Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes
byLaura Díaz-García, Maria Chuvochina, Golo Feuerriegel, Boyke Bunk, Cathrin
Spröer, Wolfgang R. Streit, Luis M. Rodriguez-R, Jörg Overmann, Diego Javier
Jiménez
An easy and straightforward way to engineer microbial environmental communities is by
setting up liquid enrichment cultures containing a specific substrate as the sole source of
carbon. Here, we analyzed twenty single-contig high-quality metagenome-assembled
genomes (MAGs) retrieved from a microbial consortium (T6) that was selected by the
dilution-to-stimulation approach using Andean soil as inoculum and lignocellulose as a
selection pressure. Based on genomic metrics (e.g., average nucleotide and amino acid
identities) and phylogenomic analyses, 15 out of 20 MAGs were found to represent novel
bacterial species, with one of those (MAG_26) belonging to a novel genus closely related
to Caenibius spp. (Sphingomonadaceae). Following the rules and requirements of the
SeqCode, we propose the name Andeanibacterium colombiense gen. nov., sp. nov. for this
taxon. A subsequent functional annotation of all MAGs revealed that MAG_7
(Pseudobacter hemicellulosilyticus sp. nov.) contains 20, 19 and 16 predicted genes from
carbohydrate-active enzymes families GH43, GH2 and GH92, respectively. Its
lignocellulolytic gene profile resembles that of MAG_2 (the most abundant member) and
MAG_3858, both of which belong to the Sphingobacteriaceae family. Using a database
that contains experimentally verified plastic-active enzymes (PAZymes), twenty-seven
putative bacterial polyethylene terephthalate (PET)-active enzymes (i.e., alpha/beta-fold
hydrolases) were detected in all MAGs. A maximum of five putative PETases were found
in MAG_3858, and two PETases were found to be encoded by A. colombiense. In
conclusion, we demonstrate that lignocellulose-enriched liquid cultures coupled with
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genome-resolved metagenomics are suitable approaches to unveil the hidden bacterial
diversity and its polymer-degrading potential in Andean soil ecosystems.