Amending woodchip bioreactors with corncobs reduces nitrogen removal cost.

Woodchip denitrification bioreactors are an effective agricultural practice to reduce nitrogen (N) export from subsurface drainage via the conversion of nitrate (NO3-) to nitrogen gas (N2), but there are challenges associated with limited woodchip supplies and increasing prices. Previous lab studies indicate that corncobs could be a promising woodchip alternative from the perspectives of N removal rate and cost. This field study aimed to provide early performance and cost assessment of denitrification bioreactors with two woodchip-corncob treatments. The objectives were to i) compare N removal rates of bioreactors with different carbon and hydraulic retention time (HRT) treatments, ii) compare bioreactor N removal costs, and iii) conduct sensitivity analysis on full-scale bioreactors (FBR) N removal costs with varying corncob lifespans and prices. Nine replicated field pilot-scale bioreactors (PBRs) using three carbon treatments and three HRTs were assessed for N removal efficiency. The carbon treatments were woodchip-only (WC100), 25% (by vol.) corncobs + 75% woodchips media (CC25) in series, and 75% corncobs + 25% woodchips (CC75) in series set at HRTs of 2, 8, and 16 h. N concentrations were monitored at each PBR inlet and outlet, and the PBR N removal efficiencies were used to estimate FBR N removal rates and costs. At respective HRTs, the estimated N removal rates of CC75 were 1.6- to 10.1-fold higher than WC100, but CC25 exhibited 0.9-fold lower (at 8-hr HRT) to 2.8-fold higher than WC100. A 15-yr cost assessment indicated CC75 ($10.56 to $13.89 kg-1 N) was the most cost-efficient treatment, followed by WC100 ($13.30 to $88.11 kg-1 N) and CC25 ($22.41 to $60.13 kg-1 N). This assessment showed CC75 as a promising alternative to WC100 in terms of N removal rate and cost, but CC25 did not provide sufficient N removal rate increase for it to be a cost-efficient option. Nonetheless, using corncobs as a bioreactor medium is a relatively new approach, and we encourage more field studies to explore the long-term opportunities and challenges.

Hydrophobic laser-induced graphene potentiometric ion-selective electrodes for nitrate sensing.

Current solid-contact ion-selective electrodes (ISEs) suffer from signal-to-noise drift and short lifespans partly due to water uptake and the development of an aqueous layer between the transducer and ion-selective membrane. To address these challenges, we report on a nitrate ISE based on hydrophobic laser-induced graphene (LIG) coated with a poly(vinyl) chloride-based nitrate selective membrane. The hydrophobic LIG was created using a polyimide substrate and a double lasing process under ambient conditions (air at 23.0 ± 1.0 °C) that resulted in a static water contact angle of 135.5 ± 0.7° (mean ± standard deviation) in wettability testing. The LIG-ISE displayed a Nernstian response of - 58.17 ± 4.21 mV dec-1 and a limit-of-detection (LOD) of 6.01 ± 1.44 µM. Constant current chronopotentiometry and a water layer test were used to evaluate the potential (emf) signal stability with similar performance to previously published work with graphene-based ISEs. Using a portable potentiostat, the sensor displayed comparable (p > 0.05) results to a US Environmental Protection Agency (EPA)-accepted analytical method when analyzing water samples collected from two lakes in Ames, IA. The sensors were stored in surface water samples for 5 weeks and displayed nonsignificant difference in performance (LOD and sensitivity). These results, combined with a rapid and low-cost fabrication technique, make the development of hydrophobic LIG-ISEs appealing for a wide range of long-term in situ surface water quality applications.

Stacked conservation practices reduce nitrogen loss: A paired watershed study.

