Comparison of Actinobacteria communities from human-impacted and
pristine karst caves
Abstract
Actinobacteria are important cave inhabitants, but knowledge of how
anthropization and anthropization-related visual marks affect this
community on cave walls is lacking. We compared Actinobacteria
communities among four French limestone caves (Mouflon, Reille,
Rouffignac, Lascaux) ranging from pristine to anthropized, and within
Lascaux Cave between marked (wall visual marks) and unmarked areas in
different rooms (Sas-1, Passage, Apse, Diaclase). In addition to the 16S
rRNA gene marker, 441 bp fragments of the hsp65 gene were used and an
hsp65-related taxonomic database was constructed for identification of
Actinobacteria to the species level by Illumina-MiSeq analysis. The
hsp65 marker revealed higher resolution for species and higher richness
(99% OTU cutoff) versus 16S rRNA gene; however, more taxa were
identified at higher taxonomic ranks. Actinobacteria communities varied
between Mouflon and Reille caves (both pristine), and Rouffignac and
Lascaux (both anthropized). Rouffignac displayed high diversity of
Nocardia, suggesting human inputs, and Lascaux exhibited high
Mycobacterium relative abundance, whereas Gaiellales were typical in
pristine caves and the Diaclase (least affected area of Lascaux Cave).
Within Lascaux, Pseudonocardiaceae dominated on unmarked walls and
Streptomycetaceae (especially Streptomyces mirabilis) on marked walls,
indicating a possible role in mark formation. A new taxonomic database
(https://zenodo.org/record/5576074) was developed. Although not all
Actinobacteria species were represented, the use of the hsp65 marker
enabled species-level variations of the Actinobacteria community to be
documented based on the extent of anthropogenic pressure. This approach
proved effective when comparing different limestone caves or specific
conditions within one cave.