Sediment was collected from the back barrier tidal flat Janssand (N53°44.151’ and E07°41.945’) located in the German Wadden Sea, in January 2011 at low tide. The upper two centimeters of the tidal flat were sampled with a flat trowel.
Continuous cultivation
The sediment was mixed vigorously in a ratio of 1:1 with red sea salt medium (33.4 g/l; Aquaristic.net). After the sediment grains had settled the overlying suspension was used as inoculum for the continuous culture. Cycloheximide (50 mg/l) was added to prevent eukaryotic growth and thus protect bacteria from being grazed. Continuous cultivation was performed in a 3 l glass vessel at controlled temperature (20±1°C). Electron donors and acceptors were separated in an acidic and an alkaline medium, which were pumped into the vessel at a ratio of 1:1 and a pump speed of 1.5 ml/min each (overall dilution rate 1.6 d-1).
This dilution rate was chosen according to an estimate of the average growth rate of the microbial community of the sampling site based on codon usage bias in the sampling site's metagenome (Accession number: SRP015924; Marchant et al., submitted) according to Vieira-Silva and Rocha (2010).
The pH of the two media were adjusted in such a way that the resulting pH was 8 ± 0.2 in the culture. Substrate concentrations in the media were gradually increased. The final composition of the acidic medium (pH=2.2) was (g/l): Red Sea Salt (Aquaristic.net) 66.8, NaH2PO4.1H2O0.276, glucose 0.870, acetate 0.204, glutamic acid 0.207, aspartic acid 0.254,
alanine 0.166, serine 0.107, tyrosine 0.118, histidine 0.023, methionine 0.048 and trace element solution 0.5ml/l. The trace element solution contained (g/l): FeSO4.7H20 0.21,
H3BO3 0.03, MnCl2.2H20 0.1, CoCl2.6H20 0.12, NiCl2.6H20 0.024, ZnCl2 0.07,
Na2MoO4.2H20 0.036, CuSO4.5H2O 0.015. The alkaline medium (pH= 12.2±0.2) contained
(g/l): NaNO2 2.76 and NaNO3 0.34. Medium pH was adjusted with HCl or NaOH. The liquid
volume in the culture vessel was 2.8 l. The pH and oxidation/reduction potential were monitored by gel-filled electrodes with an Ag/AgCl reference system (Mettler-Toledo, Giessen, Germany). To maintain anaerobiosis the culture was continuously flushed with argon (purity >99,998 %, Air Liquide, Germany) at a flow rate of 10 ml/min dosed by a mass flow controller (Alicat Scientific, USA). The culture was mixed by pumping (1.2 l/min;
Chapter 4
121 pump: Watson Marlow 620S, USA) gas from the headspace through a sintered glass membrane inserted into the bottom of the culture vessel, from where it bubbled through the culture. To prevent growth of photosynthetic organisms, the culture vessel was covered with a neoprene cover.
Analytical procedures
Nitrite, nitrate, ammonium and dissolved organic carbon concentrations and protein content in the enrichment culture as well as dinitrogen production were measured as described in the supplementary information.
Catalyzed Reporter Deposition Fluorescence In Situ hybridization (CARD-FISH) CARD-FISH was performed as described in the supplementary information.
Automated ribosomal intergenic spacer analysis (ARISA)
DNA for ARISA was extracted using the protocol of Martin-Platero et al (2007). The quantity of DNA was set to 10 ng per PCR amplification (quantified by a ND-1000 Nanodrop). The ARISA, including evaluation of the raw fingerprint profiles and binning into operational taxonomic units (OTUs), was performed as described by Ramette (2009). Primers (ITSF/ITSReub) are listed in supplementary table S4.
Sequencing, assembly, binning and annotation
DNA extraction and sequencing was performed as described in the supplementary information. Assembly was performed with MetaVelvet-v0.3 (supplementary table S2). Binning of assembled contigs was performed with the Metawatt binner according to Strous et
al (2012). More detailed information about the assembly and binning and information about
full length 16S rRNA reconstruction and phylogenetic analyses are described in the supplementary information.
Data submission
Illumina sequencing data sets were submitted to the Short Read Archive (http://www.ncbi.nlm.nih.gov/Traces/sra/), and the assembled contigs were submitted to the Whole Genome Shotgun Submission Portal (https://submit.ncbi.nlm.nih.gov/subs/wgs/).
122
Both reads and contigs are accessible under the BioProject PRJNA226580 and the BioSamples: SAMN02391470 / SRS498469 (day 6), SAMN02391471 / SRS498472 (day 18), SAMN02391472 / SRS498471 (day 33), SAMN02391473 / SRS498488 (day 46). This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accessions AYRE00000000, AYRF00000000, AYRG00000000, AYRH00000000. The version described in this paper is version AYR(E-H)01000000.
Acknowledgements
We thank Theresa Hargesheimer for CARD-FISH analysis and Ines Kattelmann and Regina Vahrenhorst for their support in metagenomic sequencing and analysis. We kindly thank Lars Schreiber and Karen Lloyd for providing their archaeal CSCG alignment. This research was funded by an ERC starting grant to Marc Strous (MASEM) and the German Federal State North Rhine Westfalia.
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