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Ruminantia is the mammalian group of ruminants, including goats, sheep and deer. Regurgitation and rechewing interact with microbial foregut fermentation. Digestive function therefore depends on both the host’s anatomy and associated microorganisms.

Sawdust consists of small particles of wood produced by cutting or abrasion. Relative to an intact piece of wood, its larger exposed surface affects exchange with the surroundings and access by decomposing microorganisms.

Selenium sulfide is a selenium-containing material used in topical preparations acting on superficial skin and associated microorganisms. Its formulation matters because a dispersed topical material is not equivalent to freely dissolved selenium compounds.

Silvia G. Acinas is a researcher in marine microbial ecology, genomics and evolution. Her institutional research profile describes work connecting the genetic diversity of marine microorganisms with their ecological capabilities, using approaches including metagenomics and cultivation.^[ref]

Acinas was first author of a 2004 study of variation among 16S ribosomal RNA sequences encoded within individual genomes. A genome can contain multiple copies of a 16S ribosomal RNA gene; those copies can be identical or differ in sequence. The study compared copy numbers, sequence divergence and redundancy. These properties complicate the interpretation of diversity estimates based on the marker.^[ref]

An invented example separates two effects. Suppose three microbial cells each have two marker-gene copies and two other cells each have five. With one complete genome per cell and no other biases, there are $3\times 2+2\times 5=16$ marker copies among five cells. Their contributions to the copy pool are $6/16$ and $10/16$, whereas their contributions to cell number are $3/5$ and $2/5$. Marker abundance and cell abundance have different denominators. If copies within a single genome also differ in sequence, multiple sequence variants can originate from one organism.

This work illustrates a recurring measurement issue in microbial ecology: a molecular marker is a biological object whose own variation affects the inference. Acinas and colleagues investigated that variation directly, rather than simply equating each recovered sequence with a separate kind of microorganism.^[ref]

Soil is a natural body at the land surface composed of solid minerals and organic matter, together with liquids and gases in the spaces between them. Its development reflects interactions among parent material, climate and living organisms. Soil horizons and the capacity to support rooted plants are important in its description; a loose mineral powder alone does not capture the whole concept.^[ref]

An original volume example shows why the pore space matters. In $100\mathrm{c}{\mathrm{m}}^3$ of soil, suppose solids occupy $60\mathrm{c}{\mathrm{m}}^3$, water occupies $25\mathrm{c}{\mathrm{m}}^3$ and air occupies $15\mathrm{c}{\mathrm{m}}^3$. The pore volume is $40\mathrm{c}{\mathrm{m}}^3$, giving porosity $40/100=0.40$. The volumetric soil water content is $25/100=0.25$, while the water-filled pore space fraction is $25/40=0.625$. These three fractions use different denominators.

At unchanged pore volume, adding water replaces some of the air rather than increasing the solid fraction. Consequently, a description by dry solid composition alone can miss a major change in conditions experienced by roots and microorganisms. The example assumes fixed total volume and explicitly specified phase volumes; swelling, compaction or incomplete sampling can require a different model.

Cultivation of microorganisms from urine. Growth can support investigation of urinary infection, but contamination, sampling method and clinical context affect interpretation of the organisms and quantities recovered.

Transfer of microorganisms between parent and offspring. Evidence of transfer does not by itself demonstrate host benefit or genetic determination of the transfer.