The role of phase separation and feed cycle length in leach beds coupled to methanogenic reactors for digestion of a solid substrate (Part 1): Optimisation of reactors' performance

A two-phase system composed by a leach bed and a methanogenic reactor was modified for the first time to improve volumetric substrate degradation and methane yields from a complex substrate (maize; Zeamays). The system, which was operated for consecutive feed cycles of different durations for 120 days, was highly flexible and its performance improved by altering operational conditions. Daily substrate degradation was higher the shorter the feed cycle, reaching 8.5 g TS_destroyed d⁻¹ (7-day feed cycle) but the overall substrate degradation was higher by up to 55% when longer feed cycles (14 and 28 days) were applied. The same occurred with volumetric methane yields, reaching 0.839 m³ (m³)⁻¹ d⁻¹. The system performed better than others on specific methane yields, reaching 0.434 m³ kg⁻¹ TS_added, in the 14-day and 28-day systems. The UASB and AF designs performed similarly as second stage reactors on methane yields, SCOD and VFA removal efficiencies.     

Autotrophic denitrification using hydrogen generated from metallic iron corrosion

Hydrogenotrophic denitrification was demonstrated using hydrogen generated from anoxic corrosion of metallic iron. For this purpose, a mixture of hydrogenated water and nitrate solution was used as reactor feed. A semi-batch reactor with nitrate loading of 2000 mg m⁻³ d⁻¹ and hydraulic retention time (HRT) of 50 days produced effluent with nitrate concentration of 0.27 mg N L⁻¹ (99% nitrate removal). A continuous flow reactor with nitrate loading of 28.9 mg m⁻³ d⁻¹ and HRT of 15.6 days produced effluent with nitrate concentration of ∼0.025 mg N L⁻¹ (95% nitrate removal). In both cases, the concentration of nitrate degradation by-products, viz., ammonia and nitrite, were below detection limits. The rate of denitrification in the reactors was controlled by hydrogen availability, and hence to operate such reactors at higher nitrate loading rates and/or lower HRT than reported in the present study, hydrogen concentration in the hydrogenated water must be significantly increased.     

Influence of substrate concentration and moisture content on the specific methanogenic activity of dry mesophilic municipal solid waste digestate spiked with propionate

The objective of this study was to evaluate the influence of substrate concentration and moisture content on the specific methanogenic activity (SMA) of a fresh dry mesophilic digestate from a municipal solid waste digester plant. For this purpose, SMA tests were performed under mesophilic conditions into glass bottles of 500 mL volume used as batch reactors, during a period of 20-25 days. Propionate was used as substrate at concentrations ranging from 1 to 10 gCOD/kg. Four moisture contents were studied: 65%, 75%, 80% and 82%. Experimental results showed that propionate concentration and moisture content strongly influenced the SMA. The highest SMA was observed at a substrate concentration of 10 gCOD/kg (11.3 mgCOD gVS⁻¹ d⁻¹ for the second dose of propionate) and at a moisture content of 82% (7.8 mgCOD gVS⁻¹ d⁻¹ for the second dose of propionate, at a concentration of 5 gCOD/kg). SMA was found to decrease linearly when decreasing the moisture content.     

Development of a simultaneous partial nitrification and anaerobic ammonia oxidation process in a single reactor

Up-flow oxygen-controlled biofilm reactors equipped with a non-woven fabric support were used as a single reactor system for autotrophic nitrogen removal based on a combined partial nitrification and anaerobic ammonium oxidation (anammox) reaction. The up-flow biofilm reactors were initiated as either a partial nitrifying reactor or an anammox reactor, respectively, and simultaneous partial nitrification and anammox was established by careful control of the aeration rate. The combined partial nitrification and anammox reaction was successfully developed in both biofilm reactors without additional biomass inoculation. The reactor initiated as the anammox reactor gave a slightly higher and more stable mean nitrogen removal rate of 0.35 (± 0.19) kg-N m⁻³ d⁻¹ than the reactor initiated as the partial nitrifying reactor (0.23 (± 0.16) kg-N m⁻³ d⁻¹). FISH analysis revealed that the biofilm in the reactor started as the anammox reactor were composed of anammox bacteria located in inner anoxic layers that were surrounded by surface aerobic AOB layers, whereas AOB and anammox bacteria were mixed without a distinguishable niche in the biofilm in the reactor started as the partial nitrifying reactor. However, it was difficult to efficiently maintain the stable partial nitrification owing to inefficient aeration in the reactor, which is a key to development of the combined partial nitrification and anammox reaction in a single biofilm reactor.     

