Methane removal is an essential step in drinking water production from methane-rich groundwaters. Conventional aeration-based stripping results in significant direct methane emissions, contributing up to one-third of a treatment plant's total carbon footprint. To address this, a full-scale trickling filter was operated for biological methane oxidation upstream of a submerged sand filter, and its performance was compared to a conventional aeration–submerged sand filtration set-up. Full-scale data were combined with ex-situ batch assays and metagenome-resolved metaproteomics to quantify the individual contribution of the main (a)biotic processes and characterize the enriched microbial communities. Both treatment setups fully removed methane, iron, ammonium, and manganese, yet the underlying mechanisms differed significantly. Methane was completely removed from the effluent after trickling filtration, with stripping and biological oxidation each accounting for half of the removal, thereby halving overall methane emissions. Methane-oxidizing bacteria not only outcompeted nitrifiers in the trickling filter, but also likely contributed directly to ammonia oxidation. In contrast to the submerged filter preceded by methane stripping, signatures of biological iron oxidation were almost completely absent in the trickling filter, suggesting that the presence of methane directly or indirectly promotes chemical iron oxidation. All systems had similar ex-situ manganese oxidation capacities, yet removal occurred only in the submerged filters but not the trickling filter. Ultimately, our results demonstrate that trickling filtration is effective in promoting biological methane oxidation at comparable produced drinking water quality, highlighting its potential for advancing sustainable drinking water production.@en

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

Rapid sand filters (RSF) are an established and widely applied technology for the removal of dissolved iron (Fe²⁺) and ammonium (NH₄⁺) among other contaminants in groundwater treatment. Most often, biological NH₄⁺oxidation is spatially delayed and starts only upon complete Fe²⁺ depletion. However, the mechanism(s) responsible for the inhibition of NH₄⁺oxidation by Fe²⁺ or its oxidation (by)products remains elusive, hindering further process control and optimization. We used batch assays, lab-scale columns, and full-scale filter characterizations to resolve the individual impact of the main Fe²⁺ oxidizing mechanisms and the resulting products on biological NH₄⁺ oxidation. modeling of the obtained datasets allowed to quantitatively assess the hydraulic implications of Fe²⁺ oxidation. Dissolved Fe²⁺ and the reactive oxygen species formed as byproducts during Fe²⁺ oxidation had no direct effect on ammonia oxidation. The Fe³⁺ oxides on the sand grain coating, commonly assumed to be the main cause for inhibited ammonia oxidation, seemed instead to enhance it. modeling allowed to exclude mass transfer limitations induced by accumulation of iron flocs and consequent filter clogging as the cause for delayed ammonia oxidation. We unequivocally identify the inhibition of NH₄⁺oxidizing organisms by the Fe³⁺ flocs generated during Fe²⁺ oxidation as the main cause for the commonly observed spatial delay in ammonia oxidation. The addition of Fe³⁺ flocs inhibited NH₄⁺oxidation both in batch and column tests, and the removal of Fe³⁺ flocs by backwashing completely re-established the NH₄⁺removal capacity, suggesting that the inhibition is reversible. In conclusion, our findings not only identify the iron form that causes the inhibition, albeit the biological mechanism remains to be identified, but also highlight the ecological importance of iron cycling in nitrifying environments.

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Gravity-driven sand filters are the dominant groundwater treatment technology for drinking water production. In the past, physicochemical reactions were often assumed to play the main role in the removal of contaminants, but recent breakthroughs showcase the vital role of microorganisms. In this Current Opinion, we thoroughly assess the current understanding of biology in sand filters and explore the potential benefits of shifting toward designs aimed at promoting biological reactions. We highlight the main bottlenecks and propose key areas to be explored toward the next generation of sustainable, resource-efficient groundwater biofilters.@en

Nitrate leaching from agricultural soils is increasingly found in groundwater, a primary source of drinking water worldwide. This nitrate influx can potentially stimulate the biological oxidation of iron in anoxic groundwater reservoirs. Nitrate-dependent iron-oxidizing (NDFO) bacteria have been extensively studied in laboratory settings, yet their ecophysiology in natural environments remains largely unknown. To this end, we established a pilot-scale filter on nitrate-rich groundwater to elucidate the structure and metabolism of nitrate-reducing iron-oxidizing microbiomes under oligotrophic conditions mimicking natural groundwaters. The enriched community stoichiometrically removed iron and nitrate consistently with the NDFO metabolism. Genome-resolved metagenomics revealed the underlying metabolic network between the dominant iron-dependent denitrifying autotrophs and the less abundant organoheterotrophs. The most abundant genome belonged to a new Candidate order, named Siderophiliales. This new species, “Candidatus Siderophilus nitratireducens,” carries genes central genes to iron oxidation (cytochrome c cyc2), carbon fixation (rbc), and for the sole periplasmic nitrate reductase (nap). Using thermodynamics, we demonstrate that iron oxidation coupled to nap based dissimilatory reduction of nitrate to nitrite is energetically favorable under realistic Fe3+/Fe2+ and NO3−/NO2− concentration ratios. Ultimately, by bridging the gap between laboratory investigations and nitrate real-world conditions, this study provides insights into the intricate interplay between nitrate and iron in groundwater ecosystems, and expands our understanding of NDFOs taxonomic diversity and ecological role.@en

