Soil Teeming with Life: New Frontiers for Soil Science - Sustainable Management of Soil Organic Matter - page 398

screening for mutations in specific genes (Hacia et al ., 1996), identifying
genes involved in genetic diseases (Heller et al ., 1997), evolutionary
sequence comparisons of closely related species (Hacia et al ., 1998),
studying mutation incurred during adaptive evolution (Ferea et al ., 1999)
and detecting genetic variants, or genetic expression studies in temporally
expressed viral genes (Chambers et al ., 1999). Oligonucleotide arrays are
also used for DNA sequencing and genotyping (Gingeras et al ., 1998),
which is a promising application of the high-density oligonucleotide
hybridization platform. Affymetrix (Santa Clara, California) is developing
sequencing by hybridization technology, and currently is marketing
oligonucleotide-based arrays (GeneChips) in which the probes are
synthesized in situ utilizing photolithographic technology, in which all
oligonucleotides are synthesized in parallel. Currently, GeneChips for
rat, human and yeast open reading frames are available, with applications
directed

towards expression analysis, polymorphism analysis and

genotyping, and disease management.
Development of microarray technology for studies in microbial ecology
is just being launched (Guschin et al ., 1997; Kelly et al ., 1999). The use of
microarrays in prokaryote applications is also in its infancy, though the
number of funded projects in the field of functional genomics, and the
numbers of biotechnology and pharmaceutical companies involved in
microarray research, is growing rapidly, suggesting that the future in this
field is very promising. There are several microbiology/microbial ecology-
oriented research areas that will benefit from microarray technology such
as: determining the metabolic effects of novel antibiotics or mutations;
identifying the presence of specific messages, DNA sequences or genomes
in natural samples; understanding gene regulation coincident with patho-
genicity; identifying pathways and regulatory networks involved in
bioremediation and biogeochemical processes; and screening natural
populations for evolutionary divergence. Commercial chips for soil bacteria
are not likely to be available; the market is too small. Hence, we will need
to make our own.

Microarray basics

Due to the variety of schemes for which DNA microarrays can be used, we
will discuss, in general, the types of equipment and gene information that
will be necessary for development of DNA microarrays that appear to be
useful for microbial ecological studies. For specific methods, we refer the
reader to a recent publication by Eisen and Brown (1999), which covers
cDNA microarray technology as applied to gene expression studies.
The flowchart in Fig. 6.5 depicts the basic strategy for a microarray
project. Only general attributes of the scheme have been listed, as this is