= Microbial ecology
<Microbial ecology> studies how <microorganisms> interact with one another and their surroundings, and how those interactions affect their abundance, distribution and activities. A <microbial community> can be investigated as part of a <soil>, an aquatic <ecosystem> or a living <host (biology)>. Identifying its members, counting them and measuring what they do are related but distinct tasks.
An invented counting example makes the distinction concrete. A population increases from one hundred to two hundred cells while all other cells in the same sample increase from nine hundred to eighteen hundred. Its abundance doubles, but its fraction of the total remains $100/1000=200/2000=0.10$. A report of unchanged relative abundance could therefore conceal a large change in absolute abundance. Sampling volume and the measurement denominator must be explicit.
Molecular measurements add further interpretation. A <16S ribosomal RNA gene> is a useful marker, but <genomes> can contain different numbers of copies and different sequences among those copies. Marker counts and sequence variants cannot automatically be equated with cell counts and distinct <species>.<Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons by Silvia G. Acinas and others>[Abstract, copy number, intragenomic divergence and diversity estimates]{ref}
Experiments can move from association to intervention. In a controlled <Arabidopsis thaliana> system, adding particular <Sphingomonas> strains changed the outcome of a subsequent bacterial challenge. Comparing defined microbial conditions tested an interaction that a list of organisms on healthy leaves alone could not establish.<Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system by Gerd Innerebner and others>[Abstract, defined plant-associated communities and protection assay]{ref}
The questions range from local interactions to <biogeochemical cycles>. A convincing ecological explanation connects the organisms present, the environmental conditions and an explicitly measured process; abundance of a genetic marker alone is not a direct rate measurement.
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