Dataset characterising dominant bacterial phylotypes across animal manure-enriched composting microcosms for crude oil waste sludge bioremediation.

The dataset provides a complete record of microbial, functional, physicochemical, and contaminant dynamics from controlled co-composting microcosms designed to remediate petroleum refinery sludge using targeted animal manure amendments. Five treatments-cow, pig, horse, and poultry manures, as well as an unamended control-were monitored over 300 days. The study incorporated amplicon-based 16S rRNA gene sequencing, functional gene inference, culture-based validation, bulk chemistry, and chromatographic analyses. Illumina MiSeq profiling of the V1-V3 regions identified 359 bacterial genera (raw OTU-level assignments prior to quality and abundance filtering) across 17 phyla, with taxonomic inventories structured from phylum to genus. Alpha and beta diversity measures demonstrated treatment-dependent community assembly, with the highest richness and diversity observed in cow-manure microcosms-pig and poultry amendments selectively enriched hydrocarbon-degrading taxa, including Pseudomonas. Functional predictions generated using PICRUSt2 (NSTI = 0.02-0.16) indicated enrichment of pathways involved in xenobiotic degradation, aromatic compound metabolism, and benzoate catabolism. These predictions were supported by culture-based evidence, including redox indicator screening and detection of the cbzE gene, which encodes catechol 2,3-dioxygenase, a key enzyme in chlorobenzoate/chlorocatechol degradation pathways and functionally analogous to the widely recognised xylE gene in aromatic hydrocarbon-degrading microorganisms. Collectively, these determinations provide complementary genomic and phenotypic evidence for the biodegradation potential of the microbial community and its capacity to transform aromatic and other environmentally relevant xenobiotic compounds. Additional datasets document total organic carbon, nitrogen, and phosphorus profiles of feedstocks and sludge. At the same time, Soxhlet extraction GC-MS measurements quantify polycyclic aromatic hydrocarbon (PAH) attenuation, with up to 99.9% removal achieved for multiple compounds in pig, horse, and poultry-amended systems. Through the combination of taxonomic profiling, PICRUSt2-based functional inference, chemical transformation analyses, and degradation kinetic measurements, this dataset affords a comprehensive characterisation of microbial community structure, predicted metabolic potential, and biodegradation performance associated with crude oil sludge co-composting at the sampled time point.