Application of metagenomic methods for selection of an optimal growth medium for bacterial diversity analysis of microbiocenoses on historical stone surfaces

Identification of microorganisms on the surfaces of historical objects traditionally involves classical microbiology techniques. Cultivation methods allow, to a limited extent, the investigation of microbial biodiversity occurring in the environment. The aim of this study was to select microbiological media, the use of which enables cultivation of bacteria in proportions and diversity most similar to that observed in situ in the microbiocenoses of historical stone objects. We carried out scanning electron microscopy (SEM) imaging, quantitative analysis of microorganisms using culture-dependent methods and high-throughput sequencing of the bacterial communities taken from the surfaces of the Pergola located at the Wilanow Palace gardens in Warsaw (Poland). Total DNA was isolated directly from the collected samples and from the grown colonies of microorganisms grouped together from a particular type of microbiological agar media. Amplification of the V3-V4 region of the 16S rRNA gene for Bacteria was performed for each sample. Illumina MiSeq technology was used for sequencing. Metagenomic analysis of the sequences revealed that the agar Wort medium is the best choice to determine the bacterial diversity present in situ in the biocenoses grown on historical sandstone surfaces.