Investigating Hydrogenase Operon Distribution in Candidatus Methanospirare jalkutatii

Because only two of the five genomes of ‘Candidatus Methanospirare jalkutatii’ have an operon encoding a hydrogenase, we performed additional analysis to better understand this intraspecies distribution. On the one hand, we mapped the metagenomic reads from samples with genomes of ‘Candidatus Methanospirare jalkutatii’ (12019, FW4382_bin126, NA091.008, PR1007, PR1031B) to the MAGs containing the hydrogenase operon (FW4382_bin126, NA091.008_bin1) to check if reads mapping this operon are also present in samples from where the MAGs without the hydrogenase were recovered. For mapping the reads, we used bowtie2 v.2.4.2 (ref. 62 (link)) then transformed the sam files to bam using samtools (http://www.htslib.org/) and extracted the coverage depth for each position. Additionally, we performed a genomic comparison of the genomes with a hydrogenase operon (FW4382_bin126, NA091.008_bin1) with the genome FWG175 that was assembled into a single scaffold. For this, we used the genome-to-genome aligner Sibelia v.3.0.7 (ref. 63 ) and we visualized the results using Circos (http://circos.ca/).