Fig. 6: Metatranscriptomics of hot-spring sediment incubated with 0.02% (m/v) DHP, eucalyptus kraft lignin (EKL), Eucalyptus milled-wood lignin (EMWL), vanillin (VAN), and control incubations with no exogenous carbon (NC).
A Strategies for taxonomic identification and binning of metatranscriptome contigs. B BBMap read mapping to MAGS (MB2), refined genomes (L.E.), GTDB reference genomes (GC), and binned transcriptome assemblies (AB, CO, LS). Mapped read counts per bin were normalized using length of the contig assembly and depth of sampling. p values generated from the multcomp implementation of Tukey-HSD pairwise-GLM analysis of normalized counts for lignin substrate shotgun metatranscriptome libraries against NC libraries (p < 0.05 shown). C Transcripts putatively involved in catabolic pathways for methoxylated monoaromatics (vanillate/syringate). Taxonomy determined using Kaiju and GTDB-Tk classification of assembled transcriptomes as shown in (A). Results of DESeq2 differential expression (DE) analysis against NC libraries provided as log2 fold change values if (padj < 0.1). Transcripts that are differentially expressed with padj < 0.05 are denoted with an asterisk (*). D Transcripts putatively involved in aromatic oligomer degradation. E CAZyme transcripts. F Proteobacterial protocatechuate meta-cleavage (lig) gene clusters identified in genome and transcriptome bins. Clusters are aligned to the start position of the ligJ/I reading frame. G Vanillate and syringate meta-cleavage by des, van, and lig gene products in the eucalyptus kraft lignin (EKL) transcriptomes. H Degradation of guaiacylglycerol-β-guaiacyl ether (GGE), 5,5′-dehydrodivanillate (DDVA), and other oligomeric compounds. Lightened genes were not detected in transcriptome.
