Microorganisms encoding for the N2O reductase (NosZ) are the only known biological sink of the potent greenhouse gas N2O and are central to global N2O mitigation efforts. Clade II NosZ populations are of particular biotechnological interest as they usually feature high N2O affinities and often lack other denitrification genes. We focus on the yet-unresolved ecological constraints selecting for different N2O-reducers strains and controlling the assembly of N2O-respiring communities. Two planktonic N2O-respiring mixed cultures were enriched at low dilution rates under limiting and excess dissolved N2O availability to assess the impact of substrate affinity and N2O cytotoxicity, respectively. Genome-resolved metaproteomics was used to infer the metabolism of the enriched populations. Under N2O limitation, clade II N2O-reducers fully outcompeted clade I affiliates, a scenario previously only theorized based on pure-cultures. All enriched N2O-reducers encoded and expressed the sole clade II NosZ, while also possessing other denitrification genes. Two Azonexus and Thauera genera affiliates dominated the culture, and we hypothesize their coexistence to be explained by the genome-inferred metabolic exchange of cobalamin intermediates. Under excess N2O, clade I and II populations coexisted; yet, proteomic evidence suggests that clade II affiliates respired most of the N2O, de facto outcompeting clade I affiliates. The single dominant N2O-reducer (genus Azonexus) notably expressed most cobalamin biosynthesis marker genes, likely to contrast the continuous cobalamin inactivation by dissolved cytotoxic N2O concentrations (400 μM). Ultimately, our results strongly suggest the solids dilution rate to play a pivotal role in controlling the selection among NosZ clades, albeit the conditions selecting for genomes possessing the sole nosZ remain elusive. We furthermore highlight the potential significance of N2O-cobalamin interactions in shaping the composition of N2O-respiring microbiomes.@en

Seawater desalination has become an essential part of the drinking water supply of many arid countries in the world – including Cyprus and the wider Mediterranean – Middle Eastern region. In this study, the microinvertebrate fauna near the outfall sites of 2 seawater desalination plants, Dhekelia and Larnaca, in Cyprus was assessed by microscopy-based classical taxonomy and eDNA metabarcoding. The results show impact of desalination brine discharge on marine benthic communities. The community structure and the impact of abiotic factors was more prominent in the sediments than the water, and the alpha diversity results from metabarcoding were consistent with the results from microscopy but differed taxonomically.@en

The wastewater treatment sector embraces mixed-culture biotechnologies for sanitation, environmental protection, and resource recovery. Bioprocess design, monitoring and control thrive on microbial processes selected in complex microbial communities. Microbial ecology and systems microbiology help access microbiomes and characterize microorganisms, metabolisms and interactions at increased resolution and throughput. Big datasets are generated from the sequencing of informational molecules extracted from biomasses sampled across process schemes. However, they mostly remain on science benches and computing clusters, without reaching the industry in a clear engineering objective function. A bilateral bridge should actionize this information. As systems microbiologists, we miss that engineering designs and operations rely on stoichiometry and kinetics. The added-value provided by microbial ecology and systems microbiology to improve capital (CAPEX) and operating expenditures (OPEX) needs to be addressed. As engineers, we miss that microbiology can be provide powerful microbial information on top of physical-chemical measurements for quantitative process design (e.g., nutrient removal systems) with detailed scientific description of phenomena inside microbiomes. In this perspective article, we allied academia and industry to address the state of shared knowledge, successes and failures, and to establish joint investigation platforms. Our roadmap involves three milestones to (i) elaborate an essential list of microbiological information needed to implement methods at the process line; (ii) characterize microbiomes from microorganisms to metabolisms, and shape conceptual ecosystem models as primer for process ecology understanding; (iii) bridge engineering and mathematical models with an analytical toolbox for fast- vs. high-throughput analyses to discover new microbial processes and engineer assemblies. We praise for a harmonized "language of love"(incorporating common vocabulary, units, protocols) across the water and environmental biotechnology sector to team up mindsets for a sewer- and plant-wide integration of systems microbiology and engineering.

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The authors regret that there is an error in one stoichiometric coefficient and in the process rate of NOB in Table 1 of the original publication. The correct table is shown below. The authors would like to apologise for any inconvenience caused.

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The control of nitrite-oxidizing bacteria (NOB) challenges the implementation of partial nitritation and anammox (PN/A) processes under mainstream conditions. The aim of the present study was to understand how operating conditions impact microbial competition and the control of NOB in hybrid PN/A systems, where biofilm and flocs coexist. A hybrid PN/A moving-bed biofilm reactor (MBBR; also referred to as integrated fixed film activated sludge or IFAS) was operated at 15 °C on aerobically pre-treated municipal wastewater (23 mg _NH4-N L ⁻¹ ). Ammonium-oxidizing bacteria (AOB) and NOB were enriched primarily in the flocs, and anammox bacteria (AMX) in the biofilm. After decreasing the dissolved oxygen concentration (DO) from 1.2 to 0.17 mg _O2 L ⁻¹ - with all other operating conditions unchanged - washout of NOB from the flocs was observed. The activity of the minor NOB fraction remaining in the biofilm was suppressed at low DO. As a result, low effluent NO ₃ ⁻ concentrations (0.5 mg _N L ⁻¹ ) were consistently achieved at aerobic nitrogen removal rates (80 mg _N L ⁻¹ d ⁻¹ ) comparable to those of conventional treatment plants. A simple dynamic mathematical model, assuming perfect biomass segregation with AOB and NOB in the flocs and AMX in the biofilm, was able to qualitatively reproduce the selective washout of NOB from the flocs in response to the decrease in DO-setpoint. Similarly, numerical simulations indicated that flocs removal is an effective operational strategy to achieve the selective washout of NOB. The direct competition for NO ₂ ⁻ between NOB and AMX - the latter retained in the biofilm and acting as a “NO ₂ -sink” - was identified by the model as key mechanism leading to a difference in the actual growth rates of AOB and NOB (i.e., μ _NOB < μ _AOB in flocs) and allowing for the selective NOB washout over a broad range of simulated sludge retention times (SRT = 6.8–24.5 d). Experimental results and model predictions demonstrate the increased operational flexibility, in terms of variables that can be easily controlled by operators, offered by hybrid systems as compared to solely biofilm systems for the control of NOB in mainstream PN/A applications.

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