Complex bacterial diversity in the white biofilms of the Catacombs of St. Callixtus in Rome evidenced by different investigation strategies

Abstract

Roman Catacombs are affected by different kinds of biofilms that were extensively investigated in the last 14 years. In particular, the areas far from the lamps are often covered by white biofilms of different extension, consistency and nature. The aim of this paper is to describe the profile of the microbial community present in two areas of the Ocean's Cubiculum (CSC13), characterized by similar alterations described as white biofilms, by using a multistep approach that included direct microscopy observations, culture-dependent and culture-independent methodologies through the extraction of DNA and RNA directly from the sampled areas. In addition to this, we extracted the DNA directly from the Petri dishes containing R2A and B4 media after incubation and growth of bacteria. Our results evidenced that a complex bacterial community (mainly constituted by filamentous Actinobacteria, as well as Firmicutes and Proteobacteria) colonizes the two different white biofilms, and its detection, quantitative and qualitative, could be revealed only by different approaches, each method giving different information that only partially overlap.

Nature and origin of the violet stains on the walls of a Roman tomb

“…The dominance of Streptomyces, either in Roman tombs as reported here, in catacombs (Albertano and Urzì, 1999;Krakova et al, 2015) or Etruscan tombs (Agarossi, 1994) highlights the ability of species of this genus to colonize subsurface environments, a fact also observed in many caves (Groth et al, 1999;Maciejewska et al, 2016). cyanobacteria in experimental cyanobacterium-actinomycete associations.…”

Elucidating the ecological networks in stone‐dwelling microbiomes

“…We used both high-throughput amplicon (targeting the 16S rRNA gene) and whole metagenome shotgun sequencing on stone ruins from three distinct climates in Tunisia and Algeria to achieve our objectives. Although climate has been shown to have an impact on stone microbes of the Mediterranean basin (Macedo et al, 2009), most previous research on the microbiome of stone structures of Europe, North America, and South America has instead focused on stone geochemistry as drivers of diversity and functional variation (Cockell et al, 2009;Krakova et al, 2015;Chimienti et al, 2016;Brewer and Fierer, 2017;Gaylarde et al, 2017a,b). In this study, we aimed to determine what aspects of the climate, including precipitation, temperature and others, were associated with specific microbial community variation, particularly in representation of Actinobacteria and Cyanobacteria colonizers.…”

Microbial composition and ecological features of phototrophic biofilms proliferating in the Moidons Caves (France): investigation at the single-cell level

“…Finally, FCM analysis in such a context allowed us to determine major bacterial dynamics according to the environmental factors within the cave (oligotrophic conditions), but not with precise identification of bacterial communities involved in the complex structure and characteristics of the biofilms. Following the conclusions of Krakova et al (2015), we remain aware that a combination of several analytical methods (culture dependent and independent) is the best strategy to gain a better understanding of bacterial diversity and complexity. The black arrow indicates a group of photosynthetic eukaryotes, probably green algae (group R4).…”

“…Several authors such as Groth et al (1999) and Stomeo et al (2008) have reported a high and complex bacterial diversity in several caves in Spain (Altamira, Tito Bustillo, Dona Trinidad, and Santimamiñe) forming white biofilms responsible for the rock alterations. Recently, Krakova et al (2015) have also argued that the bacterial community involved in the formation of white alterations in the Roman Catacombs is larger than expected. In these studies, the authors also used several methods based on culturable and unculturable approaches like cultivation and isolation on plates, microscopic observations, and 16S rRNA gene sequencing.…”