Soil Teeming with Life: New Frontiers for Soil Science - Sustainable Management of Soil Organic Matter - page 397

genomics is extracting functional and evolutionary information from these
large data sets and, from an ecological point of view, applying genomics
technology to relevant questions in microbial ecology. This technology can
have a tremendous impact on soil microbiology. Hence, in this section, we
introduce DNA microarray technology, describe the basic method and
detail some of the potential applications of this technology to microbial
ecology as well as some of the current limitations in this field. We hope that
this introduction will facilitate entry of this technology into soil science.
DNA microarrays are microscopic arrays of large sets of DNA
sequences immobilized on solid substrates. Microarrays are used in hybrid-
ization experiments designed to detect gene expression under defined
experimental conditions, or to detect the presence of the arrayed sequences
in a given sample. There are two general types of arrays: (i) cDNA
microarrays, which are constructed either with partial (expressed sequence
tag; EST) or full-length complementary DNA (cDNA) sequences typically
generated with PCR; and (ii) oligonucleotide microarrays, which are con-
structed with short (15-40 mer) or longer (i.e. 75 mer) oligonucleotide
sequences, designed to be complementary to specific coding regions of
interest. In cases when short oligonucleotides are used, often 10-20 probes
per gene and mismatch probes are put on the array. There are numerous
advantages of microarrays over other hybridization strategies: (i) the high
capacity of printing the array on solid substrate (either microscope slides, or
1 1cm 2 wafers) allows tens of thousands of samples to be arrayed; (ii) the

overall reduction in size of the experiment reduces amounts of probe and
hybridization volume, and increases sample concentration and reaction
kinetics (Eisen and Brown, 1999); (iii) global information can be accessed
in studies with completely sequenced genomes, or with large numbers of
ESTs, such that coverage is broad, and a collective picture of whole organ-
ism gene expression can be developed; (iv) speed and high throughput
design using robotic printing of DNA samples allows the mass production
of cDNA arrays, increasing quality control; (v) parallel design facilitates
substantial data acquisition; and (vi) when used with two-colour fluores-
cence detection, direct comparison of independent experimental samples is
readily obtained.
Microarray hybridization approaches promise to revolutionize biology,
much in the same way that DNA sequencing and PCR have in recent years.
DNA microarrays allow thousands of genes to be surveyed under copious
experimental conditions in parallel. Initial studies used cDNA microarrays
to determine gene function (i.e. Schena et al ., 1995, 1996). For organisms
in which the complete genome sequence information is available, it is possi-
ble to study the expression of all genes in a single experiment (Eisen and
Brown, 1999). Studies have been completed in this regard utilizing the full
sequence of Saccharomyces cerevisiae (i.e. DeRisi et al ., 1997; Wodicka et al .,
1997). Additional applications of microarray technology have included

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