Unearthing microbial diversity, environmental and human impacts in cave ecosystems

Abstract

Caves are spatially confined, subsurface environments widespread on Earth, where peculiar abiotic factors and microclimatic conditions impose special adaptations to microbial life-forms. Yet, the growing touristic interest and transformation of natural hypogean sites into authentic tourist attractions, coupled with global climate instability, dramatically challenges the preservation of these fascinating underground ecosystems and their cultural and natural heritage. This thesis aims to investigate cave microbial communities to provide new insights about changes in compositional and diversity patterns as a response to the impact of human activities and external environmental drivers still lacking to date. Advanced sequencing technologies led to the assembly of an extensive sediment microbiomes dataset from 4 tourist and 1 natural Italian caves for the first time. Overall, our findings indicated how showcaves share common microbial traits in contrast to the natural one and some evidence of potential direct microbiome cave contamination by human-related bacteria and commensal/opportunistic human associated fungi were reported. Then, by adopting an advanced ecological framework approach, we highlighted how bacteria was the most sensitive microbial assemblage to tourism pressure and that the stochastic forces (Drift) were the dominant selective processes in driving composition of microbial communities across anthropized habitats. Finally, by using a meta-analysis approach, we investigated, for the first time, cave microbiomes at global scale and we found that climatic variables were the stronger predictors of compositional and diversity patterns of top dominant phylotypes. This knowledge is critical to further develop long-term approaches and strategies aimed at preserving the astounding natural and cultural heritage of caves worldwide.