Biogeochemical processes in intensive zero-effluent marine fish culture with recirculating aerobic and anaerobic biofilters

The biogeochemical processes that drive nutrient transformations and recycling in organic marine sediment-water environments were studied for 17 months in a zero-effluent intensive recirculating culture system. The system consisted of a 10 m³ gilthead seabream (Sparus aurata) tank coupled to aerobic and anaerobic water treatment elements. Nutrients and alkalinity were measured in the system to quantify the main biogeochemical processes. Fractions of the carbon fed in feed were found in fish (18.3%) and in sludge (11%); the missing carbon was respired by fish (45%) and by aerobic (8.4%) and anaerobic (7.7%) microorganisms. Fractions of the nitrogen fed in feed were found in fish (15.4%) and in sludge (14.3%); the missing nitrogen was eliminated by nitrification-denitrification. Most of the phosphorus and ash fed in feed and not found in fish accumulated within the sludge in the system. The rates of nitrification, denitrification and sulphate reduction increased with time, reaching 0.3 g N m^− 2 d^− 1, 53 g N m^− 2 d^− 1 and 145 g S m^− 2 d^− 1, respectively. Nitrification developed more rapidly than denitrification, leading at first to nitrate accumulation (to 20 mmol NO₃ l^− 1 by day 200) and a decrease in alkalinity. Once denitrification surpassed nitrification, nitrate concentrations decreased, eventually being reduced to < 0.3 mmol NO₃ l^− 1 by day 510, and alkalinity stabilized. Toxic hydrogen sulphide, generated within the anaerobic sludge, was oxidized by oxygen and nitrate as it diffused through the anaerobic-aerobic sediment-water interface. When nitrate levels in the water above the sludge dropped below 2 mmol l^− 1, sulphide was also oxidized in the fluidized bed reactor. Denitrification reduced nitrate in the water, respired (jointly with sulphate reduction) carbon in the sludge, oxidized the hydrogen sulphide, and contributed to stabilization of alkalinity and accumulation of polyphosphate in bacteria as a major sink of labile P.     

Enhanced biomethanation of kitchen waste by different pre-treatments

Five different pre-treatments were investigated to enhance the solubilisation and anaerobic biodegradability of kitchen waste (KW) in thermophilic batch and continuous tests. In the batch solubilisation tests, the highest and the lowest solubilisation efficiency were achieved with the thermo-acid and the pressure-depressure pre-treatments, respectively. However, in the batch biodegradability tests, the highest cumulative biogas production was obtained with the pressure-depressure method. In the continuous tests, the best performance in terms of an acceptable biogas production efficiency of 60% and stable in-reactor COD_s and VFA concentrations corresponded to the pressure-depressure reactor, followed by freeze-thaw, acid, thermo-acid, thermo and control. The maximum OLR (5 g COD L⁻¹ d⁻¹) applied in the pressure-depressure and freeze-thaw reactors almost doubled the control reactor. From the overall analysis, the freeze-thaw pre-treatment was the most profitable process with a net potential profit of around 11.5 € ton⁻¹ KW.     

