Denitrifying Woodchip Bioreactors: A Microbial Solution for Nitrate in Agricultural Wastewater-A Review.

Nitrate (NO3-) is highly water-soluble and considered to be the main nitrogen pollutants leached from agricultural soils. Its presence in aquatic ecosystems is reported to cause various environmental and public health problems. Bioreactors containing microbes capable of transforming NO3- have been proposed as a means to remediate contaminated waters. Woodchip bioreactors (WBRs) are continuous flow, reactor systems located below or above ground. Below ground systems are comprised of a trench filled with woodchips, or other support matrices. The nitrate present in agricultural drainage wastewater passing through the bioreactor is converted to harmless dinitrogen gas (N2) via the action of several bacteria species. The WBR has been suggested as one of the most cost-effective NO3--removing strategy among several edge-of-field practices, and has been shown to successfully remove NO3- in several field studies. NO3- removal in the WBR primarily occurs via the activity of denitrifying microorganisms via enzymatic reactions sequentially reducing NO3- to N2. While previous woodchip bioreactor studies have focused extensively on its engineering and hydrological aspects, relatively fewer studies have dealt with the microorganisms playing key roles in the technology. This review discusses NO3- pollution cases originating from intensive farming practices and N-cycling microbial metabolisms which is one biological solution to remove NO3- from agricultural wastewater. Moreover, here we review the current knowledge on the physicochemical and operational factors affecting microbial metabolisms resulting in removal of NO3- in WBR, and perspectives to enhance WBR performance in the future.

Isotopic constraints confirm the significant role of microbial nitrogen oxides emissions from the land and ocean environment.

Nitrogen oxides (NOx, the sum of nitric oxide (NO) and N dioxide (NO2)) emissions and deposition have increased markedly over the past several decades, resulting in many adverse outcomes in both terrestrial and oceanic environments. However, because the microbial NOx emissions have been substantially underestimated on the land and unconstrained in the ocean, the global microbial NOx emissions and their importance relative to the known fossil-fuel NOx emissions remain unclear. Here we complied data on stable N isotopes of nitrate in atmospheric particulates over the land and ocean to ground-truth estimates of NOx emissions worldwide. By considering the N isotope effect of NOx transformations to particulate nitrate combined with dominant NOx emissions in the land (coal combustion, oil combustion, biomass burning and microbial N cycle) and ocean (oil combustion, microbial N cycle), we demonstrated that microbial NOx emissions account for 24 ± 4%, 58 ± 3% and 31 ± 12% in the land, ocean and global environment, respectively. Corresponding amounts of microbial NOx emissions in the land (13.6 ± 4.7 Tg N yr-1), ocean (8.8 ± 1.5 Tg N yr-1) and globe (22.5 ± 4.7 Tg N yr-1) are about 0.5, 1.4 and 0.6 times on average those of fossil-fuel NOx emissions in these sectors. Our findings provide empirical constraints on model predictions, revealing significant contributions of the microbial N cycle to regional NOx emissions into the atmospheric system, which is critical information for mitigating strategies, budgeting N deposition and evaluating the effects of atmospheric NOx loading on the world.

Towards a more labor-saving way in microbial ammonium oxidation: A review on complete ammonia oxidization (comammox).

In the Anthropocene, nitrogen pollution is becoming an increasing challenge for both mankind and the Earth system. Microbial nitrogen cycling begins with aerobic nitrification, which is also the key rate-limiting step. For over a century, it has been accepted that nitrification occurs sequentially involving ammonia oxidation, which produces nitrite followed by nitrite oxidation, generating nitrate. This perception was changed by the discovery of comammox Nitrospira bacteria and their metabolic pathway. In addition, this also provided us with new knowledge concerning the complex nitrogen cycle network. In the comammox process, ammonia can be completely oxidized to nitrate in one cell via the subsequent activity of the enzyme complexes, ammonia monooxygenase, hydroxylamine dehydrogenase, and nitrite oxidodreductase. Over the past five years, research on comammox made great progress. However, there still exist a lot of questions, including how much does comammox contribute to nitrification? How large is the diversity and are there new strains to be discovered? Do comammox bacteria produce the greenhouse gas N2O, and how or to which extent may they contribute to global climate change? The above four aspects are of great significance on the farmland nitrogen management, aquatic environment restoration, and mitigation of global climate change. As large number of comammox bacteria and pathways have been detected in various terrestrial and aquatic ecosystems, indicating that the comammox process may exert an important role in the global nitrogen cycle.

Soil Microbial Indicators within Rotations and Tillage Systems.

Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses.

