Oxygen availability and distance to surface environments determine community composition and abundance of ammonia-oxidizing prokaroytes in two superimposed pristine limestone aquifers in the Hainich region, Germany

Abstract

We followed the abundance and compared the diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the groundwater of two superimposed pristine limestone aquifers located in the Hainich region (Thuringia, Germany) over 22 months. Groundwater obtained from the upper aquifer (12 m depth) was characterized by low oxygen saturation (0-20%) and low nitrate concentrations (0-20 μM), contrasting with 50-80% oxygen saturation and 40-200 μM nitrate in the lower aquifer (48 m and 88 m depth). Quantitative PCR targeting bacterial and archaeal amoA and 16S rRNA genes suggested a much higher ammonia oxidizer fraction in the lower aquifer (0.4-7.8%) compared with the upper aquifer (0.01-0.29%). In both aquifers, AOB communities were dominated by one phylotype related to Nitrosomonas ureae, while AOA communities were more diverse. Multivariate analysis of amoA DGGE profiles revealed a stronger temporal variation of AOA and AOB community composition in the upper aquifer, pointing to a stronger influence of surface environments. Parallel fluctuations of AOA, AOB, and total microbial abundance suggested that hydrological factors (heavy rain falls, snow melt) rather than specific physicochemical parameters were responsible for the observed community dynamics.

Large Fractions of CO 2 -Fixing Microorganisms in Pristine Limestone Aquifers Appear To Be Involved in the Oxidation of Reduced Sulfur and Nitrogen Compounds

“…Groundwater bacterial 16S rRNA gene numbers, providing an approximation of the total microbial population, ranged from 3.11 ϫ 10 5 to 2.69 ϫ 10 8 genes liter Ϫ1 at the three different sites, as reported previously (44). Archaeal 16S rRNA genes were ϳ2 orders of magnitude less abundant than bacterial 16S rRNA genes, and their numbers ranged from 1.3 ϫ 10 3 to 4.6 ϫ 10 5 genes liter Ϫ1 (44). Similar to the RubisCO-encoding genes, there were strong temporal fluctuations but no significant differences among the three sampling sites.…”

“…Substantial temporal fluctuations of cbbL and cbbM gene abundances of 2 orders of magnitude at each site were observed but without significant differences in the abundances of these genes between the upper and lower aquifers or between the two wells of the lower aquifer. Groundwater bacterial 16S rRNA gene numbers, providing an approximation of the total microbial population, ranged from 3.11 ϫ 10 5 to 2.69 ϫ 10 8 genes liter Ϫ1 at the three different sites, as reported previously (44). Archaeal 16S rRNA genes were ϳ2 orders of magnitude less abundant than bacterial 16S rRNA genes, and their numbers ranged from 1.3 ϫ 10 3 to 4.6 ϫ 10 5 genes liter Ϫ1 (44).…”

How Deep Can Surface Signals Be Traced in the Critical Zone? Merging Biodiversity with Biogeochemistry Research in a Central German Muschelkalk Landscape

“…The prokaryotic population densities are similar in the target aquifers of the two aquifer assemblages, ranging from 2.7 × 10 6 to 3.8 × 10 8 cells L −1 over time (Opitz et al, 2014), which is similar to microbial abundances observed in spring water of alpine karst aquifers (Farnleitner et al, 2005). Quantitative PCR targeting bacterial and archaeal 16S rRNA genes suggested that archaea form a fraction of 0.03-8.2% of the total microbial population across different transect locations.…”

“…DOC and TOC show a relative decrease with presumed flow direction in both assemblages. Microbial processes in the different aquifer assemblages may thus be more important than surface inputs in controlling the amount and composition of DOC and TOC with progressively longer flow distances (Opitz et al, 2014).…”

“…Initial investigations have identified two factors which appear to be key drivers of microbial community composition and thus also strongly influence the potential for biogeochemical processes to take place: (i) the strong differences in oxygen availability between the two aquifers, and (ii) the distance to surface soils and thus the likelihood of the input and potential establishment of soil-derived microbial groups in the aquifer microbial communities (Opitz et al, 2014;Herrmann et al, 2015). Comparative investigations of microbial community structure in the groundwater using next generation amplicon sequencing of 16S rRNA genes and transcripts revealed that members of the Betaproteobacteria and the CytophagalesFlavobacteria-Bacteroidetes group dominate in the upper, anoxic aquifer while members of the Deltaproteobacteria and Nitrospira dominate the communities in the oxic, lower aquifer .…”