A low volumetric exchange ratio allows high autotrophic nitrogen removal in a sequencing batch reactor

Sequencing batch reactors (SBRs) have several advantages, such as a lower footprint and a higher flexibility, compared to biofilm based reactors, such as rotating biological contactors. However, the critical parameters for a fast start-up of the nitrogen removal by oxygen-limited autotrophic nitrification/denitrification (OLAND) in a SBR are not available. In this study, a low critical minimum settling velocity (0.7 m h⁻¹) and a low volumetric exchange ratio (25%) were found to be essential to ensure a fast start-up, in contrast to a high critical minimum settling velocity (2 m h⁻¹) and a high volumetric exchange ratio (40%) which yielded no successful start-up. To prevent nitrite accumulation, two effective actions were found to restore the microbial activity balance between aerobic and anoxic ammonium-oxidizing bacteria (AerAOB and AnAOB). A daily biomass washout at a critical minimum settling velocity of 5 m h⁻¹ removed small aggregates rich in AerAOB activity, and the inclusion of an anoxic phase enhanced the AnAOB to convert the excess nitrite. This study showed that stable physicochemical conditions were needed to obtain a competitive nitrogen removal rate of 1.1 g N L⁻¹ d⁻¹.     

Maximum removal rate of propionic acid as a sole carbon source in UASB reactors and the importance of the macro- and micro-nutrients stimulation

The maximum propionic acid (HPr) removal rate (R_HPr) was investigated in two lab-scale Upflow Anaerobic Sludge Bed (UASB) reactors. Two feeding strategies were applied by modifying the hydraulic retention time (HRT) in the UASB_HRT and the influent HPr concentration in the UASB_HPr, respectively. The experiment was divided into three main phases: phase 1, influent with only HPr; phase 2, HPr with macro-nutrients supplementation and phase 3, HPr with macro- and micro-nutrients supplementation. During phase 1, the maximum R_HPr achieved was less than 3 g HPr-COD L⁻¹ d⁻¹ in both reactors. However, the subsequent supplementation of macro- and micro-nutrients during phases 2 and 3 allowed to increase the R_HPr up to 18.1 and 32.8 g HPr-COD L⁻¹ d⁻¹, respectively, corresponding with an HRT of 0.5 h in the UASB_HRT and an influent HPr concentration of 10.5 g HPr-COD L⁻¹ in the UASB_HPr. Therefore, the high operational capacity of these reactor systems, specifically converting HPr with high throughput and high influent HPr level, was demonstrated. Moreover, the presence of macro- and micro-nutrients is clearly essential for stable and high HPr removal in anaerobic digestion.     

The treatment of cheese whey wastewater by sequential anaerobic and aerobic steps in a single digester at pilot scale

The treatment of reconstituted whey wastewater was performed in a 400 L digester at 20 °C, with an anaerobic digestion step, followed by a step of aerobic treatment at low oxygen concentration in the same digester. In a first set of 48 cycles, total cycle time (T_C) of 2, 3 and 4 days were tested at varying organic loading rates (OLR). The COD removal reached 89 ± 4, 97 ± 3 and 98 ± 2% at T_C of 2, 3 and 4 days and OLR of 0.56, 1.04 and 0.78 gCOD L⁻¹ d⁻¹, respectively. The activity of the biomass decreased for the methanogenic population, while increasing by 400% for the acidogens, demonstrating a displacement in the predominant trophic group in the biomass bed. A second set of 16 cycles was performed with higher soluble oxygen concentration in the bulk liquid (0.5 mg L⁻¹) during the aerobic treatment at a T_C of 2 days and an OLR of 1.55 gCOD L⁻¹ d⁻¹, with a soluble COD removal of 88 ± 3%. The biomass specific activities showed a compartmentalization of the trophic group with methanogenic activity maintained in the biomass bed and a high acidogenic activity in the suspended flocs.     

Laboratory scale examination of the effects of overloading on the anaerobic digestion by glycerol

The anaerobic digestion of pure glycerol, which produces a baseline acetic acid to propionic acid ratio of 0.2, was studied in laboratory scale reactors (3 l working volume) at mesophilic temperature (37 °C) with 3000 mg chemical oxygen demand (COD) l⁻¹d⁻¹. During the experiment tVFA and C2-C6 VFA analysis and daily biogas yield measurement were carried out. Following 10 days of a 15% d⁻¹ increase in the organic loading rate (OLR) of 3.0-10.5 g COD l⁻¹d⁻¹, the concentration of propionic acid increased to 6200-8000 mg l⁻¹. Then the inoculum was divided into three parts feeding with 100% glycerol, 50% glycerol + 50% acetic acid, and 50% glycerol + 50% thick stillage, (presented in % of 2.60 g COD l⁻¹d⁻¹ OLR), respectively. The application of co-substrates reduced the recovery period by 5 days compared to feeding with pure glycerol. When the reactors were loaded with glycerol again (10% OLR raise per day) the previously applied co-substrates had a positive effect on the VFA composition and the biogas yield as well.     

