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Archaea
Volume 2017, Article ID 2136287, 13 pages
https://doi.org/10.1155/2017/2136287
Research Article

Archaeal Diversity and CO2 Fixers in Carbonate-/Siliciclastic-Rock Groundwater Ecosystems

1Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
2Department of Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
3German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
4Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
5U.S. Geological Survey National Research Program, Reston, VA, USA
6Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany

Correspondence should be addressed to Kirsten Küsel; ed.anej-inu@leseuk.netsrik

Received 16 November 2016; Revised 22 February 2017; Accepted 18 April 2017; Published 13 June 2017

Academic Editor: Chuanlun Zhang

Copyright © 2017 Cassandre Sara Lazar et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

Figure S1. Concentrations of DNA from each fraction, for each sample, obtained using PicoGreen staining. DNA concentrations of the control (12C) bottle samples are shown in dashes. For more details on the Bottle IDs please refer to the Supplemental Table S2. LF, light fraction; HF, heavy fraction. Figure S2. Phylogenetic trees showing the affiliations of selected representative archaeal 16S rRNA gene reads from groundwater (GW), soil and rock, SIP using filtered groundwater (SIPf or SIP filter), and SIP using passive sampler material (SIPps or SIP passive sampler) samples. The trees were calculated with 575 bp by neighbor-joining analysis in ARB. Bootstrap values are based on 1,000 replicates and are indicated at nodes for values ≥50 %. (A) Thaumarchaeota, (B) Euryarchaeota, (C) Woesearchaeota, and (D) Bathyarchaeota. Figure S3. Dendrogram from cluster analysis of archaeal 16S rRNA gene diversity from the groundwater samples recovered in June, August and September 2014, using the R software and the pvclust package. Bar indicates dissimilarity values. Approximately Unbiased (AU) p-values are shown in red, and Bootstrap Probability (BP) values are shown in green at each node. Histograms represent the phylogenetic affiliations of the RNA-based (A) and DNA- based (B) 16S rRNA gene reads. Color legends are the same as in Figure 1. Figure S4. Phylogenetic affiliations of archaeal 16S rRNA gene reads in percent of total reads, in the colonized passive sampler material exposed in well H4-1 for 6 months (T0), and in the SIP heavy (HF) and light (LF) DNA fractions. y, year. Table S1. List of the rock cores samples used for DNA extraction and 16S rRNA gene diversity analysis. Table S2. List of the different types of material, labelled substrates, incubation times and conditions used for the SIP experiments. Table S3. Relative proportion (%) of archaeal taxa in each soil (August 2014), rock and groundwater (June, August and September 2014) sample, based on 16S rRNA gene diversity. Table S4. Physicochemical parameters measured in groundwater during sampling, from all sampled wells at the 3 time points (June, August and September 2014). Table S5. Phylogenetic affiliation of archaeal 16S rRNA gene reads in relative in the light (LF) and heavy (HF) DNA fractions from the anoxic H4-3 and H5-2 and oxic H4-1 and H5-1 groundwater samples (filter pieces) and H4-1 passive sampler material; using labelled 13C-CO2 and 13C-labelled veratric acid (VA). Only incubation bottles for which both fractions had ≥5 reads are shown. The odds ratio (OR) and ratio of odds ratio (RoOR) were calculated. VA, Veratric Acid. Table S6. Physicochemical parameters measured in groundwater during the 13CO2 and 13C-veratric acid SIP incubations using filtered groundwater from the oxic and anoxic aquifers. VA, veratric acid; na, not applicable; nd, not detected; T0, start of the incubation; Te, end of the incubation; DOC, dissolved organic carbon; DIC, dissolved inorganic carbon.

  1. Supplementary Material