Combinations of best management practices (BMPs) are needed to achieve nutrient reduction goals in the Mississippi/Atchafalaya River Basin (MARB), but field results are crucial to encourage stacked adoption of BMPs. A paired catchment-scale study (2015-18) was done to assess the impact of (i) BMPs, (ii) precipitation patterns, and (iii) seasonality on nitrogen (N) export. Flow-weighted samples were collected and analyzed for total ammonia nitrogen (TAN), nitrate (NO3-N), and total nitrogen (TN). Catchments Low-BMP 11 and High-BMP 12 had 27.6% and 87.6% areal coverage of BMPs, respectively. No significant difference (p > 0.05) in TAN concentrations was found between Low-BMP 11 (0.023 mg L-1) and High-BMP 12 (0.020 mg L-1). However, NO3-N and TN concentrations were significantly higher (p < 0.05) at Low-BMP 11 (NO3-N: 26.0 mg L-1, TN: 28.7 mg L-1) than at High-BMP 12 (NO3-N: 8.8 mg L-1, TN: 9.2 mg L-1). Two precipitation factors that affected N export patterns were observed. First, N flushing could continue for several years after a drought as elevated NO3-N concentrations were observed in 2015 (i.e., two years after the 2011-2013 drought). Second, higher annual N export was observed when more precipitation occurred during the pre-planting or early-growing season versus later periods. For both catchments, the highest 50% of flows were responsible for majority of the NO3-N export. We estimated that 33-37%, 61-62%, and 82-85% of the NO3-N loads occurred in the 90th, 75th, and 50th flow percentiles, respectively. As demonstrated in High-BMP 12, stacked BMP application effectively lowered NO3-N and TN loads by 60.3% and 59.1%, respectively, relative to Low-BMP 11. Although 27.6% BMP coverage area in Low-BMP 11 was considered low for this study, this coverage area is higher than many other parts of the MARB. This research highlights the importance of joint efforts between landowners in a watershed to meet downstream water quality goals.

Catchment-scale Phosphorus Export through Surface and Drainage Pathways.

The site-specific nature of P fate and transport in drained areas exemplifies the need for additional data to guide implementation of conservation practices at the catchment scale. Total P (TP), dissolved reactive P (DRP), and total suspended solids (TSS) were monitored at five sites-two streams, two tile outlets, and a grassed waterway-in three agricultural subwatersheds (221.2-822.5 ha) draining to Black Hawk Lake in western Iowa. Median TP concentrations ranged from 0.034 to 1.490 and 0.008 to 0.055 mg P L for event and baseflow samples, respectively. The majority of P and TSS export occurred during precipitation events and high-flow conditions with greater than 75% of DRP, 66% of TP, and 59% of TSS export occurring during the top 25% of flows from all sites. In one subwatershed, a single event (annual recurrence interval < 1 yr) was responsible for 46.6, 84.0, and 81.0% of the annual export of TP, DRP, and TSS, respectively, indicating that frequent, small storms have the potential to result in extreme losses. Isolated monitoring of surface and drainage transport pathways indicated significant P and TSS losses occurring through drainage; over the 2-yr study period, the drainage pathway was responsible for 69.8, 59.2, and 82.6% of the cumulative TP, DRP, and TSS export, respectively. Finally, the results provided evidence that particulate P losses in drainage were greater than dissolved P losses. Understanding relationships between flow, precipitation, transport pathway, and P fraction at the catchment scale is needed for effective conservation practice implementation.

Nitrous oxide and methane production from denitrifying woodchip bioreactors at three hydraulic residence times.

Denitrifying bioreactors remove nitrate (NO3-) from agricultural drainage and are slated to be an integral part of nitrogen reduction strategies in the Mississippi River Basin. However, incomplete denitrification can result in nitrous oxide (N2O) production and anaerobic conditions within bioreactors may be conducive to methane (CH4) production via methanogenesis. Greenhouse gas production has the potential to trade excess NO3- in surface water with excess greenhouses gases in the atmosphere. Our study examined N2O and CH4 production from pilot scale (6.38 m3) bioreactors across three hydraulic residence times (HRTs), 2, 8, and 16 h. Production was measured from both the surface of the bioreactors and dissolved in the bioreactor effluent. Nitrous oxide and CH4 was produced across all HRTs, with the majority dissolved in the effluent. Nitrous oxide production was significantly greater (P < 0.05) from 2 h HRTs (478.43 mg N2O m-3 day-1) than from 8 (29.95 mg N2O m-3 day-1) and 16 (36.61 mg N2O m-3 day-1) hour HRTs. Methane production was significantly less (P < 0.05) from 2 h HRTs (0.51 g C m3 day-1) compared to 8 (1.50 g C m3 day-1) and 16 (1.69 g C m3 day-1) hour HRTs. The 2 h HRTs had significantly greater (P = 0.05) impacts to climate change compared to 8 and 16 h HRTs. Results from this study suggest managing HRTs between 6 and 8 h in field bioreactors could minimize total greenhouse gas production and maximize NO3- removal.

