Discovery of lignin-transforming bacteria and enzymes in thermophilic environments using stable isotope probing

Characterizing microorganisms and enzymes involved in lignin biodegradation in thermal ecosystems can identify thermostable biocatalysts. We integrated stable isotope probing (SIP), genome-resolved metagenomics, and enzyme characterization to investigate the degradation of high-molecular weight, C-13-ring-labeled synthetic lignin by microbial communities from moderately thermophilic hot spring sediment (52 degrees C) and a woody hog fuel pile (53 and 62 degrees C zones). C-13-Lignin degradation was monitored using IR-GCMS of (CO2)-C-13, and isotopic enrichment of DNA was measured with UHLPC-MS/MS. Assembly of 42 metagenomic libraries (72 Gb) yielded 344 contig bins, from which 125 draft genomes were produced. Fourteen genomes were significantly enriched with C-13 from lignin, including genomes of Actinomycetes (Thermoleophilaceae, Solirubrobacteraceae, Rubrobacter sp.), Firmicutes (Kyrpidia sp., Alicyclobacillus sp.) and Gammaproteobacteria (Steroidobacteraceae). We employed multiple approaches to screen genomes for genes encoding putative ligninases and pathways for aromatic compound degradation. Our analysis identified several novel laccase-like multi-copper oxidase (LMCO) genes in C-13-enriched genomes. One of these LMCOs was heterologously expressed and shown to oxidize lignin model compounds and minimally transformed lignin. This study elucidated bacterial lignin depolymerization and mineralization in thermal ecosystems, establishing new possibilities for the efficient valorization of lignin at elevated temperature.

Automated summary

Characterizing microorganisms and enzymes involved in lignin biodegradation in thermal ecosystems can identify thermostable biocatalysts. This study explored the degradation of lignin by microbial communities from thermophilic environments using stable isotope probing, metagenomics, and enzyme characterization. The researchers identified novel ligninase genes and elucidated bacterial lignin depolymerization and mineralization, providing new possibilities for lignin valorization at high temperatures.