Microbial Ecology

, Volume 74, Issue 2, pp 264–277 | Cite as

Attached and Suspended Denitrifier Communities in Pristine Limestone Aquifers Harbor High Fractions of Potential Autotrophs Oxidizing Reduced Iron and Sulfur Compounds

  • M HerrmannEmail author
  • S Opitz
  • R Harzer
  • KU Totsche
  • K Küsel
Microbiology of Aquatic Systems


Oxygen and nitrate availability as well as the presence of suitable organic or inorganic electron donors are strong drivers of denitrification; however, the factors influencing denitrifier abundance and community composition in pristine aquifers are not well understood. We explored the denitrifier community structure of suspended and attached groundwater microorganisms in two superimposed limestone aquifer assemblages with contrasting oxygen regime in the Hainich Critical Zone Exploratory (Germany). Attached communities were retrieved from freshly crushed parent rock material which had been exposed for colonization in two groundwater wells (12.7 and 48 m depth). Quantitative PCR and amplicon pyrosequencing of nirK and nirS genes encoding copper-containing or cytochrome cd1 heme-type nitrite reductase, respectively, and of bacterial 16S ribosomal RNA genes showed a numerical predominance of nirS-type denitrifiers in both attached and suspended groundwater communities and a dominance of nirS-type denitrifiers closely related to the autotrophic thiosulfate- and hydrogen-oxidizing Sulfuritalea hydrogenivorans and the iron- and sulfide-oxidizing Sideroxydans lithotrophicus ES-1. Potential rates of nitrate reduction in association with exposed crushed rock material were higher with an inorganic electron donor (thiosulfate) compared to an organic electron donor (fumarate/acetate) in the upper aquifer assemblage but similar in the lower, oxic aquifer. Our results have clearly demonstrated that groundwater from pristine limestone aquifers harbors diverse denitrifier communities which appear to selectively attach to rock surfaces and harbor a high potential for nitrate reduction. Our findings suggest that the availability of suitable inorganic versus organic electron donors rather than oxygen availability shapes denitrifier communities and their potential activity in these limestone aquifers.


Groundwater Denitrification nirS nirK 



We thank Patricia Geesink, Erika Köhnke, Holger Hartmann, Robert Lehmann, and Heiko Minkmar for their help with the field and laboratory work. This work was financially supported by the Deutsche Forschungsgemeinschaft (CRC 1076 AquaDiva) and the Free State of Thuringia (ProExcellence Initiative “AquaDiv@Jena” and ProChance Programmlinie A1, Friedrich Schiller University Jena). Sequencing was financially supported by the German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, funded by the DFG (FZT118). The climate chambers to conduct experiments under controlled temperature conditions were financially supported by the Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft (TMWWDG; project B 715-09075).

Compliance with Ethical Standards

We confirm that all of the reported work is original. The material has not been submitted for publication elsewhere.

Conflict of Interest

The authors declare that they have no conflicts of interest.

Supplementary material

248_2017_950_MOESM1_ESM.docx (73 kb)
ESM 1 (DOCX 73 kb)


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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • M Herrmann
    • 1
    • 2
    Email author
  • S Opitz
    • 1
  • R Harzer
    • 1
  • KU Totsche
    • 3
  • K Küsel
    • 1
    • 2
  1. 1.Aquatic Geomicrobiology, Institute of EcologyFriedrich Schiller University JenaJenaGermany
  2. 2.German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzigGermany
  3. 3.Institute of GeosciencesFriedrich Schiller University JenaJenaGermany

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