Long-term impact of poultry manure on crop yield, soil and water quality, and crop revenue.

A long-term poultry manure fertilizer study was initiated in 1998 and continued until 2009 under corn-soybean (CS) rotation. To match changing landscape trends, the plots were switched to continuous corn (CC) from 2010 to 2017. In both CS and CC phases, poultry manure (PM) was applied at the crop rotation recommended agronomic N rate and either half (CC phase) or double (CS phase) the recommended rate. Urea-ammonium nitrate (UAN) was applied to comparison plots at the crop recommended application rate (168 kg N ha-1 and 224 kg N ha-1 for the CS and CC phases, respectively) throughout the study. The objectives of this study include evaluation of the economic benefits of long-term PM application at various rates (PM2, PM, and PM0.5), and the impact of poultry manure application on soil health and nutrient levels, crop yield, and drainage water quality. Lower NO3-N concentrations were reported in drainage from PM treated plots when compared to UAN fertilizer applied at the same agronomic rate. Of the parameters tested for soil health analysis after twenty years of repeat application, particulate organic matter (POM) present was significantly greater in the PM treated soils (6.1-6.7 g kg soil-1) when compared to UAN plots (4.6 g kg soil-1), showing potential for stabilized soil particles, increased infiltration and water-holding capacity. The results show a consistent positive impact of manure application on corn and soybean yields when compared to yields observed in UAN treated plots. During the CS phase, we estimated the same average revenue per dollar spent for PM and UAN treatments, while the average return rate for PM2 was 1% lower; during CC phase,15% increased return rates were observed when PM0.5 and PM were compared against the UAN treatment. When managed properly, PM application to cropland is a sustainable option for diversifying agroecosystems, improving soil health and improving farm economics.

Distinguishing between metabolically active and dormant bacteria on paper.

Switching between metabolically active and dormant states provides bacteria with protection from environmental stresses and allows rapid growth under favorable conditions. This rapid growth can be detrimental to the environment, e.g., pathogens in recreational lakes, or to industrial processes, e.g., fermentation, making it useful to quickly determine when the ratio of dormant to metabolically active bacteria changes. While a rapid increase in metabolically active bacteria can cause complications, a high number of dormant bacteria can also be problematic, since they can be more virulent and antibiotic-resistant. To determine the metabolic state of Escherichia coli and Salmonella Typhimurium, we developed two paper-based colorimetric assays. The color changes were based on oxidoreductases reducing tetrazolium salts to formazans, and alkaline phosphatases cleaving phosphates from nitrophenyl phosphate salt. Specifically, we added iodophenyl-nitrophenyl-phenyl tetrazolium salt (INT) and methylphenazinium methyl sulfate to metabolically active bacteria on paper and INT and para-nitrophenyl phosphate salt to dormant bacteria on paper. The color changed in less than 60 min and was generally visible at 103 CFU and quantifiable at 106 CFU. The color changes occurred in both bacteria, since oxidoreductases and alkaline phosphatases are common bacterial enzymes. On one hand, this feature makes the assays suitable to a wide range of applications, on the other, it requires specific capture, if only one type of bacterium is of interest. We captured Salmonella or E. coli with immobilized P22 or T4 bacteriophages on the paper, before detecting them at levels of 102 or 104 CFU, respectively. Determining the ratio of the metabolic state of bacteria or a specific bacterium at low cost and in a short time, makes this methodology useful in environmental, industrial and health care settings.

Water and Sediment Microbial Quality of Mountain and Agricultural Streams.

