisms; cooperation and patchiness.

Biofilms

Surface-attached microbial communities with structured organization.

Flocs

Loose, suspended microbial aggregates.

Diurnal oscillations

Daily cycles in microbiome composition/activity.

Perturbations

Antibiotics, infections, and xenobiotics causing changes.

Recovery trajectory

Path back to baseline or shift to a new stable state after perturbation.

Succession

Temporal changes in community composition; development or seasonal changes.

Coevolution

Long-term mutual adaptation between hosts and microbiomes.

Hysteresis

Lag in returning to the original state after perturbation is removed.