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Palm Oil Mill Effluents (POME) are complex fermentative substrates which habour diverse native microbial contaminants. However, knowledge on the microbiota community shift caused by the anthropogenic effects of POME in the environment is up to date still to be extensively documented. In this study, the bacterial and archaeal communities of POME from two palm oil processing systems (artisanal and industrial) were investigated by Illumina MiSeq Platform. Despite the common characteristics of these wastewaters, we found that their microbial communities were significantly different with regard to their diversity and relative abundance of their different Amplicon Sequence Variants (ASV). Indeed, POME from industrial plants harboured as dominant phyla  Firmicutes  (46.24%),  Bacteroidetes  (34.19%),  Proteobacteria  (15.11%), with the particular presence of  Spirochaetes ,  verrucomicrobia  and  Synergistetes , while those from artisanal production were colonized by  Firmicutes  (92.06%),  Proteobacteria  (4.21%) and  Actinobacteria  (2.09%). Furthermore, 43 AVSs of archaea were detected only in POME from industrial plants and assigned to  Crenarchaeota ,  Diapherotrites ,  Euryarchaeota  and  Nanoarchaeaeota  phyla, populated mainly by many methane-forming archaea. Definitively, the microbial community composition of POME from both type of processing was markedly different, showing that the history of these ecosystems and various processing conditions have a great impact on each microbial community structure and diversity. By improving knowledge about this microbiome, the results also provide insight into the potential microbial contaminants of soils and rivers receiving these wastewaters.

High-throughput 16S rRNA gene sequencing of the microbial community associated with palm oil mill effluents of two oil processing systems