Ribosomal and metabolic (pmoA and mcrA) gene reconstruction from metagenomic data in HMMV sediment samples@en

16S rRNA and metabolic gene abundances as well as gene reconstructions were generated using a novel, modified version of the phyloFlash pipeline (https://github.com/HRGV/phyloFlash) called funcFlash for metabolic genes. In brief, the generated reads were mapped with BBMap at minimal global nucleotide identity of 70% against curated nucleotide databases: The SILVA SSURef v119 database [75], a published dsrAB gene database (http://www.microbial-ecology.net/db_download/dsr_v3.zip, [83]) and two newly generated pmoA and mcrA gene databases that are publicly available at PANGAEA, see [61]. The mapped read pairs were counted when at least one read had a positive mapping. Full length (>70% of the target length) genes were assembled with SPAdes [84] or reconstructed with EMIRGE [85]. The mapping of reconstructed metabolic genes to curated databases using funcFlash can be used to distinguish, whether a gene of interest is affiliated with organisms performing the reductive or oxidative pathway. In our case this new analysis allowed us to distinguish between dsrAB genes from sulfate reducers and from sulfur oxidizers, as well as between mcrA genes from methanogens and from methanotrophs.