Catalogue of bacterial and archaeal Metagenome Assembled Genomes from 'Ledro Alps and Judicaria' UNESCO MAB Biosphere Reserve (North Eastern Italian Alps)

A catalogue of Metagenome Assembled Genomes (MAGs) retrieved from 19 locations within the ‘Ledro Alps and Judicaria’ MAB UNESCO Biosphere Reserve, which comprises a great variety of Alpine freshwater habitats and contributes to a rich and varied biodiversity (https://www.unesco.org/en/mab/ledro-alps-and-judicaria). 19 paired water and surface sediment samples (n=38) were collected along a physiographic gradient including deep and shallow lakes, lake ponds, pasture ponds, ponds and peat bogs. A total of 566 quality-filtered MAGs were initially recovered from the sampled sites. After de-replication, we obtained 496 representative bacterial and archaeal MAGs, with a majority of bacterial MAGs (n=485) and a minority of archaeal MAGs (n=11). We found that 72% (n=352) of the identified bacterial species and 73% (n=8) of the archaeal species were novel, i.e. currently absent in the curated environmental bacterial database GTDB (RS220). In other words, out of 496 MAGs, only 133 bacterial and 3 archaeal MAGs could be classified at the species level based on 95% whole-genome average nucleotide identity (ANI). Regarding completeness and contamination, 36% of bacterial MAGs scored a high-quality score (Completeness > 90% and Contamination < 5%), while 64% scored a medium-quality score (Completeness > 50% and Contamination < 10%). 2% of archaeal MAGs had a high-quality and 98% a medium-quality score. The data presented here include 485 bacterial MAGs (bacteria_metagenome_assembled_genomes.zip) and 11 archaeal MAGs (archaea_metagenome_assemled_genomes.zip), their taxonomic classification data along with genome quality data (bacteria_mag_taxonomy.csv, archaea_mag_taxonomy.csv) and metadata associated to each sample (metadata_samples.csv). The phylogenetic trees (newick files) constructed with the bacterial and archaeal MAGs are also downloadable.