Clarifying prokaryotic and eukaryotic biofilm microbiomes in anaerobic membrane bioreactor by non-destructive microscopy and high-throughput sequencing

Abstract

Anaerobic membrane bioreactor (AnMBR) is used for the treatment of organic solid waste. Clogging of filtration membrane pores, called membrane fouling, is one of the most serious issues for the sustainable operation of AnMBR. Although the physical and chemical mechanisms of the membrane fouling have been widely studied, the biological mechanisms are still unclear. The biofilm formation and development on the membrane might cause the membrane fouling. In this study, the prokaryotic and eukaryotic microbiomes of the membrane-attached biofilms in an AnMBR treating a model slurry of organic solid waste were investigated by non-destructive microscopy and high-throughput sequencing of 16S and 18S rRNA genes. The non-destructive visualization indicated that the biofilm was layered with different structures. The lowermost residual fouling layer was mesh-like and composed of filamentous microorganisms, while the upper cake layer was mainly the non-dense and non-cell region. The principal coordinate and phylogenetic analyses of the sequence data showed that the biofilm microbiomes were different from the sludge. The lowermost layer consisted of operational taxonomic units that were related to Leptolinea tardivitalis and Methanosaeta concilii (9.53–10.07% and 1.14–1.64% of the total prokaryotes, respectively) and Geotrichum candidum (30.22–82.31% of the total eukaryotes), all of which exhibited the filamentous morphology. Moreover, the upper layer was inhabited by the presumably cake-degrading bacteria and predatory eukaryotes. The biofilm microbiome features were consistent with the microscope-visualized structure. These results demonstrated that the biofilm structure and microbiome were the layer specific, which provides better understanding of biological mechanisms of membrane fouling in the AnMBR.