Journal cover Journal topic
Biogeosciences An interactive open-access journal of the European Geosciences Union
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Volume 14, issue 10
Biogeosciences, 14, 2697–2714, 2017
https://doi.org/10.5194/bg-14-2697-2017
© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 3.0 License.
Biogeosciences, 14, 2697–2714, 2017
https://doi.org/10.5194/bg-14-2697-2017
© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 3.0 License.

Research article 31 May 2017

Research article | 31 May 2017

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

Valérie F. Schwab1,2, Martina Herrmann3,4, Vanessa-Nina Roth5, Gerd Gleixner5, Robert Lehmann1, Georg Pohnert2, Susan Trumbore5, Kirsten Küsel3,4, and Kai U. Totsche1 Valérie F. Schwab et al.
  • 1Friedrich Schiller University, Institute of Geosciences, Jena, Germany
  • 2Friedrich Schiller University, Institute for Inorganic and Analytical Chemistry, Jena, Germany
  • 3Friedrich Schiller University, Institute of Ecology, Jena, Germany
  • 4German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
  • 5Max-Planck-Institute for Biogeochemistry, Jena, Germany

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.

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We used phospholipid fatty acids (PLFAs) to link specific microbial markers to the spatio-temporal changes of groundwater physico-chemistry. PLFA-based functional groups were directly supported by DNA/RNA results. O2 resulted in increased eukaryotic biomass and abundance of nitrite-oxidizing bacteria but impeded anammox, sulphate-reducing and iron-reducing bacteria. Our study demonstrates the power of PLFA-based approaches to study the nature and activity of microorganisms in pristine aquifers.
We used phospholipid fatty acids (PLFAs) to link specific microbial markers to the...
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