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Microorganisms in groundwater play an important role in aquifer biogeochemical cycles and water quality. However, the mechanisms linking the functional diversity of microbial populations and the groundwater physicochemistry are still not well understood due to the complexity of interactions between surface and subsurface. Here, we used phospholipid fatty acids (PLFAs) relative abundances to link specific biochemical markers within the microbial communities to the spatio-temporal changes of the groundwater physicochemistry. PLFAs were isolated from groundwater of two physicochemically distinct aquifer assemblages in central Germany (Thuringia). The functional diversities of the microbial communities were mainly correlated with groundwater chemistry, including dissolved O2, Fet and NH4+ concentrations. Abundances of PLFAs derived from eukaryotes and potential nitrite oxidizing bacteria (11MeC16:0 as biomarker for Nitrospira moscoviensis) were high at sites with elevated O2 concentration where groundwater recharge supplies both bioavailable organic substrates and NH4+ needed to sustain heterotrophic growth and nitrification processes. In anoxic groundwaters more rich in Fet, PLFAs abundant in sulphate reducing bacteria (SRB), iron-reducing bacteria and fungi increased with Fet and HCO3− concentrations suggesting the occurrence of active iron-reduction and the possible role of fungi in meditating iron solubilisation and transport in those aquifer domains. In NH4+ richer anoxic groundwaters, anammox bacteria and SRB- derived PLFAs increased with NH4+ concentration further evidencing the dependence of the anammox process on ammonium concentration and potential links between SRB and anammox bacteria. Additional support of the PLFA-based bacterial communities was found in DNA and RNA-based Illumina MiSeq amplicon sequencing of bacterial 16S rRNA genes, which evidenced high predominance of nitrite-oxidizing bacteria Nitrospira e.g. Nitrospira moscoviensis in oxic zones of the aquifers and of anammox bacteria in NH4+ richer anoxic groundwater. Higher relative abundances of sequence reads in the RNA-based data sets affiliated with iron-reducing bacteria in Fet richer groundwater supported the occurrence of active dissimilatory iron-reduction. The functional diversity of the microbial communities in these biogeochemically distinct groundwater assemblages can be largely attributed to the redox conditions linked to changes in bioavailable substrates and input of substrates with the seepage. Our results demonstrate the power of complementary information derived from PLFA-based and sequencing-based approaches

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We examined the molecular composition of forest soil water during three different seasons at three different sites, using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS). We examined oxic soils and tested the hypothesis that pH and season correlate with the molecular composition of dissolved organic matter (DOM). We used molecular formulae and their relative intensity from ESI-FT-ICR-MS for statistical analysis. Applying unconstrained and constrained ordination methods, we observed that pH, dissolved organic carbon (DOC) concentration and season were the main factors correlating with DOM molecular composition. This result is consistent with a previous study where pH was a main driver of the molecular differences between DOM from oxic rivers and anoxic bog systems in the Yenisei River catchment. At a higher pH, the molecular formulae had a lower degree of unsaturation and oxygenation, lower molecular size and a higher abundance of nitrogen-containing compounds. These characteristics suggest a higher abundance of tannin connected to lower pH that possibly inhibited biological decomposition. Higher biological activity at a higher pH might also be related to the higher abundance of nitrogen-containing compounds. Comparing the seasons, we observed a decrease in unsaturation, molecular diversity and the number of nitrogen-containing compounds in the course of the year from March to November. Temperature possibly inhibited biological degradation during winter, which could cause the accumulation of a more diverse compound spectrum until the temperature increased again. Our findings suggest that the molecular composition of DOM in soil pore waters is dynamic and a function of ecosystem activity, pH and temperature.