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chemistry (types of organic carbon, available), hence is it the vegetation in
soil that determines biogeographic patterns?
3.
Can microbial activity be mapped at the microaggregate scale? Are
microbes in the centre of aggregates inactive relics? Are microbial processes
primarily patchy? At what size scales? When? In response to what
conditions? The primary regulation of cell activity is thought to be at the
level of gene expression. Can mRNA synthesis be measured at aggregate
scales? How fast is that expression under realistic soil conditions?
For example, what is the time scale for molecular events controlling
denitrification following a rainfall?
4.
What is the degree of coupling between redox active elements and
microbial processes? Are these couplings tight, in effect a symbiosis? How
does such coupling influence soil geochemistry over time?
5.
What poorly studied processes might be triggered by the microbes'
in
situ
environment? Does the starvation state induce synthesis of a protective
coat, e.g. produce hydrophobic organic matter, or a physiological state
resistant to stresses such as desiccation? Such responses could change the
nature of soil carbon and result in a physiology that we do not yet recognize.
For example, obligate non-spore-forming anaerobes survive in well-drained
aerobic sandy soils; why?
6.
How can we introduce or manage desired microbial populations to
be more effective? How do we improve their dissemination, by earthworms
or similar animal vehicles? By a combination of chemotaxis and water
management, or by mechanical devices? Once the organisms are dispersed,
how do we ensure gene expression?
The three following sections illustrate some of the points made above
and hopefully show opportunities for better understanding of the soil com-
munity in the future. The first shows how spatial isolation provided by the
soil matrix apparently sustains soil diversity, the second suggests that soil
populations are geographically distinct and the third provides an introduc-
tion to the use of genomic and DNA microarray technologies in microbial
ecology studies. The latter is projected to have great value for understand-
ing microbes in nature and should provide a natural synergy for collabora-
tive research between basic biologists and environmental scientists.
What is the Role of the Soil Matrix in Structuring
Microbial Communities?
While there is likely to be general acceptance among microbiologists that
soil microbial populations are highly complex, recent advances in the
molecular analysis of soil communities have revealed a level of diversity
previously unimagined. For example, small subunit ribosomal DNA
(rDNA)-based studies have shown that clone libraries constructed from
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