Autotrophic denitrification supported by biotite dissolution in crystalline aquifers (1): New insights from short-term batch experiments

In situ incubation of iron(II)-bearing minerals and Fe(0) reveals insights into metabolic flexibility of chemolithotrophic bacteria in a nitrate polluted karst aquifer

Groundwater nitrate pollution is a major reason for deteriorating water quality and threatens human and animal health. Yet, mitigating groundwater contamination naturally is often complicated since most aquifers are limited in bioavailable carbon. Since metabolically flexible microbes might have advantages for survival, this study presents a detailed description and first results on our modification of the BacTrap© method, aiming to determine the prevailing microbial community's potential to utilize chemolithotrophic pathways. Our microbial trapping devices (MTDs) were amended with four different iron sources and incubated in seven groundwater monitoring wells for ∼3 months to promote growth of nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOxB) in a nitrate-contaminated karst aquifer. Phylogenetic analysis based on 16S rRNA gene sequences implies that the identity of the iron source influenced the microbial community's composition. In addition, high throughput amplicon sequencing revealed increased relative 16S rRNA gene abundances of OTUs affiliated to genera such as Thiobacillus, Rhodobacter, Pseudomonas, Albidiferax, and Sideroxydans. MTD-derived enrichments set up with Fe(II)/nitrate/acetate to isolate potential NRFeOxB, were dominated by e.g., Acidovorax spp., Paracoccus spp. and Propionivibrio spp. MTDs are a cost-effective approach for investigating microorganisms in groundwater and our data not only solidifies the MTD's capacity to provide insights into the metabolic flexibility of the aquifer's microbial community, but also substantiates its metabolic potential for anaerobic Fe(II) oxidation.

Deep denitrification: Stream and groundwater biogeochemistry reveal contrasted but connected worlds above and below

Excess nutrients from agricultural and urban development have created a cascade of ecological crises around the globe. Nutrient pollution has triggered eutrophication in most freshwater and coastal ecosystems, contributing to a loss in biodiversity, harm to human health, and trillions in economic damage every year. Much of the research conducted on nutrient transport and retention has focused on surface environments, which are both easy to access and biologically active. However, surface characteristics of watersheds, such as land use and network configuration, often do not explain the variation in nutrient retention observed in rivers, lakes, and estuaries. Recent research suggests subsurface processes and characteristics may be more important than previously thought in determining watershed-level nutrient fluxes and removal. In a small watershed in western France, we used a multi-tracer approach to compare surface and subsurface nitrate dynamics at commensurate spatiotemporal scales. We combined 3-D hydrological modeling with a rich biogeochemical dataset from 20 wells and 15 stream locations. Water chemistry in the surface and subsurface showed high temporal variability, but groundwater was substantially more spatially variable, attributable to long transport times (10-60 years) and patchy distribution of the iron and sulfur electron donors fueling autotrophic denitrification. Isotopes of nitrate and sulfate revealed fundamentally different processes dominating the surface (heterotrophic denitrification and sulfate reduction) and subsurface (autotrophic denitrification and sulfate production). Agricultural land use was associated with elevated nitrate in surface water, but subsurface nitrate concentration was decoupled from land use. Dissolved silica and sulfate are affordable tracers of residence time and nitrogen removal that are relatively stable in surface and subsurface environments. Together, these findings reveal distinct but adjacent and connected biogeochemical worlds in the surface and subsurface. Characterizing how these worlds are linked and decoupled is critical to meeting water quality targets and addressing water issues in the Anthropocene.

Advanced synergetic nitrogen removal of municipal wastewater using oxidation products of refractory organic matters in secondary effluent by biogenic manganese oxides as carbon source