Acidification in corn monocultures favor fungi, ammonia oxidizing bacteria, and nirK-denitrifier groups.

Agricultural practices of no-till and crop rotations are critical to counteract the detrimental effects of monocultures and tillage operations on ecosystem services related to soil health such as microbial N cycling. The present study explored the main steps of the microbial N cycle, using targeted gene abundance as a proxy, and concerning soil properties, following 19 and 20 years of crop monocultures and rotations of corn (Zea mays L.), and soybean [Glycine max (L.) Merr.], either under no-till or chisel tillage. Real-time quantitative polymerase chain reaction (qPCR) was implemented to estimate phylogenetic groups and functional genes related to the microbial N cycle: nifH (N2 fixation), amoA (nitrification) and nirK, nirS, and nosZ (denitrification). Our results indicate that long-term crop rotation and tillage decisions affect soil health as it relates to soil properties and microbial parameters. No-till management increased soil organic matter (SOM), decreased soil pH, and increased copy numbers of AOB (ammonia oxidizing bacteria). Crop rotations with more corn increased SOM, reduced soil pH, reduced AOA (ammonia oxidizing archaea) copy numbers, and increased AOB and fungal ITS copy numbers. NirK denitrifier groups were also enhanced under continuous corn. Altogether, the more corn years included in a crop rotation multiplies the amount of N needed to sustain yield levels, thereby intensifying the N cycle in these systems, potentially leading to acidification, enhanced bacterial nitrification, and creating an environment primed for N losses and increased N2O emissions.

Source, contribution and microbial N-cycle of N-compounds in China fresh snow.

The importance and contribution of nitrogen compounds and the related microbial nitrogen cycling processes in fresh snow are not well understood under the current research background. We collected fresh snow samples from 21 cities that 80% are from China during 2016 and 2017. Principal component analysis showed that SO42- were in the first principal component, and N-compounds were the second. Furthermore, the main pollutant ions SO42- and NO3- were from anthropogenic sources, and SO42- contributed (61%) more to the pollution load than NO3- (29%), which were confirmed through a series of precipitation mechanism analysis. We selected five N-cycle processes (consist of oxidation and reduction processes) for molecular biology experiments, including Ammonia-oxidation process, Nitrite-oxidation process, Denitrification process, Anaerobic-ammoxidation process (Anammox) and Dissimilatory nitrate reduction to ammonium process (DNRA). Except ammonia-oxidizing archaeal (AOA) and bacterial (AOB) amoA genes (above 107 copies g-1), molecular assays of key functional genes in various nitrogen conversion processes showed a belowed detection limit number, and AOB abundance was always higher than AOA. The determination of the microbial transformation rate using the 15N-isotope tracer technique showed that the potential rate of five N-conversion processes was very low, which is basically consistent with the results from molecular biology studies. Taken together, our results illustrated that microbial nitrogen cycle processes are not the primary biological processes causing the pollution in China fresh snow.

Long-term N fertilization imbalances potential N acquisition and transformations by soil microbes.

Nitrogen (N) fertilization in agricultural soils has been receiving worldwide attention due to its detrimental effects on ecosystem services, particularly on microbial N transformation. However, few studies provide a complete picture of N-fertilization effects on the N transformation cycle within a single agricultural ecosystem. Here, we explored the main steps of the microbial N cycle, using targeted gene abundances as proxies, in relation to soil properties, following 35 years of N-fertilization at increasing rates (0, 202 and 269 kg N/ha) in continuous corn (Zea mays L.) and corn-soybean [Glycine max (L.) Merr.] rotations. We used real-time quantitative polymerase chain reaction (qPCR) for the quantification of phylogenetic groups and functional gene screening of the soil microbial communities, including genes encoding critical enzymes of the microbial N cycle: nifH (N2 fixation), amoA (first step of nitrification), nirK and nirS (first step of denitrification), and nosZ (last step of denitrification). Our results showed that long term N-fertilization increased the abundance of fungal communities likely related to decreases in pH, and an enrichment of Al3+ and Fe3+ in exchange sites at the expense of critical macro and micronutrients. At the same time, long term N-fertilization damaged potential biological N2 fixation by significantly reducing the abundance of nifH genes in both continuous and rotated corn systems, while accelerating potential nitrification activities under continuous corn by increasing the abundance of bacterial amoA. Fertilization did not affect the abundance of denitrifying groups. Altogether, these results suggest that N fertilization in corn crops potentially decreases N2 acquisition by free-living soil microbes and stimulates nitrification activities, thus creating a vicious loop that makes the overall agricultural system even more dependent on external N inputs.