Longitudinal metabarcode analysis of karst bacterioplankton microbiomes provide evidence of epikarst to cave transport and community succession

Abstract

Caves are often assumed to be static environments separated from weather changes experienced on the surface. The high humidity and stability of these subterranean environments make them attractive to many different organisms including microbes such as bacteria and protists. Cave waters generally originate from the surface, may be filtered by overlying soils, can accumulate in interstitial epikarst zones underground, and emerge in caves as streams, pools and droplets on speleothems. Water movement is the primary architect of karst caves, and depending on the hydrologic connectivity between surface and subsurface, is the most likely medium for the introduction of microbes to caves. Recently published metabarcoding surveys of karst cave soils and speleothems have suggested that the vast majority of bacteria residing in these habitats do not occur on the surface, calling into question the role of microbial transport by surface waters. The purpose of this study was to use metabarcoding to monitor the aquatic prokaryotic microbiome of a cave for 1 year, conduct longitudinal analyses of the cave’s aquatic bacterioplankton, and compare it to nearby surface water. Water samples were collected from two locations inside Panel Cave in Natural Tunnel State Park in Duffield, VA and two locations outside of the cave. Of the two cave locations, one was fed by groundwater and drip water and the other by infiltrating surface water. A total of 1,854 distinct prokaryotic ASVs were detected from cave samples and 245 (13.1%) were not found in surface samples. PCo analysis demonstrated a marginal delineation between two cave sample sites and between cave and surface microbiomes suggesting the aquatic bacterioplankton in a karst cave is much more similar to surface microbes than reported from speleothems and soils. Most surprisingly, there was a cave microbe population and diversity bloom in the fall months whereas biodiversity remained relatively steady on the surface. The cave microbiome was more similar to the surface before the bloom than during and afterwards. This event demonstrates that large influxes of bacteria and particulate organic matter can enter the cave from either the surface or interstitial zones and the divergence of the cave microbiome from the surface demonstrates movement of microbes from the epikarst zones into the cave.

Lampenflora in a Show Cave in the Great Basin Is Distinct from Communities on Naturally Lit Rock Surfaces in Nearby Wild Caves

“…Other environmental factors might also impact microbial and lampenflora diversity in caves. A year-long longitudinal study of microbial succession in a karst cave system in Virginia, USA, showed that large influxes of aquatic microbes and particulate organic matter can enter the cave from either the surface or interstitial zones [54]. This results in aquatic bacterioplankton communities within caves that are highly similar to those occurring near the surface when there is a direct hydrologic connection [54].…”

“…A year-long longitudinal study of microbial succession in a karst cave system in Virginia, USA, showed that large influxes of aquatic microbes and particulate organic matter can enter the cave from either the surface or interstitial zones [54]. This results in aquatic bacterioplankton communities within caves that are highly similar to those occurring near the surface when there is a direct hydrologic connection [54]. In contrast, the majority of microbes on rock walls, speleothems, and cave soils often form endemic communities [22,25,55].…”

Microbial ecology of tourist Paleolithic caves

“…Caves represent underground and enclosed environments, but they are connected with the surrounding environment present outside the cave (Garcia-Anton et al, 2013;Hershey and Barton, 2018;Morse et al, 2021). Thus, microorganisms may enter in caves and karst ecosystems following passive dissemination by infiltrating water (Dupont et al, 2007;Davis et al, 2020) or air currents (Engel and Northup, 2008;Cuezva et al, 2009;Vanderwolf et al, 2013).…”

“…Overall, oligotrophic conditions on rock surfaces lead to low growth rates (Portillo and Gonzalez, 2010), where the availability of organic carbon is often limiting (Stomeo et al, 2009). In such cases, inputs of organic matter into the cave (through infiltrating water, air-borne particles, human inputs, incoming fauna or flooding by subterranean streams in certain cases; Cañveras et al, 2001;Morse et al, 2021) will play an important role (Jurado et al, 2010;Garcia-Anton et al, 2013). Experimental analysis of sterilized rock tablets placed in Altamira Cave showed that bacterial and fungal colonization, based on visible growth and scanning electron microscopy, needed several months (Jurado et al, 2009).…”

“…Even though microorganisms from other environments can be transferred into caves, where they may represent environmental contaminants rather than endemic cave inhabitants (Vanderwolf et al, 2013;Davis et al, 2020;Morse et al, 2021), they are confronted to strong Darwinian selection once in caves (Hershey and Barton, 2018). Therefore, microbial communities in cave may display taxa common to those from other environments, but present at very different population levels.…”