Quantitative PCR (qPCR) is broadly used as the gold standard to quantify microbial community fractions in environmental microbiology and biotechnology. Benchmarking efforts to ensure the comparability of qPCR data for environmental bioprocesses are still scarce. Also, for partial nitritation/anammox (PN/A) systems systematic investigations are still missing, rendering meta-analysis of reported trends and generic insights potentially precarious. We report a baseline investigation of the variability of qPCR-based analyses for microbial communities applied to PN/A systems. Round-robin testing was performed for three PN/A biomass samples in six laboratories, using the respective in-house DNA extraction and qPCR protocols. The concentration of extracted DNA was significantly different between labs, ranged between 2.7 and 328 ng mg⁻¹ wet biomass. The variability among the qPCR abundance data of different labs was very high (1−7 log fold) but differed for different target microbial guilds. DNA extraction caused maximum variation (3–7 log fold), followed by the primers (1–3 log fold). These insights will guide environmental scientists and engineers as well as treatment plant operators in the interpretation of qPCR data.

This study aimed at evaluating the nitrous oxide (N2O) emissions from membrane bioreactors (MBRs) for wastewater treatment. The study investigated the N2O emissions considering multiple influential factors over a two-year period: (i) different MBR based process configurations; (ii) wastewater composition (municipal or industrial); (iii) operational conditions (i.e. sludge retention time, carbon-to-nitrogen ratio, C/N, hydraulic retention time); (iv) membrane modules. Among the overall analysed configurations, the highest N2O emission occurred from the aerated reactors. The treatment of industrial wastewater, contaminated with salt and hydrocarbons, provided the highest N2O emission factor (EF): 16% of the influent nitrogen for the denitrification/nitrification-MBR plant. The lowest N2O emission (EF = 0.5% of the influent nitrogen) was obtained in the biological phosphorus removal-moving bed-MBR plant likely due to an improvement in biological performances exerted by the co-presence of both suspended and attached biomass. The influent C/N ratio has been identified as a key factor affecting the N2O production. Indeed, a decrease of the C/N ratio (from 10 to 2) promoted the increase of N2O emissions in both gaseous and dissolved phases, mainly related to a decreased efficiency of the denitrification processes.

A distinctive red biofilm was observed in a glycerol-fed digester liquid effluent treatment process coupling partial nitrification (nitritation) and partial denitrification (denitritation) processes. Based on initial phylogenetic screening using 16S rRNA clone libraries and quantitative polymerase chain reaction, the biofilm was enriched in novel anaerobic ammonium oxidizing bacteria (AMX/anammox) closely related to Candidatus “Brocadia caroliniensis”. The metabolic functionality of the C. “Brocadia caroliniensis” enrichment was further explored using high-throughput sequencing and de novo metagenome assembly. The population anammox genome that was binned from the metagenome consisted of 209 contigs with a total of 3.73 Mbp consensus sequences having 43.3% GC content, and 27.4 average coverage depth. The assembled metagenome bin was comprised of 3582 open reading frames (ORFs). Based on 16S rRNA similarity the binned metagenome was closely related with Candidatus “Brocadia caroliniensis”, Candidatus “Brocadia fulgida”, planctomycete KSU-1, and Candidatus “Kuenenia stuttgartiensis” with 99%, 96%, 92% and 93% similarity, respectively. Essential genes in anammox metabolic functions including ammonium and nitrite transport, hydrazine synthesis, electron transfer for catabolism, and inorganic carbon fixation, among several other anabolic pathways, were also observed in the population genome of the C. “Brocadia caroliniensis” related enrichment. Our results demonstrate the wider profusion of anammox bacteria in engineered nitrogen removal systems than expected. The utility of metagenomics approaches to deciphering such novel functionality in these systems is also highlighted.