Denitrifying community in coastal sediments performs aerobic and anaerobic respiration simultaneously

Electric syntrophy-driven modulation of Fe0-dependent microbial denitrification

In natural or engineered anaerobic environments, iron oxidation-driven microbial denitrification plays a critical role in the water or wastewater treatment. Herein, we report a previously unidentified metallic iron (Fe0)-dependent denitrification mode driven by the electro-syntrophic interaction between electroactive microorganism and denitrifier. In a model denitrifying consortium of Shewanella oneidensis and Pseudomonas aeruginosa, we find that P. aeruginosa can accept electrons for nitrate reduction via the constructed electron transfer system of Fe0-S. oneidensis-P. aeruginosa. In the electro-syntrophic consortium, the membrane-bound CymA-OmcA-MtrC protein complexes of S. oneidensis drive the generation, transfer and consumption of electrons, thus enabling modulation of microbial metabolic activity. Specially, using Fe0 as the sole electron donor, S. oneidensis can act as a bio-engine to harvest electrons and conserve energy from Fe0 biocorrosion. Electrons released by S. oneidensis are utilized by P. aeruginosa for accomplishing microbial denitrification. Metatranscriptomics analysis demonstrated that the direct electron cross-feeding process facilitates the expression of genes encoding for denitrification enzymes, intracellular electron transfer proteins, and quorum sensing of P. aeruginosa. The Fe0-dependent electronic syntrophy in this work could provide a metabolic window for the growth of denitrifiers that is a new insight into nitrate removal or global nitrogen cycle.

Growth of sulfate-reducing Desulfobacterota and Bacillota at periodic oxygen stress of 50% air-O2 saturation

BACKGROUND

Sulfate-reducing bacteria (SRB) are frequently encountered in anoxic-to-oxic transition zones, where they are transiently exposed to microoxic or even oxic conditions on a regular basis. This can be marine tidal sediments, microbial mats, and freshwater wetlands like peatlands. In the latter, a cryptic but highly active sulfur cycle supports their anaerobic activity. Here, we aimed for a better understanding of how SRB responds to periodically fluctuating redox regimes.

RESULTS

To mimic these fluctuating redox conditions, a bioreactor was inoculated with peat soil supporting cryptic sulfur cycling and consecutively exposed to oxic (one week) and anoxic (four weeks) phases over a period of > 200 days. SRB affiliated to the genus Desulfosporosinus (Bacillota) and the families Syntrophobacteraceae, Desulfomonilaceae, Desulfocapsaceae, and Desulfovibrionaceae (Desulfobacterota) successively established growing populations (up to 2.9% relative abundance) despite weekly periods of oxygen exposures at 133 µM (50% air saturation). Adaptation mechanisms were analyzed by genome-centric metatranscriptomics. Despite a global drop in gene expression during oxic phases, the perpetuation of gene expression for energy metabolism was observed for all SRBs. The transcriptional response pattern for oxygen resistance was differentiated across individual SRBs, indicating different adaptation strategies. Most SRB transcribed differing sets of genes for oxygen consumption, reactive oxygen species detoxification, and repair of oxidized proteins as a response to the periodical redox switch from anoxic to oxic conditions. Noteworthy, a Desulfosporosinus, a Desulfovibrionaceaea, and a Desulfocapsaceaea representative maintained high transcript levels of genes encoding oxygen defense proteins even under anoxic conditions, while representing dominant SRB populations after half a year of bioreactor operation.

CONCLUSIONS

In situ-relevant peatland SRB established large populations despite periodic one-week oxygen levels that are one order of magnitude higher than known to be tolerated by pure cultures of SRB. The observed decrease in gene expression regulation may be key to withstand periodically occurring changes in redox regimes in these otherwise strictly anaerobic microorganisms. Our study provides important insights into the stress response of SRB that drives sulfur cycling at oxic-anoxic interphases. Video Abstract.

The influence of bioturbator activity on sediment bacterial structure and function is moderated by environment

Bioturbation in coastal sediments plays a crucial role in biogeochemical cycling. However, a key knowledge gap is the extent to which bioturbation influences bacterial community diversity and ecosystem processes, such as nitrogen cycling. This study paired bacterial diversity, bioturbation activity and in situ flux measurements of oxygen and nitrogen from bioturbated sediments at six estuaries along the East coast of Australia. Bacterial community diversity, composition and predicted functional profiles were similar across burrow and surface sediments but were significantly influenced by bioturbator activity (measured as number of burrows) at sites with higher fine grain content. Sediment oxygen demand increased with bioturbator activity but changes in nitrogen cycling (as measured by fluxes and predicted bacterial functional gene analysis) were more spatially variable and were unrelated to bioturbator activity and bacterial community shifts. This study highlights how bioturbator activity influences bacterial community structure and functioning and what implications this has for biogeochemical cycles in estuarine sediments.

