High Microbial Diversity Despite Extremely Low Biomass in a Deep Karst Aquifer

Abstract

Despite the importance of karst aquifers as a source of drinking water, little is known about the role of microorganisms in maintaining the quality of this water. One of the limitations in exploring the microbiology of these environments is access, which is usually limited to wells and surface springs. In this study, we compared the microbiology of the Madison karst aquifer sampled via the potentiometric lakes of Wind Cave with surface sampling wells and a spring. Our data indicated that only the Streeter Well (STR), which is drilled into the same hydrogeologic domain as the Wind Cave Lakes (WCL), allowed access to water with the same low biomass (1.56–9.25 × 103 cells mL-1). Filtration of ∼300 L of water from both of these sites through a 0.2 μm filter allowed the collection of sufficient cells for DNA extraction, PCR amplification of 16S rRNA gene sequences, and identification through pyrosequencing. The results indicated that bacteria (with limited archaea and no detectable eukaryotic organisms) dominated both water samples; however, there were significant taxonomic differences in the bacterial populations of the samples. The STR sample was dominated by a single phylotype within the Gammaproteobacteria (Order Acidithiobacillales), which dramatically reduced the overall diversity and species richness of the population. In WCL, despite less organic carbon, the bacterial population was significantly more diverse, including significant contributions from the Gammaproteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Planctomycetes, Fusobacter, and Omnitrophica phyla. Comparisons with similar oligotrophic environments suggest that karst aquifers have a greater species richness than comparable surface environs. These data also demonstrate that Wind Cave provides a unique opportunity to sample a deep, subterranean aquifer directly, and that the microbiology of such aquifers may be more complex than previously anticipated.

Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA

“…The relative abundances of bacterial and archaeal 16S rRNA gene sequences in the springs were similar to the abundances found in other aquifer studies, and some similar taxa have also been reported previously (41)(42)(43)(44). Proteobacteria and Cyanobacteria composed a large portion of the 16S rRNA gene sequences from all of the Florida springs investigated here.…”

Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN

“…Field samples were collected from a global set of diverse environments ( Figure 1 ) that were found to contain candidate phyla of Bacteria and Archaea in prior studies ( Rinke et al, 2013 ; Thomas et al, 2013 ; Moser et al, 2015 ; Becraft et al, 2017 ; Hershey et al, 2018 ; Sackett, 2018 ; Sackett et al, 2018 , 2019 ). Immediately after collection, samples were amended with sterile 5% glycerol and 1 mM EDTA (final concentrations) and stored at −80°C.…”

Decomposition of Organic Matter in Caves

“…Microbial biomass is an important driver of decomposition rates in surface freshwater (Hieber and Gessner, 2002), but the influence on the decomposition can also be more affected by the community composition and enzymatic activity than by the microbial biomass alone (Hieber and Gessner, 2002;Chapin et al, 2011). Nutrient limited caves are known to have high microbial diversity (Barton, 2015;Hershey et al, 2018), this diversity may potentially stimulate the decomposition process inside caves. On the other hand, in caves where invertebrates are more abundant, we expect the decomposition to be stimulated by their physical breakdown of substrates (Chapin et al, 2011).…”