Due to the high operational cost and secondary pollution of the conventional advanced nitrogen removal of municipal wastewater, a novel concept and technique of advanced synergetic nitrogen removal of partial-denitrification anammox and denitrification was proposed, which used the oxidation products of refractory organic matters in the secondary effluent of municipal wastewater treatment plant (MWWTP) by biogenic manganese oxides (BMOs) as carbon source. When the influent NH₄⁺-N in the denitrifying filter was about 1.0, 2.0, 3.0, 4.0, 5.0 and 7.0 mg/L, total nitrogen (TN) in the effluent decreased from about 22 mg/L to 11.00, 7.85, 6.85, 5.20, 4.15 and 2.09 mg/L, and the corresponding removal rate was 49.15, 64.82, 69.40, 76.70, 81.36 and 90.58%, respectively. The proportional contribution of the partial-denitrification anammox pathway to the TN removal was 12.00, 26.45, 39.70, 46.04, 54.97 and 64.01%, and the actual COD_cr consumption of removing 1 mg TN was 0.75, 1.43, 1.26, 1.17, 1.08 and 0.99 mg, respectively, which was much lower than the theoretical COD_cr consumption of denitrification. Furthermore, COD_cr in the effluent decreased to 8.12 mg/L with a removal rate of 72.40%, and the removed organic matters were mainly non-fluorescent organic matters. Kinds of denitrifying bacteria, anammox bacteria, hydrolytic bacteria and manganese oxidizing bacteria (MnOB) were identified in the denitrifying filter, which demonstrated that the advanced synergetic nitrogen removal was achieved. This novel technology presented the advantages of high efficiency of TN and COD_cr removal, low operational cost and no secondary pollution.

Advanced nitrogen removal performance and microbial community structure of a lab-scale denitrifying filter with in-situ formation of biogenic manganese oxides

Advanced nitrogen removal faces the challenges of high operational cost resulted from the additional carbon source and secondary pollution caused by inaccurate carbon source dosage in municipal wastewater. To address these problems, a novel carbon source was developed, which was the oxidation products of refractory organic matters in the secondary effluent of municipal wastewater treatment plant (MWWTP) by in-situ generated biogenic manganese oxides (BMOs) in the denitrifying filter. In the steady phase, the effluent chemical oxygen demand (COD_cr), NO₃^--N and total nitrogen (TN) in the denitrifying filter 2^# with BMOs was 11.27, 9.03 and 10.36 mg/L, and the corresponding removal efficiency was 54.79%, 51.85% and 48.03%, respectively, which was significantly higher than those in the control denitrifying filter 1^# that the removal efficiency of COD_cr, NO₃^--N and TN was only 32.30%, 28.58% and 29.36%, respectively. Kinds of denitrifying bacteria (Candidatus Competibacter, Defluviicoccus, Dechloromonas, Candidatus Competibacter, Dechloromonas, Pseudomonas, Thauera, Acinetobacter, Denitratisoma, Anaerolineae and Denitratisoma) and anammox bacteria (Pirellula, Gemmata, Anammoximicrobium and Brocadia) were identified in the denitrifying filters 1^# and 2^#, which explained why the actual COD_cr consumption (1.55 and 1.44 mg) of reducing 1 mg NO₃^--N was much lower than the theoretical COD_cr consumption. While manganese oxidizing bacteria (MnOB, Bacillus, Crenothrix and Pedomicrobium) was only identified in the denitrifying filter 2^#. This novel technology presented the advantages of no additional carbon source, low operational cost and no secondary pollution. Therefore, the novel technology has superlative application value and broad application prospect.

New insights on simultaneous nitrate and phosphorus removal in pyrite-involved mixotrophic denitrification biofilter for a long-term operation: Performance change and its underlying mechanism

Simultaneous nitrate and phosphorus removal can be completed by pyrite- and influent organics-involved mixotrophic denitrification and chemical phosphorus removal via iron precipitation. However, so far, how their removal performances change with iron precipitation accumulation remains unclear. In this study, the differences in nitrate and phosphorus removal from municipal tailwater between volcanic and pyrite supported biofilters (V-BF, P-BF) for a long-term operation were investigated, as well as the underlying mechanism for these differences. The nitrate removal efficiencies (NREs) in P-BF were greater than those in V-BF due to the synergistic effect of influent organic and pyrite, as evidenced by comparable TOC consumption and Fe²⁺/SO₄^2- production. The NREs in P-BF were gradually lower than in V-BF as a result of bacterial cell-iron encrustation observed in TEM images, which would deteriorate microbial activity. However, the phosphorus removal efficiencies (PREs) in P-BF remained consistently higher than in V-BF, resulting from chemical phosphorus removal which was confirmed that P, Fe and O elements dominated on the pyrite surface after use by SEM-EDS. The dominant denitrifying bacteria differed significantly, autotrophic and heterotrophic denitrifying microorganisms coexisted in P-BF. The relative abundances of the narG coding gene in P-BF were higher than that in V-BF, which was consistent with the total relative abundances of identified denitrifying bacteria. Besides, the mechanism of simultaneous nitrogen and phosphorus removal in the pyrite-involved mixotrophic denitrification process has been deduced. This work has significant implications for the practical application of a pyrite-involved mixotrophic denitrification process for low C/N wastewater treatment.

