Dataset for Metagenomics Insights of Microbial Communities in Chlorolignin Waste Discharged After Secondary Treatment from Pulp and Paper Mill

This dataset provides a comprehensive taxonomic and functional analysis of microbial communities exposed to chlorolignin pollutants in secondary sludge (PPES) and secondary treated effluent (PPME) from the activated sludge process used in treating pulp and paper mill wastewater. The study employs amplicon sequencing-based metagenomics and physicochemical analyses to investigate microbial composition, functional potential, and pollutant characteristics under high pollutant loads. The present dataset includes ASV_seqs, Multiqc reports, FASTQC files, Phyloseq files. Additionally, it provides functional annotation tables derived from KEGG, EC, and MetaCyc databases using PICRUSt2 analysis. Moreover, this dataset includes a QIIME2 pipeline information file, a summary, and a MultiQC report. Physicochemical analysis of PPES revealed the presence of heavy metals and various organic pollutants. Gas chromatography-mass spectrometry (GC-MS) identified organic pollutants, including fatty acids, heterocyclic compounds, phenolics, alkanes, ketone derivatives, and ketones. High-throughput amplicon sequencing was performed using Illumina NovaSeq, targeting the V3–V4 hypervariable region of the 16S rRNA gene. The sequencing yielded 67,431 sequences per read for PPES and 94,028 for PPME. After quality filtering, 15,803 amplicon sequence variants (ASVs) were identified in PPES and 26,554 in PPME. Venn diagram analysis identified 679 unique ASVs in PPES, 530 in PPME, and 25 shared ASVs, indicating a core microbial community. Taxonomic classification of the amplicon sequencing data revealed that Proteobacteria dominated both samples, constituting 39.99% of PPES and 62.31% of PPME. At the genus level, PPES was dominated by SM1A02, followed by Sulfurovum, Thiobacillus, SWB02, etc. In PPME, the microbial community was dominated by Oleiphilus, followed by Ketobacter, Hydrogenophaga, Legionella, 29 marine group, Caldithrix, and Schlesneria. Alpha Diversity analysis exhibited high microbial richness and evenness, as indicated by Pielou’s evenness, Faith’s phylogenetic diversity, Shannon entropy, and observed features. Additionally, Beta Diversity analyses revealed distinct microbial community structures between PPES and PPME, as revealed by Weighted UniFrac, Unweighted UniFrac, Jaccard, and Bray-Curtis distance metrics. Functional analysis using PICRUSt2 identified significant differences in KEGG Ontology, EC, and MetaCyc pathways between PPES and PPME. PPME microbial communities demonstrated greater taxonomic and metabolic adaptation to the pollutant-rich environment compared to PPES. The data highlight the distinct microbial communities and their metabolic adaptations to high pollutant loads in pulp and paper mill wastewater. These findings can inform the optimization of wastewater treatment processes for improved efficiency and pollutant degradation.