The Plate Debate: Cultivable communities have no utility in contemporary environmental microbial ecology

Abstract

Contention: ‘Community-scale characterizations based on cultivable microbes are so unrepresentative that they have no utility in contemporary environmental microbial ecology’ . Microbes are, by definition, very small. Individual microbial cells and isolated fungal hyphae are invisible to the unaided human eye, and remained intangible until the invention of microscopes in the 17th Century. Aggregations of microbial cells to form larger-scale and visible entities occur naturally and can be spectacularly manifest, for example as bacterial slimes, myxomycete plasmodia, and fungal basidiocarps. In the history of microbiology, there was an imperative not just simply to visualize microbial cells, but to enumerate them and understand their form, physiology, function and relationships with their environment. This required the isolation, purification and multiplication of cells to provide sufficient biomass to enable analyses. This was conveniently achieved using dispersal and dilution techniques, most commonly in an aqueous medium, followed by modest enrichment on semisolid media, such that ostensibly separated cells proliferated and formed visible colonies; enumeration was then based on these so-called CFUs, in recognition of the fact that it was not necessarily a single cell that was the originator. Such techniques were pioneered by Koch in the 1880s, who first used cut surfaces of boiled potatoes as an enrichment surface, and then adopted hydrated gelatine films, which were better suited to visualization of colonies. Methods then evolved which adopted other gelling agents, most notably agar, and a huge variety of nutritional supplements to such media as it became apparent that different organisms grew more or less effectively on a variety of substrates. Media were devised that were apparently selective to restricted groups or even species of microbe. These techniques revolutionized both medical and environmental microbiology. In a medical context, the ability to isolate disease-causing microorganisms in a selective manner enabled Koch to formulate and apply …