Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes

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 genome-resolved metagenomics are suitable approaches to unveil the hidden bacterial diversity and its polymer-degrading potential in Andean soil ecosystems.

An archaeal lid-containing feruloyl esterase degrades polyethylene terephthalate

Polyethylene terephthalate (PET) is a commodity polymer known to globally contaminate marine and terrestrial environments. Today, around 80 bacterial and fungal PET-active enzymes (PETases) are known, originating from four bacterial and two fungal phyla. In contrast, no archaeal enzyme had been identified to degrade PET. Here we report on the structural and biochemical characterization of PET46 (RLI42440.1), an archaeal promiscuous feruloyl esterase exhibiting degradation activity on semi-crystalline PET powder comparable to IsPETase and LCC (wildtypes), and higher activity on bis-, and mono-(2-hydroxyethyl) terephthalate (BHET and MHET). The enzyme, found by a sequence-based metagenome search, is derived from a non-cultivated, deep-sea Candidatus Bathyarchaeota archaeon. Biochemical characterization demonstrated that PET46 is a promiscuous, heat-adapted hydrolase. Its crystal structure was solved at a resolution of 1.71 Å. It shares the core alpha/beta-hydrolase fold with bacterial PETases, but contains a unique lid common in feruloyl esterases, which is involved in substrate binding. Thus, our study widens the currently known diversity of PET-hydrolyzing enzymes, by demonstrating PET depolymerization by a plant cell wall-degrading esterase.

Plastics degradation by hydrolytic enzymes: The plastics-active enzymes database-PAZy

Petroleum-based plastics are durable and accumulate in all ecological niches. Knowledge on enzymatic degradation is sparse. Today, less than 50 verified plastics-active enzymes are known. First examples of enzymes acting on the polymers polyethylene terephthalate (PET) and polyurethane (PUR) have been reported together with a detailed biochemical and structural description. Furthermore, very few polyamide (PA) oligomer active enzymes are known. In this article, the current known enzymes acting on the synthetic polymers PET and PUR are briefly summarized, their published activity data were collected and integrated into a comprehensive open access database. The Plastics-Active Enzymes Database (PAZy) represents an inventory of known and experimentally verified enzymes that act on synthetic fossil fuel-based polymers. Almost 3000 homologs of PET-active enzymes were identified by profile hidden Markov models. Over 2000 homologs of PUR-active enzymes were identified by BLAST. Based on multiple sequence alignments, conservation analysis identified the most conserved amino acids, and sequence motifs for PET- and PUR-active enzymes were derived.

T2-relaxation time of cartilage repair tissue is associated with bone remodeling after spongiosa-augmented matrix-associated autologous chondrocyte implantation

OBJECTIVE

To investigate whether T2 relaxation time measurements of cartilage repair tissue and structural changes of the knee joint are associated with subchondral bone architecture after spongiosa-augmented matrix-associated autologous chondrocyte implantation (MACI).

DESIGN

Both knees of 25 patients (25.5 ± 7.8y; 10 women) were examined preoperatively and 2.7 years after unilateral spongiosa-augmented MACI with 3T magnetic resonance (MR) imaging. Cartilage composition was assessed using T2 relaxation time measurements, subchondral trabecular bone microstructure was quantified using a 3D phase-cycled balanced steady state free-precision sequence. Structural knee joint changes were assessed using the modified Whole-Organ Magnetic Resonance Imaging Score (WORMS). The Magnetic Resonance Observation of Cartilage Repair Tissue (MOCART) score was used for the postoperative description of the area that underwent MACI. Correlations were assessed using Spearman's rank correlation coefficients.

RESULTS

Hypertrophy of the cartilage repair tissue was found in 2 of 25 patients, both after a MACI procedure at the patella, 21 patients showed congruent filling. In subchondral bone of the cartilage repair compartment, apparent trabecular thickness was significantly higher in compartments with elevated cartilage T2 (n = 17; 0.37 ± 0.05 mm) compared to those showing no difference in cartilage T2 compared to the same compartment in the contralateral knee (n = 8; 0.27 ± 0.05 mm; P = 0.042). Significant correlations were found between the overall progression of WORMS and the ipsilateral vs contralateral ratio of average trabecular thickness (r = 0.48, P = 0.031) and bone fraction (r = 0.57, P = 0.007).

CONCLUSIONS

After spongiosa-augmented MACI, T2 values of cartilage repair tissue and structural knee joint changes correlated with the quality of the underlying trabecular bone.