Blog Intro

This blog shows information about nucleic acids and proteins in soil.
The great challenge in microbial ecology of the inaugural decade of the
twenty-first century is to resolve and then understand the linkage between
microbial community structure and its function. This goal is based on the
fact that the primary value of microbes is their function and the belief that
understanding the composition, relative abundance, biochemical diversity
and dynamics of the microbial community will help us understand and
eventually predict or manage function in microbial communities of importance.
However, microbial communities are very diverse and complex,
and vary at very small scales and in which cells are active. Furthermore,
measurement of microbial activities at the relevant spatial and temporal
scales, especially in soil, is no less challenging. Hence, linking microbial
community structure and function in predictive ways must be considered
the Decadal Grand Challenge! The desire to link function to structure derives from microbial diversity,i.e. that microbes vary enormously in their biochemical potential.
This is understandable. They have been on earth for 3.8 billion years and
have exploited most energy niches and adapted to a tremendous range of
conditions. Their contemporary progeny carry the genetic heritage from
that extensive diversification and selection. The extant diversification represents
a continuum from a range of major features that we first think
about as functional diversity such as differences in energy-producing redox
couples, metabolic pathways, morphological adaptations (e.g. spores, filaments,
motility, surface-to-volume ratio), and tolerance to environmental
stresses such as desiccation, pHand temperature extremes, salt, and growth
kinetics (r and K selected populations). However, diversification has also
produced a number of other variants that can have major effects on function
but may bemore difficult to recognise in community structure studies
such as differences in enzyme kinetics (e.g. Km, Vmax, Ki), gene regulation
(signal transduction, regulatory networks, response time, specificity), enzyme
stability/turnover, rate and mechanisms of genetic change, and gene
redundancy in the same organism (orthologues, paralogues, isozymes).
The combination of these traits in members of the populations can create
large differences in functional diversity, e.g. low Km, psychroactive, with
rapid induction response populations, versus others that vary in these and
other traits. When certain traits of diversity can be associated with a particular
condition, usually one offering a competitive advantage, we then
have a useful linkage of community structure and function.
Given the small size of the organisms and the tendency to attach to surfaces,
individual microbial cells interact with one another only over short
distances controlled by diffusional processes and gradients. Direct competition
among microorganisms in soil is limited by spatial isolation and
resource heterogeneity among various habitats thus resulting in communities
with equally abundant and uniformly distributed bacterial species
.A two-species test of the hypothesis that spatial isolation influences microbial diversity in
soil indicates that spatial isolation, created by low moisture content, plays
an important role in structuring soil microbial communities. Habitats such as soil should also support a large number of different species expressing significant niche overlap.Mechanisticmodels for the differential performance of species over time within communities and experimental data predict that over time the average niche breadth of individualswill decrease resulting in an increased proportion of specialists.The course of succession will be constrained by selective pressures of physical,chemical and biological conditions existing within a given niche. The balancebetween generalistsandspecialists isimportant as anunpredictable extinction of community members dominated by generalists may hamper community function to a greater extent than in a community comprised of
specialists. The large number of organisms capable of performing individual
biochemical reactions enhances the probability of restoring functions
by replacing extinct, diminished or inactive populations .However, the relationship between microbial diversity–community structure and soil processes was found to be non-linear as many processes are carried out in specialised microbial consortia. Small linear changes in
microbial diversitymay result in non-linear changes in processes, especially
if the number of organisms drops below the number of original functional groups of organisms in a sample .The redundancy of function within a community serves to dampen the loss of ecosystem function in two ways: by providing functional redundancy for
the same pathway/enzyme type or by different pathways that achieve the
same processing goal. Diversity seems to contribute beneficially to redundancy
by providingmultiple ecotypes capable of performing an equivalent
function albeit with a different community structure. Under perturbed
conditions, however, significant deviations in functional traits are possible
and, as the perturbation becomesmore severe, the deviationmore likely. In
these cases numerically minor but important populations can bloom and
dominate function .In short, soil microbial diversity is enormous, the environmental responses and interactions are complex, but we are beginning to understand the causes for
some of the simpler cases.

Analysis of spatial distribution of bacteria at microhabitat levels revealed that 80% of the bacteria in fertilised soils were located in micropores of
stable soil aggregates suggesting that these habitats offer the most favourable conditions for microbial growth (water and substrate availability, gas diffusion, predation protection). Nunan
showed that the degree of randomness in the distribution of bacteria is greater in the subsoil than in topsoil suggesting that bacteria have a hot-spot distribution in bulk soil, with the hot spots being smaller in the subsoil than in the topsoil. Sessitsch showed that microbial
diversity increases with decreasing particle size and that particle size has a more notable impact on microbial diversity and community structure than does bulk pH and the amount and type of organic substrate. Other investigations of different soil types found that the type and amount of
available organic substrates strongly influence the abundance of microbial groups and their functional diversity in soil ecosystems .An emerging theme is that structure–function interactions and vice versa are not easily predicted as either can produce positive, neutral or negative effects on the other depending on the environmental context. In this respect, ecological responses tomultiple stressors over long time scales have yet to be thoroughly explored.