Rapid sand filters are established and widely applied technologies for groundwater treatment. In these filters, main groundwater contaminants such as iron, manganese, and ammonium are oxidized and removed. Conventionally, intensive aeration is employed to provide oxygen for these redox reactions. While effective, intensive aeration promotes flocculent iron removal, which results in iron oxide flocs that rapidly clog the filter. In this study, we operated two parallel full-scale sand filters at different aeration intensities to resolve the relative contribution of homogeneous, heterogeneous and biological iron removal pathways, and identify their operational controls. Our results show that mild aeration in the LOW filter (5 mg/L O2, pH 6.9) promoted biological iron removal and enabled iron oxidation at twice the rate compared to the intensively aerated HIGH filter (>10 mg/L O2, pH 7.4). Microscopy images showed distinctive twisted stalk-like iron solids, the biosignatures of Gallionella ferruginea, both in the LOW filter sand coatings as well as in its backwash solids. In accordance, 10 times higher DNA copy numbers of G. ferruginea were found in the LOW filter effluent. Clogging by biogenic iron solids was slower than by chemical iron flocs, resulting in lower backwash frequencies and yielding four times more water per run. Ultimately, our results reveal that biological iron oxidation can be actively controlled and favoured over competing physico-chemical routes. The production of more compact and practically valuable iron oxide solids is of outmost interest. We conclude that, although counterintuitive, slowing down iron oxidation in the water before filtration enables rapid iron removal in the biofilter.@en

Drinking water production works well, but we can do better.

Anaerobic groundwater is an excellent drinking water source. It presents several advantages over its counterpart, surface water, such as constant quality and temperature, and it is considered to be microbiologically safe. The main contamination sources of anaerobic groundwater are the decomposition of natural organic matter and the dissolution of soil minerals. The first one produces compounds such as ammonia, while the second introduces manganese, iron, and trace metals. Iron, ammonia and manganese must be removed from groundwater to produce drinking water. For this purpose, humans have been using rapid sand filtration - preceded by an aeration step - for over a century.

The purpose of aeration is to strip out undesired gases and to introduce oxygen up to saturation levels. At this oxidation-reduction potential, iron, ammonia and manganese are oxidized by different physical-chemical and biological processes in the subsequent rapid sand filter. As a result, most contaminants precipitate, forming solids that are captured by the filter, and clean water is produced. Although widely used and robust, solid understanding of the intricacies of rapid sand filters is still missing. A high degree of complexity is hidden behind their seemingly simple working principles.

The main reason underneath this extraordinary complexity is the high oxygen load introduced during the aeration step. The saturation of anaerobic groundwater with oxygen onsets a series of simultaneous, interwoven and uncontrolled reactions whose nature and contribution to the overall process remains unknown and generally unpredictable. This process convolution precludes understanding and optimization of rapid sand filtration.

The overarching goal of this thesis is to gain knowledge to advance towards the design of high-flow, resource-efficient sand filters. To do so, we must be able to understand the mechanisms that govern which reactions take place, in which order they occur, and how they affect each other, which will ultimately allow us to predict and control i) microbial community assembly and performance and ii) the interplay between chemical and biological reactions. In the first part of this thesis, we focused on gaining mechanistic understanding of how current sand filters work using laboratory, pilot, and full-scale experiments. In the second one, we used this freshly acquired knowledge to design and test novel systems…
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Rapid sand filters (RSF) are an established and widely applied technology for groundwater treatment. Yet, the underlying interwoven biological and physical-chemical reactions controlling the sequential removal of iron, ammonia and manganese remain poorly understood. To resolve the contribution and interactions between the individual reactions, we studied two full-scale drinking water treatment plant configurations, namely (i) one dual-media (anthracite and quartz sand) filter and (ii) two single-media (quartz sand) filters in series. In situ and ex situ activity tests were combined with mineral coating characterization and metagenome-guided metaproteomics along the depth of each filter. Both plants exhibited comparable performances and process compartmentalization, with most of ammonium and manganese removal occurring only after complete iron depletion. The homogeneity of the media coating and genome-based microbial composition within each compartment highlighted the effect of backwashing, namely the complete vertical mixing of the filter media. In stark contrast to this homogeneity, the removal of the contaminants was strongly stratified within each compartment, and decreased along the filter height. This apparent and longstanding conflict was resolved by quantifying the expressed proteome at different filter heights, revealing a consistent stratification of proteins catalysing ammonia oxidation and protein-based relative abundances of nitrifying genera (up to 2 orders of magnitude difference between top and bottom samples). This implies that microorganisms adapt their protein pool to the available nutrient load at a faster rate than the backwash mixing frequency. Ultimately, these results show the unique and complementary potential of metaproteomics to understand metabolic adaptations and interactions in highly dynamic ecosystems.

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Drinking water treatment plants (DWTPs) are designed to remove physical, chemical, and biological contaminants. However, until recently, the role of DWTPs in minimizing the cycling of antibiotic resistance determinants has got limited attention. In particular, the risk of selecting antibiotic-resistant bacteria (ARB) is largely overlooked in chlorine-free DWTPs where biological processes are applied. Here, we combined high-throughput quantitative PCR and metagenomics to analyze the abundance and dynamics of microbial communities, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) across the treatment trains of two chlorine-free DWTPs involving dune-based and reservoir-based systems. The microbial diversity of the water increased after all biological unit operations, namely rapid and slow sand filtration (SSF), and granular activated carbon filtration. Both DWTPs reduced the concentration of ARGs and MGEs in the water by circa 2.5 log gene copies mL−1, despite their relative increase in the disinfection sub-units (SSF in dune-based and UV treatment in reservoir-based DWTPs). The total microbial concentration was also reduced (2.5 log units), and none of the DWTPs enriched for bacteria containing genes linked to antibiotic resistance. Our findings highlight the effectiveness of chlorine-free DWTPs in supplying safe drinking water while reducing the concentration of antibiotic resistance determinants. To the best of our knowledge, this is the first study that monitors the presence and dynamics of antibiotic resistance determinants in chlorine-free DWTPs.@en