Metataxonomic Analysis of Bacteria Entrapped in a Stalactite’s Core and Their Possible Environmental Origins

Abstract

Much is known about microbes originally identified in caves, but little is known about the entrapment of microbes (bacteria) in stalactites and their possible environmental origins. This study presents data regarding the significant environmental distribution of prokaryotic bacterial taxa of a Greek stalactite core. We investigated the involvement of those bacteria communities in stalactites using a metataxonomic analysis approach of partial 16S rRNA genes. The metataxonomic analysis of stalactite core material revealed an exceptionally broad ecological spectrum of bacteria classified as members of Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, and other unclassified bacteria. We concluded that (i) the bacterial transport process is possible through water movement from the upper ground cave environment, forming cave speleothems such as stalactites, (ii) bacterial genera such as Polaromonas, Thioprofundum, and phylum Verrucomicrobia trapped inside the stalactite support the paleoecology, paleomicrobiology, and paleoclimate variations, (iii) the entrapment of certain bacteria taxa associated with water, soil, animals, and plants such as Micrococcales, Propionibacteriales, Acidimicrobiales, Pseudonocardiales, and α-, β-, and γ-Proteobacteria.

Phylotypic Diversity of Bacteria Associated with Speleothems of a Silicate Cave in a Guiana Shield Tepui

“…Cave microbial communities are affected by rock types and surface-soil richness/poorness, resulting in various geochemical and hydrochemical features of cave streams, such as pH, organic/inorganic nutrient availability, and buffering action [ 6 , 7 ]. On the other hand, cave microbial communities are likely involved in the formation of various geological forms, such as stalactites in limestone caves [ 8 ] and “champignons”, i.e., mushroom-like white speleothems, uniquely found in silicate caves [ 9 ]. The roles of microorganisms have been well studied but perhaps are still poorly understood [ 10 ].…”

Stalactites Core Prospect as Environmental “Microbial Ark”: The Actinomycetota Diversity Paradigm, First Reported from a Greek Cave

“…They contain small volumes of water trapped within and between the calcite crystals of commonly named liquid inclusions, like the bubbles in ice cores. Rainwater from the cave surrounding area penetrates the ground and epicarst; consequently, it is carried through microcracks and eventually drips from the soda straws suspended from the roof of the cave down on the stalagmites ( Michail et al 2021 ). Based on the above, it is difficult to find instant, unchanged water, dispersed by previous rainfall on land and in caves around the world, able to construct stalactites and stalagmites that incorporate fossil water and trap well-preserved bacteria over millennia, a natural environment ( Affolter et al 2019 ).…”

“…Recent data have shown that cave sediments, as oligotrophic environments, host a highly heterogeneous phylogenetic pluralism dominated by Actinomycetota and Proteobacteria. The prevalence of Proteobacteria species in the stalactite core structure may be related to their fast development rates in rich nutrient habitats (uppermost ground cave surroundings), establishing a substitute for the ground carbon input ( Michail et al 2021 ). De Mandal et al (2017) proposed that bacteria correspond to a significant part of a cave’s ecosystem and play an essential role in preserving a cave’s biodiversity.…”

“…Although caves have been investigated for many years, their rare microbiome is generally under-investigated and often neglected. Caves have been engaging the attention of microbiologists, in particular their microbial divergence, over the last 20 years ( Laiz et al 1999 ; Barton et al 2004 ; Barton 2006 ; Michail et al 2021 ). With the blending of exceptional conditions, including high humidity, moderate low but steady temperature, and scarce nutrients, caves are predicted to sanctum new microorganisms with biological activities like the γ-Proteobacteria, Serratia proteamaculans , and Serratia liquefaciens isolated from bat guano ( Rangseekaew and Pathom-Aree 2019 ; Michail et al 2021 ).…”

“…Caves have been engaging the attention of microbiologists, in particular their microbial divergence, over the last 20 years ( Laiz et al 1999 ; Barton et al 2004 ; Barton 2006 ; Michail et al 2021 ). With the blending of exceptional conditions, including high humidity, moderate low but steady temperature, and scarce nutrients, caves are predicted to sanctum new microorganisms with biological activities like the γ-Proteobacteria, Serratia proteamaculans , and Serratia liquefaciens isolated from bat guano ( Rangseekaew and Pathom-Aree 2019 ; Michail et al 2021 ). The harmonization of Actinomycetota to unfriendly habitats and the unveiled related synergies have led to the development of unique biotechnological capabilities ( Farda et al 2022 ).…”