Cultivation of microalgae for oil production with a cultivation strategy of urea limitation

The microalgae, Chlorella sp., were cultivated in various culture modes to assess biomass and lipid productivity in this study. In the batch mode, the biomass concentrations and lipid content of Chlorella sp. cultivated in a medium containing 0.025–0.200 g L⁻¹ urea were 0.464–2.027 g L⁻¹ and 0.661–0.326 g g⁻¹, respectively. The maximum lipid productivity of 0.124 g d⁻¹ L⁻¹ occurred in a medium containing 0.100 g L⁻¹ urea. In the fed-batch cultivation, the highest lipid content was obtained by feeding 0.025 g L⁻¹ of urea during the stationary phase, but the lipid productivity was not significantly increased. However, a semi-continuous process was carried out by harvesting the culture and renewing urea at 0.025 g L⁻¹ each time when the cultivation achieved the early stationary phase. The maximum lipid productivity of 0.139 g d⁻¹ L⁻¹ in the semi-continuous culture was highest in comparison with those in the batch and fed-batch cultivations.     

Evaluation of passive solar heating and alternative flow regimes on nitrate removal in denitrification beds

Denitrification beds are a simple and relatively inexpensive technology for removing nitrate from point source discharges. To date, operational beds have used wood media as the carbon source, as it provides a sustained nitrate removal rate (2-10 g N m⁻³ of media d⁻¹) while maintaining permeability. In pilot-scale (2.9 m⁻³) denitrification beds receiving municipal wastewater effluent dosed with KNO₃, we looked at improving nitrate removal by using alternative carbon media (maize cobs) and increasing bed temperature through passive solar heating. The influence of flow regime (horizontal-point, horizontal-diffuse, downflow and upflow) on short-circuit flow was also investigated.The long-term nitrate removal rate (21.8 g N m⁻³ d⁻¹) of the maize cob beds over the 15-month period of the trial was 2-11-fold higher than sustained removal rates reported by other researchers for wood-based beds. While passive solar heating raised the mean bed temperature by 3.4 °C, it did not cause a measurable increase in the nitrate removal rate due to the variability in the removal rate exceeding the expected increase due to temperature.Horizontal flow had more short-circuiting than vertical flow. Short-circuiting in the horizontal flow was attributed to flow being concentrated near the top surface due to the buoyancy effect of warmer water. Greater short-circuiting in the solar heated horizontal and upflow beds than in the corresponding unheated beds was attributed to the buoyancy effect being more pronounced in the solar heated beds.Overall, downflow was deemed the most effective of the four tested flow regimes. It provided the highest increase in bed temperature due to solar heating, had the highest nitrate removal rate in the latter part of the trial and had more plug-flow characteristics. While passive solar heating raised bed temperature, we were unable to demonstrate a significant difference (at 95% CL) in nitrate removal rate between the unheated and solar heated beds because of the high variability in nitrate removal rate and the increase in short-circuiting in the solar heated horizontal and upflow beds.     

Rapid acclimation of methanogenic granular sludge into denitrifying sulfide removal granules

Rapid formation of denitrifying sulfide removal granules is of practical interest to start up an expanded granular sludge bed reactor for wastewater treatment. This study demonstrates that methanogenic granules can be easily acclimated into DSR granules in one day, removing all 1.30 kg m⁻³ d⁻¹ sulfide and converting >90% of 0.56 kg-N m⁻³d⁻¹ nitrate into di-nitrogen gas. Under high loadings, reactor performance, however, declined. Under high loading rates, sulfide first inhibited the heterotrophic denitrifier (Caldithrix sp.), thereby accumulating nitrite in the system; the autotrophic denitrifier (Pseudomonas sp. C23) was then inhibited by accumulated nitrite, leading to breakdown of the entire DSR process.     

