The diameters of the aggregates were measured according to a reference scale bar

built in the eyepiece of the microscope. The biovolume was calculated assuming that both cells and aggregates have spherical shapes. For each sample, 4 individual staining were applied. For each staining 50 fields of view were counted for calculation. Cell and aggregates identification In order to evaluate which type of ANME and SRB were present and enriched in the reactor, catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) was applied on S1 and S2. The slurry samples were embedded onto GTTP filters. The filters were incubated in methanol with #Tideglusib in vivo randurls[1|1|,|CHEM1|]# 0.15% H2O2 for 30 min at room temperature before washed with water and ethanol and dried. For each sample, 2 filters were prepared. One was incubated in lysozyme solution (10 mg/ml in 0.05 M EDTA, pH 8.0; 0.1 M Tris-HCl, pH 8.0) for 15 min at 37°C to achieve permeablilization of bacterial cells, and another one was incubated in Proteinase K solution (15 μg/ml in MilliQ water) for 3 min at room temperature to achieve permeabilization of achaeal cells. Afterwards the filters were cut into 4 pieces. Each piece was for hybridization with one probe (Table 1). The hybridization was performed according to the protocol previously described [23]. After

hybridization, the filter was stained with DAPI to target all cells present on the filter. During CARD-FISH, a few steps of washing the filter may cause the loss of cells and aggregates. It was assumed that all types of cells or aggregates were washed out in the same ratio. Therefore the percentage of FHPI chemical structure ANME or SRB among the total cells did not change after washing. For each hybridization, cells and aggregates in 50 fields of view were analyzed under microscope. For each field, both probe staining and DAPI staining were counted to quantify the concentration of ANME-1 (or ANME-2, ANME-3 and SRB) among total biomass. For a more detailed investigation on the microbial Acetophenone community, the archaeal and bacterial 16S rRNA gene clone libraries were performed

on S2 according to protocol previously described [24, 25] with the primers listed in Table 1. For archaeal library, 56 clones were obtained while 50 clones were randomly picked for sequencing. For bacterial library, 110 clones were obtained while 100 clones were picked for sequencing. The sequences were compared with their best match in NCBI to classify their phylogenetic group (Additional file 1, Table S1). To calculate the percentage of each phylogenetic group into total archaeal/bacterial community, the number of clones within one phylogenetic group was divided by the number of sequenced clones within archaeal/bacterial library. All the sequences described in the paper have been deposited in the databases of GenBank, under accession numbers HQ405602 to HQ405741.