Increased public health risk caused by pathogen contamination in streams is a serious issue, and mitigating the risk requires improvement in existing microbial monitoring of streams. To improve understanding of microbial contamination in streams, we monitored in stream water columns and streambed sediment. Two distinct streams and their subwatersheds were studied: (i) a mountain stream (Merced River, California), which represents pristine and wild conditions, and (ii) an agricultural stream (Squaw Creek, Iowa), which represents an agricultural setting (i.e., crop, manure application, cattle access). Stream water column and sediment samples were collected in multiple locations in the Merced River and Squaw Creek watersheds. Compared with the mountain stream, water column concentrations in the agricultural stream were considerably higher. In both mountain and agricultural streams, concentrations in bed sediment were higher than the water column, and principal component analysis indicates that land use affected water column levels significantly ( < 0.05). The cluster analysis showed grouping of subwatersheds for each basin, indicating unique land use features of each watershed. In general, water column levels in the mountain stream were lower than the USEPA's existing water quality criteria for bacteria. However, the levels in the agricultural stream exceeded the USEPA's microbial water quality criteria by several fold, which substantiated that increased agricultural activities, use of animal waste as fertilizers, and combined effect of rainfall and temperature may act as potential determining factors behind the elevated levels in agriculture streams.

Correction to: Escherichia coli persistence kinetics in dairy manure at moderate, mesophilic, and thermophilic temperatures under aerobic and anaerobic environments.

Escherichia coli persistence kinetics in dairy manure at moderate, mesophilic, and thermophilic temperatures.

Quantifying Attachment and Antibiotic Resistance of from Conventional and Organic Swine Manure.

Broad-spectrum antibiotics are often administered to swine, contributing to the occurrence of antibiotic-resistant bacteria in their manure. During land application, the bacteria in swine manure preferentially attach to particles in the soil, affecting their transport in overland flow. However, a quantitative understanding of these attachment mechanisms is lacking, and their relationship to antibiotic resistance is unknown. The objective of this study is to examine the relationships between antibiotic resistance and attachment to very fine silica sand in collected from swine manure. A total of 556 isolates were collected from six farms, two organic and four conventional (antibiotics fed prophylactically). Antibiotic resistance was quantified using 13 antibiotics at three minimum inhibitory concentrations: resistant, intermediate, and susceptible. Of the 556 isolates used in the antibiotic resistance assays, 491 were subjected to an attachment assay. Results show that isolates from conventional systems were significantly more resistant to amoxicillin, ampicillin, chlortetracycline, erythromycin, kanamycin, neomycin, streptomycin, tetracycline, and tylosin ( < 0.001). Results also indicate that isolated from conventional systems attached to very fine silica sand at significantly higher levels than those from organic systems ( < 0.001). Statistical analysis showed that a significant relationship did not exist between antibiotic resistance levels and attachment in from conventional systems but did for organic systems ( < 0.001). Better quantification of these relationships is critical to understanding the behavior of in the environment and preventing exposure of human populations to antibiotic-resistant bacteria.

Woodchip Denitrification Bioreactors: Impact of Temperature and Hydraulic Retention Time on Nitrate Removal.

Woodchip denitrification bioreactors, a relatively new technology for edge-of-field treatment of subsurface agricultural drainage water, have shown potential for nitrate removal. However, few studies have evaluated the performance of these reactors under varied controlled conditions including initial woodchip age and a range of hydraulic retention times (HRTs) and temperatures similar to the field. This study investigated (i) the release of total organic C (TOC) during reactor start up for fresh and weathered woodchips, (ii) nitrate (NO-N) removal at HRTs ranging from 2 to 24 h, (iii) nitrate removal at influent NO-N concentrations of 10, 30, and 50 mg L, and (iv) NO-N removal at 10, 15, and 20°C. Greater TOC was released during bioreactor operation with fresh woodchips, whereas organic C release was low when the columns were packed with naturally weathered woodchips. Nitrate-N concentration reductions increased from 8 to 55% as HRT increased. Nitrate removal on a mass basis (g NO-N m d) did not follow the same trend, with relatively consistent mass removal measured as HRT increased from 1.7 to 21.2 h. Comparison of mean NO-N load reduction for various influent NO-N concentrations showed lower reduction at an influent concentration of 10 mg L and higher NO-N reductions at influent concentrations of 30 and 50 mg L. Nitrate-N removal showed a stepped increase with temperature. Temperature coefficient () factors calculated from NO-N removal rates ranged from 2.2 to 2.9.

Escherichia coli persistence kinetics in dairy manure at moderate, mesophilic, and thermophilic temperatures under aerobic and anaerobic environments.