Phenol removal from hypersaline wastewaters in a Membrane Biological Reactor (MBR): operation and microbiological characterisation

In this study, two Membrane Biological Reactors (MBR) with submerged flat membranes, one at lab-scale conditions and the other at pilot-plant conditions, were operated at environmental temperature to treat an industrial wastewater characterised by low phenol concentrations (8-16 mg L⁻¹) and high salinity (∼150-160 mS cm⁻¹). During the operation of both reactors, the phenol loading rate was progressively increased and less than 1 mg phenol L⁻¹ was detected even at very low HRTs (0.5-0.7 days). Membrane fouling was minimized by the cross flow aeration rate inside the MBRs and by intermittent permeation. Microbial community analysis of both reactors revealed that members of the genera Halomonas and Marinobacter (gammaproteobacteria) were major components. Growth-linked phenol degradation by pure cultures of Marinobacter isolates demonstrated that this bacterium played a major role in the removal of phenol from the bioreactors.     

In situ microbial treatment of landfill leachate using aerated lagoons

The aim of this study was to assess the efficiency of leachate treatment by microbial oxidation in four connected on-site aerated lagoons at a landfill site. The landfill site was found to be in an ageing methanogenic state, producing leachate with relatively low COD (mean value 1740 mg l⁻¹) and relatively high ammonium concentrations (mean value 1241 mg l⁻¹). Removal of COD averaged 75%, with retention times varying from 11 to 254 days. Overall 80% of the N load was removed within the plant, some by volatilisation of ammonium. Microbial community profiling of the water from each lagoon showed a divergent community profile, presumably a reflection of the nutrient status in each lagoon. In municipal solid waste landfills under similar conditions, leachate treatment through a facultative aerobic system in which sequential aerobic and anaerobic microbial oxidations occurred can readily be achieved using a simple two-lagoon system, suggesting this technology can be economic to install and simple to run.     

Effect of seed sludge and operation conditions on performance and archaeal community structure of low-temperature anaerobic solvent-degrading bioreactors

Two laboratory-scale expanded granular sludge bed (EGSB) anaerobic bioreactors (R1 and R2) were inoculated with biomass from different mesophilic (37 °C) treatment plants, and used for the treatment of an organic solvent-based wastewater at 9–14 °C at applied organic loading rates (OLRs) of 1.2–3.6 kg chemical oxygen demand (COD) m⁻³ d⁻¹. Replicated treatment performance was observed at 10–14 °C, which suggested the feasibility of the process at pilot-scale. Stable and efficient COD removal, along with high methane productivity, was demonstrated at 9 °C at an applied OLR of 2.4 kg COD m⁻³ d⁻¹. Clonal libraries and fluorescence in situ hybridization (FISH) indicated that the seed sludges were dominated (>60%) by acetoclastic Methanosaeta-like organisms. Specific methanogenic activity (SMA) profiles indicated shifts in the physiological profiles of R1 and R2 biomass, including the development of psychrotolerant methanogenic activity. Acetoclastic methanogenesis represented the primary route of methane production in R1 and R2, which is in contrast with several previous reports from low-temperature bioreactor trials. A reduction in the abundance of Methanosaeta-like clones (R2), along with the detection of hydrogenotrophic methanogenic species, coincided with altered granule (sludge) morphology and the development of hydrogenotrophic SMA after prolonged operation at 9 °C.     

Microbial treatment of high-strength perchlorate wastewater

To treat wastewater containing high concentrations of perchlorate, a perchlorate reducing-bacterial consortium was obtained by enrichment culture grown on high-strength perchlorate (1200 mg L⁻¹) feed medium, and was characterized in a sequence batch reactor (SBR) over a long-time operation. The consortium removed perchlorate in the SBR with high reduction rates (35-90 mg L⁻¹ h⁻¹) and stable removal efficiency over 200-day operations. The maximum specific perchlorate reduction rate (q_max), half saturation constant (K_s), and optimal pH range were 0.67 mg-perchlorate mg-dry cell weight⁻¹ h⁻¹, 193.8 mg-perchlorate L⁻¹, and pH 7-9, respectively. The perchlorate reduction yield was 0.48 mol-perchlorate mol-acetate⁻¹. A clone library prepared using the amplicons of cld gene encoding chlorate dismutase showed that the dominant (per)chlorate reducing bacteria in the consortium were Dechlorosoma sp. (53%), Ideonella sp. (28%), and Dechloromonas sp. (19%).     

