Agriculture Reference
In-Depth Information
(RDP, http://www.cme.msu.edu/RDP/html/index.html), a large resource
of sequence information is available.
3.
Environmental functional gene arrays. These arrays could come in a
variety of styles. One concept would be to prepare oligonucleotide arrays
for targeted gene expression, with genes of interest on the array. For
example, oligonucleotide probes complementary to genes coding for key
enzymes in all biogeochemical cycling processes could be arrayed. These
would be used for specific detection of expression in the environment.
Another style for an array could be designed to study functional diversity
in nature. These gene arrays could include hundreds of PCR products
representing the diversity found in nature (e.g. nitrate reductase, ammonia
monooxygenase and dechlorinase). The limitations for these two concepts
are similar. They rely on available sequence information for designing the
array. Functional gene sequencing lags far behind the information available
in SSU databases though, with the diversity of genome projects underway,
this situation is changing rapidly. Additionally, samples of varying biomass
concentration
may
present
technical
challenges,
since
large
amounts
of RNA are required for the hybridization experiments (5-10
g total
RNA per experiment). Developments in signal detection, and in signal
amplification may aid in these problems.
4.
Population biology arrays. Genetic diversity or genetic polymorphisms
within specific populations can be assessed with oligonucleotide arrays.
This has already been done with
M. tuberculosis
(Gingeras
et al
., 1998),
S. cervesiae
(Ferea
et al
., 1999), and with the human cytomegalovirus
(Chambers
et al
., 1999) in which the potential for this application was
demonstrated. Oligonucleotides representing all open reading frames of
a reference organism genome can be arrayed, then assayed against
strain-level variants. Similarly, cDNAs for a genome of interest could be
arrayed then mRNA from isolated strains could be compared with the
reference
ยต
organism
to
study
speciation
and
functional
relationships
between the isolates.
There are clearly a large number of different applications of microarray
technology that can be applied to relevant problems in environmental
microbiology. The field of soil microbiology will benefit invaluably from the
contribution to our understanding of microbial content and function in
the natural environment.
Acknowledgements
This research was supported by NSF Grant DEB9120006 to the Center
for
Microbial
Ecology
and
DOE
grants
DE-AC05-960R22464
and
DE-FG02-97ER62469.
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