Metagenomic Mining for Esterases in the Microbial Community of Los Rueldos Acid Mine Drainage Formation

Acid mine drainage (AMD) systems are extremely acidic and are metal-rich formations inhabited by relatively low-complexity communities of acidophiles whose enzymes remain mostly uncharacterized. Indeed, enzymes from only a few AMD sites have been studied. The low number of available cultured representatives and genome sequences of acidophiles inhabiting AMDs makes it difficult to assess the potential of these environments for enzyme bioprospecting. In this study, using naive and in silico metagenomic approaches, we retrieved 16 esterases from the alpha/beta-hydrolase fold superfamily with the closest match from uncultured acidophilic Acidobacteria, Actinobacteria (Acidithrix, Acidimicrobium, and Ferrimicrobium), Acidiphilium, and other Proteobacteria inhabiting the Los Rueldos site, which is a unique AMD formation in northwestern Spain with a pH of similar to 2. Within this set, only two polypeptides showed high homology (99.4%), while for the rest, the pairwise identities ranged between 4 and 44.9%, suggesting that the diversity of active polypeptides was dominated not by a particular type of protein or highly similar clusters of proteins, but by diverse non-redundant sequences. The enzymes exhibited amino acid sequence identities ranging from 39 to 99% relative to homologous proteins in public databases, including those from other AMDs, thus indicating the potential novelty of proteins associated with a specialized acidophilic community. Ten of the 16 hydrolases were successfully expressed in Escherichia coli. The pH for optimal activity ranged from 7.0 to 9.0, with the enzymes retaining 33-68% of their activities at pH 5.5, which was consistent with the relative frequencies of acid residues (from 54 to 67%). The enzymes were the most active at 30-65 degrees C, retaining 20-61% of their activity under the thermal conditions characterizing Los Rueldos (13.8 +/- 0.6 degrees C). The analysis of the substrate specificity revealed the capacity of six hydrolases to efficiently degrade (up to 1,652 +/- 75 U/g at pH 8.0 and 30 degrees C) acrylic- and terephthalic-like [including bis(2-hydroxyethyl)-terephthalate, BHET] esters, and these enzymes could potentially be of use for developing plastic degradation strategies yet to be explored. Our assessment uncovers the novelty and potential biotechnological interest of enzymes present in the microbial populations that inhibit the Los Rueldos AMD system.

Automated summary

This study identifies enzymes with potential biotechnological interest from the Los Rueldos acid mine drainage (AMD) system. The enzymes, derived from acidophilic bacteria, exhibit high diversity and potential novelty. Some of these enzymes are adapted to acidic conditions and may have potential applications in plastic degradation.