Performance of microbial fuel cell in response to change in sludge loading rate at different anodic feed pH

Performance of two dual chambered mediator-less microbial fuel cells (MFCs) was evaluated at different sludge loading rate (SLR) and feed pH. Optimum performance in terms of organic matter removal and power production was obtained at the SLR of 0.75 kg COD kg VSS⁻¹ d⁻¹. Maximum power density of 158 mW/m² and 600 mW/m² was obtained in MFC-1 (feed pH 6.0) and MFC-2 (feed pH 8.0), respectively. Internal resistance of the cell decreased with increase in SLR. When operated only with biofilm on anode, the maximum power density was 109.5 mW/m² in MFC-1 and 459 mW/m² in MFC-2, which was, respectively, 30% and 23.5% less than the value obtained in MFC-1 and MFC-2 at SLR of 0.75 kg COD kg VSS⁻¹ d⁻¹. Maximum volumetric power of 15.51 W/m³ and 36.72 W/m³ was obtained in MFC-1 and MFC-2, respectively, when permanganate was added as catholyte. Higher feed pH (8.0) favoured higher power production.     

Rates, controls and potential adverse effects of nitrate removal in a denitrification bed

Denitrification beds are a simple approach for removing nitrate (NO₃⁻) from a range of point sources prior to discharge into receiving waters. These beds are large containers filled with woodchips that act as an energy source for microorganisms to convert NO₃⁻ to nitrogen (N) gases (N₂O, N₂) through denitrification. This study investigated the biological mechanism of NO₃⁻ removal, its controlling factors and its adverse effects in a large denitrification bed (176 m × 5 m × 1.5 m) receiving effluent with a high NO₃⁻ concentration (>100 g N m⁻³) from a hydroponic glasshouse (Karaka, Auckland, New Zealand). Samples of woodchips and water were collected from 12 sites along the bed every two months for one year, along with measurements of gas fluxes from the bed surface. Denitrifying enzyme activity (DEA), factors limiting denitrification (availability of carbon, dissolved organic carbon (DOC), dissolved oxygen (DO), temperature, pH, and concentrations of NO₃⁻, nitrite (NO₂⁻) and sulfide (S²⁻)), greenhouse gas (GHG) production - as nitrous oxide (N₂O), methane (CH₄), carbon dioxide (CO₂) - and carbon (C) loss were determined. NO₃⁻-N concentration declined along the bed with total NO₃⁻-N removal rates of 10.1 kg N d⁻¹ for the whole bed or 7.6 g N m⁻³ d⁻¹. NO₃⁻-N removal rates increased with temperature (Q₁₀ = 2.0). In laboratory incubations, denitrification was always limited by C availability rather than by NO₃⁻. DO levels were above 0.5 mg L⁻¹ at the inlet but did not limit NO₃⁻-N removal. pH increased steadily from about 6 to 7 along the length of the bed. Dissolved inorganic carbon (C-CO₂) increased in average about 27.8 mg L⁻¹, whereas DOC decreased slightly by about 0.2 mg L⁻¹ along the length of the bed. The bed surface emitted on average 78.58 μg m⁻² min⁻¹ N₂O-N (reflecting 1% of the removed NO₃⁻-N), 0.238 μg m⁻² min⁻¹ CH₄ and 12.6 mg m⁻² min⁻¹ CO₂. Dissolved N₂O-N increased along the length of the bed and the bed released on average 362 g dissolved N₂O-N per day coupled with N₂O emission at the surface about 4.3% of the removed NO₃⁻-N as N₂O. Mechanisms to reduce the production of this GHG need to be investigated if denitrification beds are commonly used. Dissolved CH₄ concentrations showed no trends along the length of the bed, ranging from 5.28 μg L⁻¹ to 34.24 μg L⁻¹. Sulfate (SO₄²⁻) concentrations declined along the length of the bed on three of six samplings; however, declines in SO₄²⁻ did not appear to be due to SO₄²⁻ reduction because S²⁻ concentrations were generally undetectable. Ammonium (NH₄⁺) (range: <0.0007 mg L⁻¹ to 2.12 mg L⁻¹) and NO₂⁻ concentrations (range: 0.0018 mg L⁻¹ to 0.95 mg L⁻¹) were always very low suggesting that anammox was an unlikely mechanism for NO₃⁻ removal in the bed. C longevity was calculated from surface emission rates of CO₂ and release of dissolved carbon (DC) and suggested that there would be ample C available to support denitrification for up to 39 years.This study showed that denitrification beds can be an efficient tool for reducing high NO₃⁻ concentrations in effluents but did produce some GHGs. Over the course of a year NO₃⁻ removal rates were always limited by C and temperature and not by NO₃⁻ or DO concentration.     