A hillslope-scale aquifer-model to determine past agricultural legacy and future nitrate concentrations in rivers

The long-term fate of agricultural nitrate depends on rapid subsurface transfer, denitrification and storage in aquifers. Quantifying these processes remains an issue due to time varying subsurface contribution, unknown aquifer storage and heterogeneous denitrification potential. Here, we develop a parsimonious modelling approach that uses long-term discharge and river nitrate concentration time-series combined with groundwater age data determined from chlorofluorocarbons in springs and boreholes. To leverage their informational content, we use a Boussinesq-type equivalent hillslope model to capture the dynamics of aquifer flows and evolving surface and subsurface contribution to rivers. Nitrate transport was modelled with a depth-resolved high-order finite-difference method and denitrification by a first-order law. We applied the method to three heavily nitrate loaded catchments of a crystalline temperate region of France (Brittany). We found that mean water transit time ranged 10-32 years and Damköhler ratio (transit time/denitrification time) ranged 0.12-0.55, leading to limited denitrification in the aquifer (10-20%). The long-term trajectory of nitrate concentration in rivers appears determined by flows stratification in the aquifer. The results suggest that autotrophic denitrification is controlled by the accessibility of reduced minerals which occurs at the base of the aquifer where flows decrease. One interpretation is that denitrification might be an interfacial process in zones that are weathered enough to transmit flows and not too weathered to have remaining accessible reduced minerals. Consequently, denitrification would not be controlled by the total aquifer volume and related mean transit time but by the proximity of the active weathered interface with the water table. This should be confirmed by complementary studies to which the developed methodology might be further deployed.

Elucidating heterogeneous nitrate contamination in a small basement aquifer. A multidisciplinary approach: NO3 isotopes, CFCs-SF6, microbiological activity, geophysics and hydrogeology

Nitrate contamination of groundwater remains a major concern despite all the measures and efforts undertaken over the last decades to protect water resources. We focused on a small catchment in Brittany (France) facing nitrate pollution with concentrations over the European drinking water standard of 50 mg.L^-1. This is a common situation in catchments where - supposedly effective - measures were applied for reducing the transfer of N to groundwater. At the scale of this small (~100 ha) basement aquifer, nitrate concentrations are very heterogeneous in the groundwater, sampled up to 15-20 m below the soil surface in several observation wells (hereafter referred as piezometers) and up to 110 m deep in a borehole drilled through a faulted area near the Spring (outlet of the catchment). We used complementary and robust approaches for exploring and constraining the driving parameters of nitrate transfer and distribution in groundwater. Detailed geological work and a geophysical electrical resistivity tomography survey identified the lithologies, tectonic structures and weathering layers. This highlighted a complex geological structure with several compartments delimited by faults, as well as the highly variable thickness of the weathered layer. It also illustrated the heterogeneity of the hydrosystem, some compartments appearing to be disconnected from the general groundwater flow. This was confirmed by geochemical analyses and by the mean apparent groundwater residence time based on CFCs-SF6 and noble-gas analyses, locally revealing old and nitrate-free groundwater, and very old water with a recharge temperature below than the current average temperature in the area, reflecting water dating back to the last period of glaciation (-19 to -17 ky). Nitrate isotopes clearly showed denitrification processes in a few piezometers, which was generally supported by microbiology and molecular biology results. This highlighted the presence of functional genes involved in denitrification as well as a capacity of the groundwater microbial community to denitrify when in situ conditions are favourable. This type of combined approach - covering chemistry, isotopic methods, dissolved gases, microbiological activity, geophysics and hydrogeology - appears to be indispensable for implementing the most relevant programme of measures and for accurately assessing their effectiveness, notably by considering the timeframe between implementation of the measures and their impact on groundwater quality.

