Matrix-associated microbial communities in a nitrogen-removing on-site wastewater treatment system are largely structured by niche processes.

On-site wastewater treatment systems (OWTSs) can be designed to promote microbial communities with naturally occurring metabolic functions desirable to wastewater treatment. Among such OWTSs are nitrogen-removing biofilters (NRBs), comprising a sand layer overlying a sand-lignocellulose (sand-lc) layer and intended to promote sequential nitrification and denitrification. The design of NRBs is based on the hypothesis that niche processes like environmental selection strongly structure the microbial communities, which predicts that immigrating wastewater communities and matrix-associated communities will be distinct and that the matrix communities in the two layers will be distinct. We characterized NRB microbial communities by 16S ribosomal RNA amplicon sequencing. Selection of the matrix-associated communities was indicated by clear differences from the immigrating community. For matrix-associated communities, alpha and beta diversity differed between the matrix layers, as did the relative abundances of many functional groups and genera. Functional groups with strict metabolisms were nearly exclusively detected in either the sand (ammonia and nitrite oxidizers) or sand-lc layer (methanogens), consistent with the niche hypothesis. Contrary to expectations, denitrifiers as a functional group were not present at greater relative abundance in the sand-lc than sand matrix because of a portfolio effect: some denitrifying genera were more abundant in the sand layer, whereas others were more abundant in the sand-lc layer. This study reveals niche processes acting at different levels of community organization for different biogeochemical functions, a crucial consideration in designing effective and reliable OWTSs to mitigate nitrogen pollution.