## 4 Conclusions  
The in-depth 16S rRNA gene amplicon and metagenome information obtained in this study contribute to the understanding of the taxonomies and pathways involved in methanogenesis in the two types of bioreactors in the DWTS. The results obtained in this study showed that microbial composition was significantly different between the PSD and AnMBR. High-quality MAGs of predominated species were recruited, and the results of an in-depth dissection of the genes in the MAGs suggested a strong interaction of bacteria and archaea during methanogenesis that mainly occurs through the interspecific exchange of substances. The valuable insights obtained in this study are expected to provide guidance for the currently planned start-up of decentralized wastewater treatment systems that contain a primary sludge digestor and membrane bioreactor.  
**Supplementary Materials:** The following are available online at [[http://www.mdpi.com/2076-3417/10/1/135/s1](http://www.mdpi.com/2076-3417/10/1/135/s1)]([http://www.mdpi.com/2076-3417/10/1/135/s1](http://www.mdpi.com/2076-3417/10/1/135/s1)). Table S1, physicochemical characteristics of the influent and effluent water; Table S2, sequence numbers and alpha diversity indices of 16S rRNA genes in the PSD and AnMBR samples; Table S3, differences of the alpha diversity indices of the 16S rRNA genes between the PSD and AnMBR samples; Table S4, taxonomic profiling of the 16S rRNA genes at the family level in the PSD and AnMBR; Table S5, KEGG categories of the PSD and AnMBR metagenomes; Table S6, number of reads annotated as genes affiliated with CAzyme in the PSD and AnMBR metagenomes; Table S7, rate of ORFs in MAGs annotated by the KEGG and CAzyme databases; Figure S1, weighted PCoA clustering of the microbial communities in the PSD (blue triangles) and AnMBR (red triangles) samples based on the UniFrac distance; Figure S2, relative abundances of the KEGG categories of functional genes in the PSD and AnMBR metagenomes; Figure S3, read abundance of CAzyme in the PSD and AnMBR metagenomes; Figure S4, numbers of genes involved in the relevant acetonitrile methanogenesis pathway in archaeal MAGs; Figure S5, numbers of genes involved in the relevant methylotrophic methanogenesis pathway in archaeal MAGs; Figure S6, the relative abundances of _Syntrophaceae_ and _Methanobacteriaceae_ in PSD and AnMBR.  
**Author Contributions:** Developed and framed research questions, K.Z., Y.-L.Z., J.-T.L., J.-L.L., and J.-J.L.; Conducted the experiments, K.Z., Y.-L.Z., X.O., J.-P.L., A.Y., and G.-J.X.; Performed the data analyses, J.-L.L. and X.Y.; Wrote the first draft of the manuscript, K.Z., Y.-L.Z., and J.-L.L.; all authors revised the manuscript. All authors have read and agreed to the published version of the manuscript.  
Figure 6: Conceptual graph of the microbial network and dominant metabolic pathways of the microbial communities in the DWTS.  
**Funding:** This work was supported by the Provincial Natural Science Foundation of Guangdong, China (No. 2018A0303130014) and the project of Guangdong Provincial Education Department (No.2018 GKTSCX091, No.2017 GKQNCX004), the Excellent Youth Foundation of Guangdong Industry Polytechnic (QN2018-003), the Project of Guangzhou Science and Technology Association (K2019070101009).  
**Acknowledgments:** The authors are grateful to ECOGENE BIOTECH CO., LTD. (Shenzhen, China) for the support on bioinformatics of 16S rRNA amplicon and metagenome data.  
**Conflicts of Interest:** The authors declare no conflict of interest.