Reevaluation of the nutrient mineralization process by infaunal bivalves (Ruditapes philippinarum) in a shallow lagoon in Hokkaido, Japan

Previous estimations of nutrient mineralization in the water column by infaunal bivalves might have been overestimated because of underestimation of the uptake process by microphytobenthos in the field. We conducted field surveys of environmental conditions and quantitative sampling of Ruditapes philippinarum in a shallow lagoon system (Hichirippu Lagoon, eastern Hokkaido, Japan) in August 2006. We recorded the spatial distribution pattern and the molar ratio of dissolved inorganic nutrients to determine the limiting nutrients for microphytobenthos, to evaluate the input and output of nutrients at the entrance of the lagoon station, and to estimate potential nutrient mineralization by R. philippinarum. Our aim was to reevaluate the nutrient mineralization process by infaunal bivalve species. In this study, the mean standing stock of microphytobenthos inhabiting surface sediment (5 mm thick) on the tidal flats was 100 times higher than that of phytoplankton (1 m depth). Low N/P and high Si/N ratios (mean = 2.6 and 17.6, respectively) near the entrance of the lagoon compared to those of microphytobenthos (N:P:Si = 10.1:1:18) clearly suggest N deficiency. The flux of NH₄-N coming into the lagoon was 3.4 kmolN d^− 1, and the flux out was − 3.7 kmolN d^− 1. Thus, assuming that there would have been no phytoplankton and microphytobenthos uptake during the day, 0.3 kmolN d^− 1 of NH₄-N was produced within the lagoon. However, the NH₄-N mineralization rate of the clams has been estimated to be approximately 7.7 ± 6.8 kmolN d^− 1. Thus, 96% (7.4 kmolN d^− 1, i.e., 7.7 kmolN d^− 1 minus 0.3 kmolN d^− 1) of the NH₄-N mineralized by the clam was consumed by microphytobenthos. In contrast, if all the NH₄-N inflow (3.1 kmolN d^− 1) was consumed by the microalgae before outflow, 52% (4.0 kmolN d^− 1, i.e., 7.7 kmolN d^− 1 minus 3.7 kmolN d^− 1) of the NH₄-N mineralized by the clams should have been consumed by microphytobenthos. Microphytobenthos on the tidal flats (11.3 ± 11.8 kmolN) used all of the surplus nutrients (between 4.0 and 7.4 kmolN d^− 1), and the temporal division rate [=(NH₄-N uptake)/(standing stock of microphytobenthos)] of microphytobenthos would have to be between 0.35 and 0.65 d^− 1. Residual NH₄-N (0.3 - 3.7 kmolN d^− 1) was the water-column source and accounted for 12-148% of NH₄-N in the water column near the entrance of the lagoon (2.5 ± 1.4 kmolN) per day. This is the first field-based observation with a quantitative evaluation of nutrient mineralization by infaunal bivalves and nutrient uptake by microphytobenthos.