To assess Escherichia coli (E. coli) persistence in dairy manure, bench scale experiments were conducted under aerobic and anaerobic environments. The changes in E. coli levels in dairy manure were assessed at moderate (25 °C), mesophilic (37 °C), and thermophilic (52.5 °C) temperatures. The inactivation of E. coli at moderate, mesophilic, and thermophilic temperatures were described by linear regression equations. Subsequently, double-exponential kinetic models were developed to describe the E. coli decay curves under aerobic and anaerobic environments. The kinetics models were used to estimate E. coli log reductions at various temperatures. Results showed that the double-exponential kinetic models performed well while calculating E. coli reductions in dairy manure over the incubation period. In addition, we evaluated digestate to compare the changes in total solids and volatile solids, total organic carbon, total nitrogen, pH, and oxygen reduction potential levels in aerobic and anaerobic conditions under various temperatures. We anticipate that the results presented here will be useful for enhancing the understanding of pathogen reduction in anaerobic and aerobic processes during dairy manure treatment.

A neighborhood statistics model for predicting stream pathogen indicator levels.

Because elevated levels of water-borne Escherichia coli in streams are a leading cause of water quality impairments in the U.S., water-quality managers need tools for predicting aqueous E. coli levels. Presently, E. coli levels may be predicted using complex mechanistic models that have a high degree of unchecked uncertainty or simpler statistical models. To assess spatio-temporal patterns of instream E. coli levels, herein we measured E. coli, a pathogen indicator, at 16 sites (at four different times) within the Squaw Creek watershed, Iowa, and subsequently, the Markov Random Field model was exploited to develop a neighborhood statistics model for predicting instream E. coli levels. Two observed covariates, local water temperature (degrees Celsius) and mean cross-sectional depth (meters), were used as inputs to the model. Predictions of E. coli levels in the water column were compared with independent observational data collected from 16 in-stream locations. The results revealed that spatio-temporal averages of predicted and observed E. coli levels were extremely close. Approximately 66 % of individual predicted E. coli concentrations were within a factor of 2 of the observed values. In only one event, the difference between prediction and observation was beyond one order of magnitude. The mean of all predicted values at 16 locations was approximately 1 % higher than the mean of the observed values. The approach presented here will be useful while assessing instream contaminations such as pathogen/pathogen indicator levels at the watershed scale.

Transport and persistence of tylosin-resistant enterococci, genes, and tylosin in soil and drainage water from fields receiving Swine manure.

Land application of manure from tylosin-treated swine introduces tylosin, tylosin-resistant enterococci, and erythromycin resistant rRNA methylase () genes, which confer resistance to tylosin. This study documents the persistence and transport of tylosin-resistant enterococci, genes, and tylosin in tile-drained chisel plow and no-till agricultural fields treated with liquid swine manure in alternating years. Between 70 and 100% of the enterococci in manure were resistant to tylosin and B concentrations exceeded 10 copies g manure, while the mean F concentrations exceeded 10 copies g manure (T was not detected). The mean concentration of tylosin was 73 ng g manure. Soil collected from the manure injection band closely following application contained >10 copies g soil of both B and F in 2010 and >10 copies g soil after the 2011 application compared to 3 × 10 to 3 × 10 copies g soil in the no-manure control plots. Gene abundances declined over the subsequent 2-yr period to levels similar to those in the no-manure controls. Concentrations of enterococci in tile water were low, while tylosin-resistant enterococci were rarely detected. In approximately 75% of tile water samples, B was detected, and F was detected in 30% of tile water samples, but levels of these genes were not elevated due to manure application, and no difference was found between tillage practices. These results show that tylosin usage increased the short-term occurrence of tylosin-resistant enterococci, genes, and tylosin in soils but had minimal effect on tile drainage water quality in years of average to below average precipitation.

Nitrate-nitrogen export: magnitude and patterns from drainage districts to downstream river basins.

