ABSTRACT

Bacterial diversity is central to ecosystem sustainability and soil
biological function, for which the role of roots is important. The high
throughput potential of taxonomic microarray should match the breadth of
bacterial diversity. Here, the power of this technology was evidenced
through methodological verifications and the analysis of biological
results based on the 16S rRNA-based microarray developed from the
prototype of Sanguin et al. (2005). The current probe set was composed
of 169 probes (41 new probes in this work) that targeted essentially the
Proteobacteria. Cloning-sequencing were carried out on rhizosphere and
bulk soil DNA. All clones tested that had perfect match with
corresponding probes were positive in the hybridization experiment. The
level of taxonomic identification was variable, depending on the probe
set specificity, but the hierarchically nested probes were reliable. The
comparison of experimental and theoretical hybridizations revealed 0.91%
false positives and 0.81% false negatives. The microarray detection
threshold was estimated at 0.03% of a given DNA type based on DNA
spiking experiments. Comparing rhizosphere and bulk soil hybridization
results showed a significant rhizospheric effect with a higher
predominance of Agrobacterium in the rhizosphere as well as a lower
prevalence of Acidobacteria, Bacteroidetes, Verrucomicrobia and
Planctomycetes, a new taxa of interest in soil. In addition, well-known
taxonomic groups such as Sphingomonas spp., Rhizobiaceae and
Actinobacteria were identified in both ecosystems with strong
hybridization signals. Thus, the taxonomic microarray developed in this
study was able to discriminate and characterize bacterial community
structures in related biological samples. The microarray approach for
systematic exploration of ecosystem diversity offers extensive
possibilities.