The influence mechanism of temperature on solid phase denitrification based on denitrification performance, carbon balance, and microbial analysis

In this work, the influence mechanism of temperature on solid phase denitrification (SPD) was investigated using a pilot-scale reactor supported with polycaprolactone (PCL). The results showed that under nitrate loads of ~31.5 mg N/(L·h), as temperature decreased from 30 °C to 13 °C, the nitrate removal efficiency declined from 94% to 57%. Furthermore, denitrification rate constants were input into Arrhenius equation and the resulting temperature coefficient was 1.04. Significantly nitrite accumulation and less effluent COD residue occurred at low-temperatures. Via stoichiometry, the sludge yield coefficient and COD demand for nitrate removal both increased as a function of increasing temperature; and were calculated at 20 °C as 0.069 g MLVSS/(g COD·d) and 3.265 g COD/g N, respectively. Carbon balance analysis indicated that the COD release rate (υ) at 30 °C was twice that at 13 °C. LEfSe analysis demonstrated that Desulfomicrobium, Desulfovibrio, and Meganema were abundant at low-temperature, while Simplicispira, Aquabacterium, and Acidovorax were enriched at high-temperature. Besides, carboxylesterase (PCL depolymerase) was more abundant at high-temperature, implying an association with a fast υ. Moreover, nar was enriched at low-temperature, while nir was depleted, which led to nitrite accumulation. These results provide reference for SPD design parameter estimation and/or optimal operation strategy.

Controls on species distribution and biogeochemical cycling in nitrate-contaminated groundwater and surface water, southeastern Australia

A detailed study of groundwater and surface water nitrate over four seasons across an area of varied landuse provided insights into the mechanisms that underlie accumulation and transport of nitrate. High nitrate concentrations found in a significant percentage of surface water and shallow groundwater samples are due to anthropogenic contamination. Statistics (PCA, ANOVA, parsimonious model and general linear regression) were used to explore the relationship between NO₃^- and land use, and confirmed that areas of high NO₃^- concentration are associated with dairy pasture and horticulture. Seasonally, NO₃^- levels are greater during winter, the wettest part of the year. Values of δ¹⁵N showed that most nitrate is sourced from livestock waste, with a smaller contribution from synthetic fertilizer. Direct wash-off of animal waste from dairy farms results in higher NO₃^- concentrations in surface water than in groundwater. Denitrification is an important NO₃^- attenuation mechanism which reduces NO₃^- to NH₄, as demonstrated by the PCA analysis, which showed positive correlation of NO₃^- concentrations with dissolved oxygen and negative correlations with NH₄⁺, Fe²⁺and Mn²⁺; the latter two species may act as the electron donors necessary for reduction of NO₃^-. The often high NO₃^- concentrations in shallow groundwater are decreased by denitrification, which can occur at relatively shallow depths (<3 m). The relatively small NO₃^- concentrations in deeper groundwater are due partly to denitrification, but more to originally lower NO₃^- concentrations, as the age of deeper groundwater shows that it was recharged before agriculture was established in the study area. Overall, the study demonstrates the usefulness of hydrogeochemical characterisation and multivariate statistics in the evaluation of impacts of agricultural land-use on regional N cycling. In particular, the results show that efforts to mitigate NO₃^- pollution from farms should concentrate more on wash-off of animal waste than the contribution of nitrogenous synthetic fertilizer.

Aerobic granular sludge operation and nutrients removal mechanism in a novel configuration reactor combined sequencing batch reactor and continuous-flow reactor

A novel aerobic granular sludge (AGS) system called SBR (sequencing batch reactor)-CF (continuous-flow) system merging the advantages of sequencing batch reactors (SBRs) and continuous flow (CF) reactors was developed. The AGS was successfully operated in the SBR-CF system which consisted of four same SBRs (each served as settling tank/anaerobic feeding tank/aerobic reacting tank in turn). The effects of aeration intensity and hydraulic retention time (HRT) on the SBR-CF system were studied. The results showed strong aeration intensity (9.74 h^-1 in this study) and appropriate HRT (9 h in this study) were more favorable to the nutrients removal. The EEM-PARAFAC analysis was applied to characterize the LB-EPS, TB-EPS and domestic wastewater, as results TB-EPS was found play an important role in the biosorption in COD removal of the SBR-CF system. In addition, a preliminary conceptual reaction process model in the SBR-CF system was built using high-throughput pyrosequencing and phylogenetic assignment.