Alteration of the prairie pothole ecosystem through installation of subsurface tile drains has enabled the U.S. Corn Belt to become one of the most agriculturally productive areas in the world but has also led to increased nitrogen losses to surface water. The literature contains numerous field plot studies but few in-depth studies of nitrate exports from small, tile-drained catchments representative of agricultural drainage districts. The objectives of this study were to quantify hydrology and nitrate-nitrogen (NO-N) export patterns from three tile-drained catchments and the downstream river over a 5-yr period, compare results to prior plot-, field-, and watershed-scale studies, and discuss implications for water quality improvement in these landscapes. The tile-drained catchments had an annual average water yield of 247 mm yr, a flow-weighted NO-N concentration of 17.1 mg L, and an average NO-N loss of nearly 40 kg ha yr. Overall, water yields were consistent with prior tile drainage studies in Iowa and the upper Midwest, but associated NO-N concentrations and losses were among the highest reported for plot studies and higher than those found in small watersheds. More than 97% of the nitrate export occurs during the highest 50% of flows, at both the small catchment and river basin scale. Findings solidified the importance of working at the drainage district scale to achieve nitrate reductions necessary to meet water quality goals. They also point to the need for implementing strategies that address both hydrology and nitrogen supply in tile-drained landscapes.

Extreme low-flow conditions in a dual-chamber denitrification bioreactor contribute to pollution swapping with low landscape-scale impact.

Denitrification bioreactors are an effective edge-of-field conservation practice for nitrate (NO3) reduction from subsurface drainage. However, these systems may produce other pollutants and greenhouse gases during NO3 removal. Here a dual-chamber woodchip bioreactor system experiencing extreme low-flow conditions was monitored for its spatiotemporal NO3 and total organic carbon dynamics in the drainage water. Near complete removal of NO3 was observed in both bioreactor chambers in the first two years of monitoring (2019-2020) and in the third year of monitoring in chamber A, with significant (p < 0.01) reduction of the NO3-N each year in both chambers with 8.6-11.4 mg NO3-N L-1 removed on average. Based on the NO3 removal observed, spatial monitoring of sulfate (SO4), dissolved methane (CH4), and dissolved nitrous oxide (N2O) gases was added in the third year of monitoring (2021). In 2021, chambers A and B had median hydraulic residence times (HRTs) of 64 h and 39 h, respectively, due to varying elevations of the chambers, with drought conditions making the differences more pronounced. In 2021, significant production of dissolved CH4 was observed at rates of 0.54 g CH4-C m-3 d-1 and 0.07 g CH4-C m-3 d-1 in chambers A and B, respectively. In chamber A, significant removal (p < 0.01) of SO4 (0.23 g SO4 m-3 d-1) and dissolved N2O (0.21 mg N2O-N m-2 d-1) were observed, whereas chamber B produced N2O (0.36 mg N2O-N m-2 d-1). Considering the carbon dioxide equivalents (CO2e) on an annual basis, chamber A had loads (~12,000 kg CO2e ha-1 y-1) greater than comparable poorly drained agricultural soils; however, the landscape-scale impact was small (<1 % change in CO2e) when expressed over the drainage area treated by the bioreactor. Under low-flow conditions, pollution swapping in woodchip bioreactors can be reduced at HRTs <50 h and NO3 concentrations >2 mg N L-1.

A comparison of nutrient losses from two simulated pastureland management scenarios.

Fecal deposits by grazing animals on pasturelands have the potential to leach nutrients to runoff during rainfall events. Unlike croplands, grazing systems such as pasturelands or rangelands have little opportunity to ameliorate nutrient runoff through in-field or edge-of-field management practices. Thus, we investigated the amounts and concentrations of nutrients in overland flow from simulated grazing lands. Two grazing management scenarios were simulated: continuous grazing represented by two sparsely vegetated (SV) plots and rotational grazing represented by two densely vegetated (DV) plots. In addition, there were two control plots. The plots were treated with standard cowpats and rainfall was simulated until overland flow at the edge of the plots reached steady-state. Higher runoff was observed from DV plots (9.97 mm) than SV plots (7.05 mm), but the average total suspended solids concentration in runoff from SV plots was approximately 17 times the concentration observed in runoff from the DV plots. The average total phosphorus (TP) concentrations were highest in plots simulating continuous grazing (5.91 mg L(-1)). In both DV and SV plots at least 83% of the TP was found to be in the dissolved form. The average total Kjeldhal nitrogen (TKN) and total nitrogen concentrations observed in runoff samples from SV plots were 1.25 and 1.46 mg L(-1), respectively. Organic nitrogen comprised 95% of the TKN observed in runoff samples from SV plots. The SV plots have relatively higher loads for those nutrients in the particle associated form compared to DV plots, whereas DV plots had higher loads for those nutrients in the dissolved form. Grazing lands without any additional manure applications were found to release nutrients in high levels and vegetation did not show any effect on removing dissolved nutrients from runoff. These results are useful to inform selection of appropriate management practices to reduce nutrient transport to surface waters in watersheds dominated by grazed lands.

