Dataset: Candidatus Nitrosopelagicus brevis strain U25

Organism sources and cultivation conditions:
‘Candidatus Nitrosopelagicus brevis’ str. CN25 (Santoro et al., 2015), was propagated in ONP medium (Santoro and Casciotti, 2011), consisting of aged natural seawater (collected from 10 m depth at 15°S, 173°W on 23 October 2011; 0.2 μm pore size filtered at sea) amended with a chemolithoautotrophic nitrogen source (NH4Cl or urea, described in ‘Experimental design’), ampicillin (10.8 μM), streptomycin (68.6 μM), potassium phosphate (29.4 μM), and a chelated trace metal mix consisting of disodium ethylenediaminetetraacetic acid (14 μM), FeCl2 (7.25 μM), ZnCl2 (0.5 μM), MnCl2 (0.5 μM), H3BO3 (1 μM), CoCl2-6H2O (0.8 μM), CuCl2-2H2O (0.1 μM), NiCl2-H2O (0.1 μM), Na2MoO4-2H2O (0.15 μM). ‘Ca. N. brevis’ str. U25 was enriched from the original CN25 enrichment culture (Santoro and Casciotti, 2011) using sequential transfers of the initial enrichment into ONP medium amended with 50-100 μM urea, instead of NH4Cl, over a period of ~48 months. All enrichments were propagated in 250 mL polycarbonate flasks at 22°C in the dark and monitored for NO2- production using the Griess reagent colorimetric method (Strickland and Parsons, 1972). Cell counts were obtained with a Millipore Guava EasyCyte 5HT flow cytometer as described previously (Tripp, 2008).

Cell harvesting for and genome sequencing of ‘Ca. N. brevis’ str. U25: A Ca. N. brevis U25 enrichment culture that was grown exclusively with urea as the sole chemolithoautotrophic growth substrate for >50 generations, was harvested by filtration on to 25 mm diameter, 0.22 μm pore-size Supor-200 filters and frozen at -80°C. DNA was extracted using a DNeasy blood & Tissue DNA extraction kit (Qiagen, Valencia, CA, USA), following the manufacturer’s instructions. The DNA was treated with RNAse and examined using a Bioanlayzer 2100 (Agilent) with 500 ng serving as the input for library construction (NEBNext paired-end DNA Library Prep kit, New England Biolabs).

Instruments:
The sample was sequenced on an Illumina MiSEQ (v2 chemistry, paired 250 bp reads). Reads were quality trimmed and served as the inputs to assembly with metaSPAdes (v 0.5, 70mer) (Nurk et al., 2017). The K-mer usage of and phylogenetic annotation of the assembled contigs were then used to visually identify a putative thaumarchaeal bin (Supplementary Figure 1a) (Laczny et al., 2015). The 3 contig genome was annotated using the JGI IMG pipeline and the PGAP pipeline at NCBI.