*5.3.7 DNA microarray*

Nucleic acid (DNA/RNA) hybridization using specific probes is another qualitative and quantitative tool in molecular bacterial ecology. Oligonucleotide or polynucleotide probes designed from known sequences ranging in specificity from domain to species can be tagged with markers (fluorescent) at the 5′-end [55]. Based on nucleic hybridization, DNA microarrays are developed and are used to detect and identify bacterial species in soil or any other environmental samples. In this method, a single chip contains thousands of probes with high specificity can be used in identifying microbial species in soil or environmental samples. The amplified products from the soil DNA is hybridized against the known molecular probes, which are attached on the microarrays. The hybridized spots are detected and scored using microscopy. Its advantage is the rapid and replicated evaluation of the samples [56] but while analyzing the soil or environmental sample there may be risk of cross hybridization. Further, there are two different microarray chips namely 16S rRNA gene microarray or PhyloChip and Functional gene microarray or GeoChip (**Figure 4**).

PhyloChip is the most widely used phylogenetic array. In here, 16S rRNA genes are extracted followed by PCR amplification of metagenome DNA and then biotin labeled for PhyloChip hybridization, the signals are detected using digital image detection. It is Affymetrix-based technology consisting 25-mer oligonucleotide probes which differentiate between the 16S rRNA gene sequences in microbial communities. The recent version of the PhyloChip (G3) has probes targeting ~60,000 operational taxonomic units (OTUs), representing two domains (Archaea and Bacteria), 147 phyla, 1123 classes, 1219 orders, 1464

**Figure 4.** *DNA microarray chip (PhyloChip or GeoChip).*

families, and 10,993 subfamilies [57]. Functional gene arrays are used in targeting genes involved in various biogeochemical cycling processes which help in determining the functional composition microbial communities. GeoChip, a functional gene array is widely used which targets hundreds of functional genes involved in biogeochemical, ecological, and environmental analyses. Arrays for detecting specific functional processes, such as nitrogen cycling, methanotrophy, stress responses, hydrogen activity etc. are available. The version 5.0 GeoChip contains about 167,000 50-mer oligonucleotide probes covering ~395,000 coding sequences from >1590 functional genes related to various microbes, mineral cycling, energy metabolism, antibiotic resistance, metal homeostasis and resistance, secondary metabolism, organic remediation, stress responses, bacteriophages, and virulence [58].
