Spatial structuring of bacterial communities in epilithic biofilms in the Acquarossa river (Italy)

Abstract

Epilithic river biofilms characterize the rock surfaces along the Acquarossa river (Viterbo, Italy); they are in part red and in part black colored, maintaining a well-defined borderline. This peculiarity has raised questions about the biotic and abiotic phenomena that might avoid the mixing of the two biofilms. In this study, the structuring of bacterial communities in black and red epilithic biofilm in the Acquarossa river has been investigated with both culture dependent and independent approaches. Data obtained highlighted a (very) different taxonomic composition of black and red epilithons bacterial communities, dominated by Acinetobacter sp. and iron-oxidizing bacteria, respectively. The chemical characterization of both river water and biofilms revealed a substantial heavy metals pollution of the environment; heavy metals were also differentially accumulated in red and black epilithons. Overall, our data revealed that the structuring of red and black epilithons might be affected mainly by the antagonistic interactions exhibited by bacterial genera dominating the two biofilms. These findings suggest that biotic factors might be responsible for the structuring of natural bacterial communities, suggesting that there is a selection of populations at very small scale, and that different populations might compete for different niches.

Exploring the Bacterial Communities of Infernaccio Waterfalls: A Phenotypic and Molecular Characterization of Acinetobacter and Pseudomonas Strains Living in a Red Epilithic Biofilm

“…Along the whole river course, rocks are covered by a red and a black biofilm (epilithon). As previously described [3], these epilithons are characterized by high heavy metal concentrations, suggesting that they might represent natural "filters" for the river. Interestingly, the two kinds of epilithic biofilm are characterized by peculiar bacterial communities, from both genetic and phenotypic viewpoints.…”

“…Sequences were clustered into operational taxonomic units (OTUs) using the UPARSE pipeline [19], as described previously [3]. Briefly, raw reads were merged into a single amplicon sequence using the 'fastq_mergepairs' command.…”

“…Merged reads were then quality checked as described in [20]. An additional quality filtering step and sequences clustering were performed [3]. Representative sequences were taxonomically classified using the 'sintax' command along with the RDP training set (version 16).…”

“…Even though some information about the archaeological and historical aspects of the Infernaccio waterfalls and the Acquarossa river are available [12][13][14], from a (micro)biological viewpoint there is an almost complete lack of information, with the only exception represented by the characterization of the red and black epilithic biofilms along the river course [3]. Interestingly, the bacterial community characterization confirmed the presence of strains showing a marked antimicrobial activity against other bacterial strains of the same environments [3]. Moreover, Pseudomonas strains from the Acquarossa river, showed a marked antagonistic activity also against other strains isolated from many other environments [15].…”

“…The finding that no black epilithon was found in the Infernaccio site suggests that the chemical and physical compositions of red epilithon might differ from those of the red epilithon disclosed in the Acquarossa river, which, in turn, might imply that different bacterial communities might have been selected in Infernaccio red epilithon. Thus, this work was aimed to the characterization of the bacterial communities isolated from the red epilithic biofilm collected on the rocks surrounding the bottom of the Infernaccio waterfalls and to compare data obtained with those previously described [3].…”