Denitrifying bioreactor microbiome: Understanding pollution swapping and potential for improved performance.

Denitrifying woodchip bioreactors are a best management practice to reduce nitrate-nitrogen (NO3 -N) loading to surface waters from agricultural subsurface drainage. Their effectiveness has been proven in many studies, although variable results with respect to performance indicators have been observed. This paper serves the purpose of synthesizing the current state of the science in terms of the microbial community, its impact on the consistency of bioreactor performance, and its role in the production of potential harmful by-products including greenhouse gases, sulfate reduction, and methylmercury. Microbial processes other than denitrification have been observed in these bioreactor systems, including dissimilatory nitrate reduction to ammonia (DNRA) and anaerobic ammonium oxidation (anammox). Specific gene targets for denitrification, DNRA, anammox, and the production of harmful by-products are identified from bioreactor studies and other environmentally relevant systems for application in bioreactor studies. Lastly, cellulose depletion has been observed over time via increasing ligno-cellulose indices, therefore, the microbial metabolism of cellulose is an important function for bioreactor performance and management. Future work should draw from the knowledge of soil and wetland ecology to inform the study of bioreactor microbiomes.

Comparison of microbial communities in replicated woodchip bioreactors.

Denitrification in woodchip bioreactors is a microbial process, but the effects of variations in bioreactors operation on microbial community structure are not well understood. Here, our goals were to understand hydraulic retention time (HRT) as a factor that influences woodchip bioreactor microbial community variation and structure in replicated field bioreactors and to evaluate relationships between microbial community membership and marker genes for denitrification. We used a combination of quantitative polymerase chain reaction of nirS, nirK, nosZI, and nosZII and 16S rRNA amplicon sequencing to characterize the microbial communities of nine pilot-scale woodchip bioreactors located at Iowa State University. Our results showed dynamic microbial communities but with persistent taxa between two sampling years and three HRTs. Similarities between functional gene copy numbers across sampling year and HRT indicate that the potential for denitrification is conserved despite differences in the microbial communities. These results are evidence that there are specific and persistent taxa within replicated bioreactors. Woodchip bioreactor microbial community membership is recommended to be the focus of future studies to better understand the relationship between microbial community functions and bioreactor management.

Allelic variation of Escherichia coli outer membrane protein A: Impact on cell surface properties, stress tolerance and allele distribution.

Outer membrane protein A (OmpA) is one of the most abundant outer membrane proteins of Gram-negative bacteria and is known to have patterns of sequence variations at certain amino acids-allelic variation-in Escherichia coli. Here we subjected seven exemplar OmpA alleles expressed in a K-12 (MG1655) ΔompA background to further characterization. These alleles were observed to significantly impact cell surface charge (zeta potential), cell surface hydrophobicity, biofilm formation, sensitivity to killing by neutrophil elastase, and specific growth rate at 42°C and in the presence of acetate, demonstrating that OmpA is an attractive target for engineering cell surface properties and industrial phenotypes. It was also observed that cell surface charge and biofilm formation both significantly correlate with cell surface hydrophobicity, a cell property that is increasingly intriguing for bioproduction. While there was poor alignment between the observed experimental values relative to the known sequence variation, differences in hydrophobicity and biofilm formation did correspond to the identity of residue 203 (N vs T), located within the proposed dimerization domain. The relative abundance of the (I, δ) allele was increased in extraintestinal pathogenic E. coli (ExPEC) isolates relative to environmental isolates, with a corresponding decrease in (I, α) alleles in ExPEC relative to environmental isolates. The (I, α) and (I, δ) alleles differ at positions 203 and 251. Variations in distribution were also observed among ExPEC types and phylotypes. Thus, OmpA allelic variation and its influence on OmpA function warrant further investigation.