17Partial nitritation-anammox (PNA) is today used for nitrogen removal from highly concentrated 18 wastewater after anaerobic sludge digestion (sidestream). However, implementation of PNA for 19 treatment of municipal wastewater (mainstream), with its lower ammonium concentration and lower 20 temperature is challenging, which might be due to differences in microbial community composition 21 and/or activity. To investigate this, we compared side-by-side sidestream and mainstream PNA 22 biofilms using amplicon sequencing of 16S rDNA and rRNA, hzsB DNA and mRNA, and the genes 23 nxrB, and amoA. The two communities were different to each other with relatively more heterotrophic 24 denitrifying bacteria and less anammox bacteria in the mainstream. With hzsB and nxrB we found 25 microdiversity among Brocadia and Nitrospira, and turnover (taxa replacement) between sidestream 26 and mainstream. However, in both environments Brocadia sapporoensis represented most of the hzsB 27 DNA and mRNA reads, despite the different environmental conditions and nitrogen removal rates. All 28 of those populations present in both sidestream and mainstream had no differences in their 16S 29 rRNA:rDNA ratios, supporting recent findings that rRNA:rDNA ratios are poor indicators of bacterial 30 activity. The observed diversity within functional groups and composition differences between 31 sidestream and mainstream add complexity to our view of PNA communities with possible 32 implication for reactor function. 33 34