Sulphuric acid-mediated weathering on Taiwan buffers geological atmospheric carbon sinks

The chemical composition of the Gaoping River in Taiwan reflects the weathering of both silicate and carbonate rocks found in its metasedimentary catchment. Major dissolved ion chemistry and radiocarbon signatures of dissolved inorganic carbon (DIC) reveal the importance of pyrite-derived sulphuric acid weathering on silicates and carbonates. Two-thirds of the dissolved load of the Gaoping River derives from sulphuric acid-mediated weathering of rocks within its catchment. This is reflected in the lowest reported signatures DI¹⁴C for a small mountainous river (43 to 71 percent modern carbon), with rock-derived carbonate constituting a ¹⁴C-free DIC source. Using an inverse modelling approach integrating riverine major dissolved ion chemistry and DI¹⁴C, we provide quantitative constraints of mineral weathering pathways and calculate atmospheric CO₂ fluxes resulting from the erosion of the Taiwan orogeny over geological timescales. The results reveal that weathering on Taiwan releases 0.31 ± 0.12 MtC/yr, which is offset by burial of terrestrial biospheric organic carbon in offshore sediments. The latter tips the balance with respect to the total CO₂ budget of Taiwan such that the overall system acts as a net sink, with 0.24 ± 0.13 MtC/yr of atmospheric CO₂ consumed over geological timescales.

Plant-microbial synergism: An effective approach for the remediation of shale-gas fracturing flowback and produced water

Effective and affordable treatment of hydraulic fracturing flowback and produced water (FPW) is a major challenge for the sustainability of unconventional shale-gas exploration and development. We investigated the effectiveness of different combinations of activated sludge (AS), three microbial preparations, and ten plants (ryegrass, water dropwort, typha, reed, iris, canna, water caltrop, rape, water spinach, and Alternanthera philoxeroides) on the treatment performance of FPW. Water quality parameters (NH₄-N, NO₃-N, NO₂-N, COD_cr, and BOD) and the algal toxicity of the treated FPW were used as metrics to assess the treatment efficiency. The results showed that AS had higher treatment efficiency than the prepared microorganisms, and water dropwort was the best plant candidate for boosting performance of AS treatment of FPW. The treated FPW showed improved water quality and microbial diversity. The Shannon-Wiener index increased from 4.76 to 7.98 with FPW treatment. The relative abundance of microbes with a greater resistance to high salt conditions, such as Bacteroidetes, Firmicutes, Chloroflexi, increased substantially in the treated FPW. The combination of water dropwort and AS showed the greatest improvement in water quality, the highest algal density and microbial diversity, thus indicating good potential for this candidate in the treatment of FPW.

Stratification of reactivity determines nitrate removal in groundwater

Although groundwater is a critical source of drinking water and irrigation, it has been polluted worldwide by agriculture, industry, and domestic activity. Because assessing groundwater quality and recovery rates is challenging, we developed a method for determining where and how quickly nitrate is removed in aquifers using just a few point measurements of groundwater chemistry. This methodology opens new avenues for characterizing catchment-scale nutrient dynamics, including nitrogen, carbon, and silica, with existing datasets for ecosystems around the globe. Understanding the subsurface structure of reactivity would also improve estimates of recovery time frames for polluted ecosystems and inform sustainable limits for anthropogenic activity.

Biogeochemical reactions occur unevenly in space and time, but this heterogeneity is often simplified as a linear average due to sparse data, especially in subsurface environments where access is limited. For example, little is known about the spatial variability of groundwater denitrification, an important process in removing nitrate originating from agriculture and land use conversion. Information about the rate, arrangement, and extent of denitrification is needed to determine sustainable limits of human activity and to predict recovery time frames. Here, we developed and validated a method for inferring the spatial organization of sequential biogeochemical reactions in an aquifer in France. We applied it to five other aquifers in different geological settings located in the United States and compared results among 44 locations across the six aquifers to assess the generality of reactivity trends. Of the sampling locations, 79% showed pronounced increases of reactivity with depth. This suggests that previous estimates of denitrification have underestimated the capacity of deep aquifers to remove nitrate, while overestimating nitrate removal in shallow flow paths. Oxygen and nitrate reduction likely increases with depth because there is relatively little organic carbon in agricultural soils and because excess nitrate input has depleted solid phase electron donors near the surface. Our findings explain the long-standing conundrum of why apparent reaction rates of oxygen in aquifers are typically smaller than those of nitrate, which is energetically less favorable. This stratified reactivity framework is promising for mapping vertical reactivity trends in aquifers, generating new understanding of subsurface ecosystems and their capacity to remove contaminants.