Functional diversity of microbial communities in pristine aquifers inferred by PLFA- and sequencing-based approaches

Valérie F. Schwab,Kai U. Totsche,Susan Trumbore,Vanessa-Nina Roth,Kirsten Küsel,Robert Lehmann,Martina Herrmann,Georg Pohnert,Gerd Gleixner

doi:10.5194/bg-14-2697-2017

Abstract

Abstract. 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 physico-chemistry are still not well understood due to the complexity of interactions between surface and subsurface. Within the framework of Hainich (north-western Thuringia, central Germany) Critical Zone Exploratory of the Collaborative Research Centre AquaDiva, we used the relative abundances of phospholipid-derived fatty acids (PLFAs) to link specific biochemical markers within the microbial communities to the spatio-temporal changes of the groundwater physico-chemistry. 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 (11Me16:0 as biomarker for Nitrospira moscoviensis) were high at sites with elevated O2 concentration where groundwater recharge supplies bioavailable substrates. In anoxic groundwaters more rich in Fet, PLFAs abundant in sulfate-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 solubilization and transport in those aquifer domains. In more NH4+-rich 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 showed high predominance of nitrite-oxidizing bacteria Nitrospira, e.g. Nitrospira moscoviensis, in oxic aquifer zones and of anammox bacteria in more NH4+-rich anoxic groundwater. Higher relative abundances of sequence reads in the RNA-based datasets affiliated with iron-reducing bacteria in more Fet-rich groundwater supported the occurrence of active dissimilatory iron reduction. The functional diversity of the microbial communities in the 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.

Highlights

Continental and marine subsurface environments represent the largest habitat on Earth for microbial life and are of primary importance for energy fluxes on a global scale (Edwards et al, 2012)
We used constrained ordination to show environmental variables that significantly correlated with phospholipid-derived fatty acids (PLFAs) relative abundances in groundwater of distinct carbonaterock aquifer assemblages
Variation partitioning identified PLFA-based microbial functional groups that were directly supported by results of DNA- and RNA-based amplicon sequencing targeting bacterial 16S rRNA genes

Summary

Introduction

Continental and marine subsurface environments represent the largest habitat on Earth for microbial life and are of primary importance for energy fluxes on a global scale (Edwards et al, 2012). Deep and especially fossil groundwaters tend to reflect the chemistry of the aquifer materials They have typically lower concentrations of O2 and bioavailable substrates which cause facultative anaerobes to switch to terminal electron acceptors with lower energy yield such as NO−3 , MnO2, FeOOH and SO24− (Chapelle and Lovley, 1992). As many chemolithoautotrophs can use a variety of compounds to meet their energy needs in the dark subsurface, an increasing number of studies report the importance of chemo-lithoautotrophy in groundwater (Stevens and McKinley, 1995; Emerson et al, 2015; Herrmann et al, 2015) It is still not well understood how the composition and function of microbial communities in groundwaters depend on hydrology, chemistry and the relationship to groundwater recharge dynamics

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