Microbial diversity and proxy species for human impact in Italian karst caves

Abstract

To date, the highly adapted cave microbial communities are challenged by the expanding anthropization of these subterranean habitats. Although recent advances in characterizing show-caves microbiome composition and functionality, the anthropic effect on promoting the establishment, or reducing the presence of specific microbial guilds has never been studied in detail. This work aims to investigate the whole microbiome (Fungi, Algae, Bacteria and Archaea) of four Italian show-caves, displaying different environmental and geo-morphological conditions and one recently discovered natural cave to highlight potential human-induced microbial traits alterations. Results indicate how show-caves share common microbial traits in contrast to the natural one; the first are characterized by microorganisms related to outdoor environment and/or capable of exploiting extra inputs of organic matter eventually supplied by tourist flows (i.e. Chaetomium and Phoma for fungi and Pseudomonas for bacteria). Yet, variation in microalgae assemblage composition was reported in show-caves, probably related to the effect of the artificial lighting. This study provides insights into the potential microbiome cave contamination by human-related bacteria (e.g. Lactobacillus and Staphylococcus) and commensal/opportunistic human associated fungi (e.g. Candida) and dermatophytes. This work is critical to untangle caves microbiome towards management and conservation of these fragile ecosystems.

The geomicrobiology of limestone, sulfuric acid speleogenetic, and volcanic caves: basic concepts and future perspectives

“…Furthermore, a robust core microbiome of shared ASVs (15.1%) between five limestone caves located in different regions of Italy ( Biagioli et al, 2023 ) supported the high degree of adaptation and specialization for microbial communities in limestone caves. Different from limestone caves, studies on volcanic caves from geographically distant areas highlighted a low number of shared OTUs among microbial communities, suggesting that slight differences in lava chemistry or other microenvironmental factors may affect the microbial community structure of volcanic caves ( Hathaway et al, 2014 ; Gonzalez-Pimentel et al, 2018 ; Prescott et al, 2022 ).…”

“…Among carbonate rocks, those composed of calcite (CaCO 3 ) are the prevalent substrate for limestone cave formation ( Biagioli et al, 2023 ), as opposed to the less soluble dolomite [CaMg(CO 3 ) 2 ] rock. Limestone caves are often epigenic since generated by the acid rainwater actions that induce the dissolution of underlying calcite rocks ( Culver and Pipan, 2009 ), while SAS caves are hypogenic since formed by hydrogen sulfide (H 2 S)-rich water rising from the depths of the Earth ( Engel et al, 2004b ; D’Angeli et al, 2019a ).…”

“…Given the continuous improvement of next-generation sequencing (NGS) and analytical chemistry methods, various culture-independent approaches are being applied to cave microbiomes, e.g., 16S rRNA metataxonomic profiling ( Biagioli et al, 2023 ), metagenomic shotgun sequencing ( Wiseschart et al, 2019 ; Turrini et al, 2020 ), metatranscriptomics ( Mondini et al, 2022 ) and proteomics ( van Spanning et al, 2022 ). In parallel, high-magnification and fluorescence microscopies have contributed to unveiling biofilm-like structures on cave surfaces, identifying and quantifying specific taxa composing these communities, and studying the functional properties of individual microbial components ( Jones et al, 2023 ).…”

Microbiological exploration of the Cueva del Viento lava tube system in Tenerife, Canary Islands

“…There are two dominant bacterial groups, which alternate in first and second positions, according to different studies based on DNA analysis to determine diversity in lava tubes: Actinomycetota and Pseudomonadota (Gonzalez‐Pimentel et al, 2018 ; Hathaway et al, 2014 ; Riquelme, Marshall Hathaway, et al, 2015 ). In general, a wide microbial diversity can be found in caves, encompassing numerous bacterial phyla, with Pseudomonadota , Actinomycetota , Acidobacteriota , Nitrospirota and Bacillota as the most abundant groups (Biagioli et al, 2023 ; De Mandal et al, 2017 ; Saiz‐Jimenez, 2012 ). In addition, minority phyla such as Verrucomicrobiota , Planctomycetota , Gemmatimonadota and Chloroflexota and other phyla, considered as microbial dark matter (He, 2023 ; Lok, 2015 ) or belonging to rare biosphere (Hershey & Barton, 2018 ; Lynch & Neufeld, 2015 ; Pascoal et al, 2021 ; Saw, 2021 ) have also been detected.…”

Status of vertebrate species in Danial Cave, northern Iran

“…Cave ecosystems are often more sensitive, vulnerable and poorly studied than other ecosystems yet are often affected by human activities (Elliott, 2000; Silva et al, 2015). This is problematic for conservationists and land managers wishing to balance the ecology of caves with tourist interest in visiting caves (Medellin et al, 2017; Biagioli et al, 2023).…”