Abstract
The microflora in environmental water consists of a high density and diversity of bacterial species that form the foundation of the water ecosystem. Because the majority of these species cannot be cultured in vitro, a different approach is needed to identify prokaryotes in environmental water. A novel DNA microarray was developed as a simplified detection protocol. Multiple DNA probes were designed against each of the 97,927 sequences in the DNA Data Bank of Japan and mounted on a glass chip in duplicate. Evaluation of the microarray was performed using the DNA extracted from one liter of environmental water samples collected from seven sites in Japan. The extracted DNA was uniformly amplified using whole genome amplification (WGA), labeled with Cy3-conjugated 16S rRNA specific primers and hybridized to the microarray. The microarray successfully identified soil bacteria and environment-specific bacteria clusters. The DNA microarray described herein can be a useful tool in evaluating the diversity of prokaryotes and assessing environmental changes such as global warming.
Highlights
Diverse prokaryotic populations, including bacteria and archaea, co-exist in the microflora of various environments such as soil, air and water
Sample 6, the only lake sample, showed a unique pattern compared to others (Figure 2 and Figure S1). These results suggest that the composition of most bacteria in the environment is similar, this microarray could detect small differences in the prokaryotic species in environmental water
We examined whether DNA from pathogenic bacteria can be detected in the top 1,000 signals generated in each sample
Summary
Diverse prokaryotic populations, including bacteria and archaea, co-exist in the microflora of various environments such as soil, air and water. The analysis of marine water in the Sargasso Sea found 148 novel phylotypes and 1.2 million genes among 1.6 Gbp of DNA sequence [5] These metagenomic data were integrated with those of a global ocean sampling expedition that collected samples at 44 sites, from the Atlantic Ocean near the Nova Scotia peninsula in Canada to the Pacific. Using the DNA Data Bank of Japan (DDBJ), which has collected >140,000 16S rRNA sequences, we designed probes for a DNA microarray to detect prokaryotic species. We applied this array to the metagenomic analysis of microflora from water samples around Japan. Individual pathogenic bacteria were detected, as well as specific prokaryotic clusters that might be associated with the temperature of the water that was sampled
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