Anammox bacteria drive fixed nitrogen loss in hadal trench sediments

Benthic N2 production by microbial denitrification and anammox is the largest sink for fixed nitrogen in the oceans. Most N2 production occurs on the continental shelves, where a high flux of reactive organic matter fuels the depletion of nitrate close to the sediment surface. By contrast, N2 production rates in abyssal sediments are low due to low inputs of reactive organics, and nitrogen transformations are dominated by aerobic nitrification and the release of nitrate to the bottom water. Here, we demonstrate that this trend is reversed in the deepest parts of the oceans, the hadal trenches, where focusing of reactive organic matter enhances benthic microbial activity. Thus, at ∼8-km depth in the Atacama Trench, underlying productive surface waters, nitrate is depleted within a few centimeters of the sediment surface, N2 production rates reach those reported from some continental margin sites, and fixed nitrogen loss is mainly conveyed by anammox bacteria. These bacteria are closely related to those known from shallow oxygen minimum zone waters, and comparison of activities measured in the laboratory and in situ suggest they are piezotolerant. Even the Kermadec Trench, underlying oligotrophic surface waters, exhibits substantial fixed N removal. Our results underline the role of hadal sediments as hot spots of deep-sea biological activity, revealing a fully functional benthic nitrogen cycle at high hydrostatic pressure and pointing to hadal sediments as a previously unexplored niche for anaerobic microbial ecology and diagenesis.

Expanded Diversity and Metabolic Versatility of Marine Nitrite-Oxidizing Bacteria Revealed by Cultivation- and Genomics-Based Approaches

ABSTRACT Nitrite-oxidizing bacteria (NOB) are ubiquitous and abundant microorganisms that play key roles in global nitrogen and carbon biogeochemical cycling. Despite recent advances in understanding NOB physiology and taxonomy, currently very few cultured NOB or representative NOB genome sequences from marine environments exist. In this study, we employed enrichment culturing and genomic approaches to shed light on the phylogeny and metabolic capacity of marine NOB. We successfully enriched two marine NOB (designated MSP and DJ) and obtained a high-quality metagenome-assembled genome (MAG) from each organism. The maximum nitrite oxidation rates of the MSP and DJ enrichment cultures were 13.8 and 30.0 μM nitrite per day, respectively, with these optimum rates occurring at 0.1 mM and 0.3 mM nitrite, respectively. Each enrichment culture exhibited a different tolerance to various nitrite and salt concentrations. Based on phylogenomic position and overall genome relatedness indices, both NOB MAGs were proposed as novel taxa within the Nitrospinota and Nitrospirota phyla. Functional predictions indicated that both NOB MAGs shared many highly conserved metabolic features with other NOB. Both NOB MAGs encoded proteins for hydrogen and organic compound metabolism and defense mechanisms for oxidative stress. Additionally, these organisms may have the genetic potential to produce cobalamin (an essential enzyme cofactor that is limiting in many environments) and, thus, may play an important role in recycling cobalamin in marine sediment. Overall, this study appreciably expands our understanding of the Nitrospinota and Nitrospirota phyla and suggests that these NOB play important biogeochemical roles in marine habitats. IMPORTANCE Nitrification is a key process in the biogeochemical and global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) perform the second step of aerobic nitrification (converting nitrite to nitrate), which is critical for transferring nitrogen to other organisms for assimilation or energy. Despite their ecological importance, there are few cultured or genomic representatives from marine systems. Here, we obtained two NOB (designated MSP and DJ) enriched from marine sediments and estimated the physiological and genomic traits of these marine microbes. Both NOB enrichment cultures exhibit distinct responses to various nitrite and salt concentrations. Genomic analyses suggest that these NOB are metabolically flexible (similar to other previously described NOB) yet also have individual genomic differences that likely support distinct niche distribution. In conclusion, this study provides more insights into the ecological roles of NOB in marine environments.

Microalgae cultivation using undiluted anaerobic digestate by introducing aerobic nitrification–desulfurization treatment

A novel coupling process using an aerobic bacterial reactor with nitrification and sulfur–oxidization functions followed by a microalgal reactor was proposed for simultaneous biogas desulfurization and anaerobic digestion effluent (ADE) treatment. ADE nitrified by bacteria has a potential to be directly used as a culture medium for microalgae because ammonium nitrogen, including inhibitory free ammonia (NH3), has been converted to harmless NO3−. To demonstrate this hypothesis, Chlorella sorokiniana NIES-2173, which has ordinary NH3 tolerance; that is, 1.6 mM of EC50 compared with other species, was cultivated using untreated/treated ADE. Compared with the use of a synthetic medium, when using ADE with 1–10-fold dilutions, the specific growth rate and growth yield maximally decreased by 44% and 88%, respectively. In contrast, the algal growth using undiluted ADE treated by nitrification–desulfurization was almost the same as with using synthetic medium. It was also revealed that 50% of PO43− and most metal concentrations of ADE decreased following nitrification–desulfurization treatment. Moreover, upon NaOH addition for pH adjustment, the salinity increased to 0.66%. The decrease in metals mitigates the bioconcentration of toxic heavy metals from wastewater in microalgal biomass. Meanwhile, salt stress in microalgae and limiting nutrient supplementation, particularly for continuous cultivation, should be of concern.

