Nannipieri et al. 2003

Nannipieri P, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G. 2003. Microbial diversity and soil functions. European Journal of Soil Science 54: 655-670.

These authors present a review of the current state of knowledge about microbial diversity and ecosystem function such as organic matter decomposition in soils. They devote sections of the paper to the structure of soil as a habitat for microbes and other soil-dwelling organisms, methods of measuring microbial diversity, measuring soil functions, the current understanding of these methods and prominent results, and how these measures fit together in various contexts.

Unlike above-ground systems, soils appear to have no link between function and microbial diversity, or the direction and magnitude of the relationship varies considerably with which function is studied. General ecology theory and results suggest there should be a hump-shaped relationship between biodiversity (species richness and evenness) and productivity, such that productivity increases with diversity to some point, before declining. This relationship has not typically been found in soil systems, though there are relatively few studies of this relationship specifically in soils.
Measuring function in soils is complicated by the structure of soil. It is largely composed of non-living matter, some of which such as clay surfaces are capable of catalyzing reactions normally associated with living cells. In addition, these surfaces can adsorb large organic molecules such as enzymes and nucleic acids and protect them from degradation while still allowing some catalytic activity. Thus, even after all cells have been killed in a soil sample, enzymatic activity may be detectable. Distinguishing between biotic and abiotic chemical reactions in natural soil systems is therefore extremely difficult.

Measuring biodiversity in soil is not much easier than measuring function. Plate-count methods have been widely criticized because they will measure only culturable organisms, variously estimated to compose a small fraction of actual biodiversity. Countering this criticism, some researchers have suggested that the biomass, rather than species richness, of unculturable microbes is a minority, rendering plate counts of culturable species much more relevant to ecological studies. However, much attention has been focused recently on molecular methods, further divided into DNA-based techniques and fatty-acid based techniques.

DNA-based techniques deployed to study microbial diversity in soils often include a PCR step. However, DNA extraction methods for soil must balance several trade-offs, for example gram positive bacteria have very tough cell wall structures that require harsh treatment to break down and access their DNA. This same harsh treatment can shred DNA from less-tough cells to under 1kb fragments, which will often form chimeras during PCR, especially when using universal primers for such popular markers as 16s rDNA. Similarly, high-efficiency methods of DNA extraction and isolation are also efficient at extracting humic acids, which interfere with PCR. Despite these concerns, a large number of studies based on PCR of soil-derived DNA templates have been published, providing a large database of sequences for phylogenetic comparison.

Fatty-acid based techniques avoid the PCR-based concerns of DNA methods, but are less specific in their results: fatty acid composition is generally not species-specific the way DNA sequence data can be. However, techniques such as PFLA provide useful estimates of soil microbial biomass.

There is an ecological puzzle in the observed high biodiversity of near-surface soils. Two competing, though probably not mutually-exclusive hypotheses centre on a lack of competition among soil microbes. Under the first hypothesis, microbial microhabitats tend to be isolated from each other, preventing contact and competition. Community mixing occurs when water droplets bridge the gaps between soil aggregates, as during rainfall when soil pore spaces are filled. Countering this hypothesis is the observation that much of the near-surface soil environment is not especially prone to pore-drying, for example the plant root-soil interfaces, yet contains high species richness. The second hypothesis suggests that high specialization for organic substrates (i.e. microbe food) prevents competition among cells in close physical proximity. There are higher quantity and diversities of organic molecules in surface soils compared to greater depths, but flow channels such as cracks, fissures, and worm burrows also have high levels of organic molecules, and high microbial biomass, but do not show higher diversity than the surrounding bulk soil. The puzzle remains unsolved.

Much of the discussion of various measurements in this paper is of direct relevance to my own work. The various methods for assessing soil function, for example, are almost all measures of enzyme activity, which is precisely what my gas-flux measurements are as well. I intend to measure biodiversity, by molecular means, and the references and discussion here are valuable. Overall, this review paper does a good job of providing an overview of some issues I will also be exploring.