Nitrogen Removal by Co-Immobilized Anammox and Ammonia-Oxidizing Bacteria in Wastewater Treatment

In wastewater treatment, an alternative to the widely used aerobic nitrification with subsequent anoxic denitrification method is the combination of nitration and anammox (AMX) in one system. This study focuses on the co-immobilization of AMX and ammonia-oxidizing bacteria into a polyvinyl alcohol (PVA) hydrogel, and its effective use in nitrogen removal (NR). The NR process was performed in nine consecutive, repeated batches. By optimizing the conditions of the biotransformations, there was equal utilization of nitrogen in both sources, N–NH4+ and N–NO2−, at 100% NR during the sixth repetition. A significant increase in the immobilized co-culture activity was also detected per cycle. The maximum value of the NR rate was 3.46 mg N (L h)−1, and 100% NR efficiency was achieved with an initial concentration of 100.3 mg N L−1 for N–NH4+ and 60.1 mg N L−1 for N–NO2−, during the eighth batch biotransformation.

Treatment of Sewage Using a Constructed Soil Rapid Infiltration System Combined with Pre-Denitrification

The activated sludge process of the anaerobic/oxic (A/O) process has a good denitrification performance because it can make full use of the carbon source in the original sewage, and the denitrification can provide alkalinity for aerobic nitrification. The traditional constructed soil rapid infiltration (CSRI) system, on the other hand, has a poor nitrogen removal effect. Dividing the traditional CSRI system into two sections, one performs denitrification as an anoxic section, while the other performs nitrification as an aerobic section and is placed after the anoxic section. The nitrification liquid of the effluent from the aerobic section is mixed with the original wastewater and enters the anoxic section for denitrification. We expected that this would be improved by combining CSRI with a pre-denitrification step that would make full use of the carbon source in the original sewage. In a small-scale experimental model, the removal efficiencies of nitrogen, in the form of ammonium, nitrate, and total nitrogen (TN), as well as chemical oxygen demand (COD), were determined. The hydraulic load was varied, while the backflow reflux capacity was kept constant, to determine the effect on the pre-denitrification process. An average removal rate of 95.4% for NH4+-N and 96% for COD could be obtained when a hydraulic load of 80 cm3(cm2·d)−1 and a reflux ratio of 75% were applied. Under these conditions, the average removal rate of TN was 77.4%, which is much higher than what can be typically achieved with conventional CSRI systems.

Isotopic overprinting of nitrification on denitrification as a ubiquitous and unifying feature of environmental nitrogen cycling

Natural abundance nitrogen and oxygen isotopes of nitrate (δ15NNO3and δ18ONO3) provide an important tool for evaluating sources and transformations of natural and contaminant nitrate (NO3−) in the environment. Nevertheless, conventional interpretations of NO3−isotope distributions appear at odds with patterns emerging from studies of nitrifying and denitrifying bacterial cultures. To resolve this conundrum, we present results from a numerical model of NO3−isotope dynamics, demonstrating that deviations in δ18ONO3vs. δ15NNO3from a trajectory of 1 expected for denitrification are explained by isotopic over-printing from coincident NO3−production by nitrification and/or anammox. The analysis highlights two driving parameters: (i) the δ18O of ambient water and (ii) the relative flux of NO3−production under net denitrifying conditions, whether catalyzed aerobically or anaerobically. In agreement with existing analyses, dual isotopic trajectories >1, characteristic of marine denitrifying systems, arise predominantly under elevated rates of NO2−reoxidation relative to NO3−reduction (>50%) and in association with the elevated δ18O of seawater. This result specifically implicates aerobic nitrification as the dominant NO3−producing term in marine denitrifying systems, as stoichiometric constraints indicate anammox-based NO3−production cannot account for trajectories >1. In contrast, trajectories <1 comprise the majority of model solutions, with those representative of aquifer conditions requiring lower NO2−reoxidation fluxes (<15%) and the influence of the lower δ18O of freshwater. Accordingly, we suggest that widely observed δ18ONO3vs. δ15NNO3trends in freshwater systems (<1) must result from concurrent NO3−production by anammox in anoxic aquifers, a process that has been largely overlooked.