Sediment grain size regulates the biogeochemical processes of nitrate in the riparian zone by influencing nutrient concentrations and microbial abundance

Riparian zones play a crucial role in reducing nitrate pollution in both terrestrial and aquatic environments. Complex deposition action and dynamic hydrological processes will change the grain size distribution of riparian sediments, affect the residence time of substances, and have a cascade effect on the biogeochemical process of nitrate nitrogen (NO3--N). However, simultaneous studies on NO3--N transformation and the potential drivers in riparian zones are still lacking, especially neglecting the effect of sediment grain size (SGS). To fill this knowledge gap, we first systematically identified and quantified NO3--N biogeochemical processes in the riparian zone by integrating molecular biotechnology, 15N stable isotope tracing, and microcosmic incubation experiments. We then evaluated the combined effects of environmental variables (including pH, dissolved organic carbon (DOC), oxidation reduction potential, SGS, etc.) on NO3--N transformation through Random Forest and Structural Equation Models. The results demonstrated that NO3--N underwent five microbial-mediated processes, with denitrification, dissimilatory nitrate reduction to ammonium (DNRA) dominated the NO3--N attenuation (69.4 % and 20.1 %, respectively), followed by anaerobic ammonia oxidation (anammox) and nitrate-dependent ferric oxidation (NDFO) (8.4 % and 2.1 %, respectively), while nitrification dominated the NO3--N production. SGS emerged as the most critical factor influencing NO3--N transformation (24.96 %, p < 0.01), followed by functional genes (nirS, nrfA) abundance, DOC, and ammonia concentrations (14.12 %, 16.40 %, 13.08 %, p < 0.01). SGS influenced NO3--N transformation by regulating microbial abundance and nutrient concentrations. RF predicted that a 5 % increase in the proportion of fine grains (diameter < 50 μm) may increase the NO3--N transformation rate by 3.8 %. This work highlights the significance of integrating machine learning and geochemical analysis for a comprehensive understanding of nitrate biogeochemical processes in riparian zones, contributing valuable references for future nitrogen management strategies.

Temperature differentially regulates estuarine microbial N2O production along a salinity gradient

Nitrous oxide (N2O) is atmospheric trace gas that contributes to climate change and affects stratospheric and ground-level ozone concentrations. Ammonia oxidizers and denitrifiers contribute to N2O emissions in estuarine waters. However, as an important climate factor, how temperature regulates microbial N2O production in estuarine water remains unclear. Here, we have employed stable isotope labeling techniques to demonstrate that the N2O production in estuarine waters exhibited differential thermal response patterns between nearshore and offshore regions. The optimal temperatures (Topt) for N2O production rates (N2OR) were higher at nearshore than offshore sites. 15N-labeled nitrite (15NO2-) experiments revealed that at the nearshore sites dominated by ammonia-oxidizing bacteria (AOB), the thermal tolerance of 15N-N2OR increases with increasing salinity, suggesting that N2O production by AOB-driven nitrifier denitrification may be co-regulated by temperature and salinity. Metatranscriptomic and metagenomic analyses of enriched water samples revealed that the denitrification pathway of AOB is the primary source of N2O, while clade II N2O-reducers dominated N2O consumption. Temperature regulated the expression patterns of nitrite reductase (nirK) and nitrous oxide reductase (nosZ) genes from different sources, thereby influencing N2O emissions in the system. Our findings contribute to understanding the sources of N2O in estuarine waters and their response to global warming.

Determining how oxygen legacy affects trajectories of soil denitrifier community dynamics and N2O emissions

Denitrification - a key process in the global nitrogen cycle and main source of the greenhouse gas N2O - is intricately controlled by O2. While the transition from aerobic respiration to denitrification is well-studied, our understanding of denitrifier communities' responses to cyclic oxic/anoxic shifts, prevalent in natural and engineered systems, is limited. Here, agricultural soil is exposed to repeated cycles of long or short anoxic spells (LA; SA) or constant oxic conditions (Ox). Surprisingly, denitrification and N2O reduction rates are three times greater in Ox than in LA and SA during a final anoxic incubation, despite comparable bacterial biomass and denitrification gene abundances. Metatranscriptomics indicate that LA favors canonical denitrifiers carrying nosZ clade I. Ox instead favors nosZ clade II-carrying partial- or non-denitrifiers, suggesting efficient partnering of the reduction steps among organisms. SA has the slowest denitrification progression and highest accumulation of intermediates, indicating less functional coordination. The findings demonstrate how adaptations of denitrifier communities to varying O2 conditions are tightly linked to the duration of anoxic episodes, emphasizing the importance of knowing an environment's O2 legacy for accurately predicting N2O emissions originating from denitrification.

Influence of crop residue-induced Fe-DOC complexation on nitrate reduction in paddy soil

Although complexation between dissolved organic matter (DOM) and ubiquitous Fe is known to have a major influence on electron transferring ability in redoximorphic soil, it was unclear whether and how this complexation affected nitrate reduction and N2O productivity. The nitrate reduction of paddy soil in the presence of crop residues returning under flooding conditions was explored in this study. The rate of nitrate reduction in control soil was 0.0677 d-1, while it improved 1.99 times in treatment soil with Chinese milk vetch (CMV) straw returning. During a 28-day incubation period, N2O productivity decreased 0.08-0.91 ppb in CMV soil and 0.43-0.50 ppb in rice straw soil compared with control. The presence of crop residue increased DOC content and Fe (III) reduction rate, which aided in the formation of Fe (II)-DOC complexation. Meanwhile, the addition of CMV increased the content of DOC by 5.14-78.77 mg/kg and HCl extractable Fe (II) by 35.12-1221.03 mg/kg. Crop residues returning to soil increased the relative abundance of iron reductive and electroactive genera, as well as denitrifying genera with more copies of denitrification genes (Archangiaceae, Gemmatimonadaceae, and Burkholderiaceae). The synergistic effect of Fe-DOC complexation, electroactive genera, and denitrifying genera contributed to up-regulated expression of napA and narG (5.84 × 106 and 3.39 × 107 copies increased in the CMV soil compared to the control) numbers and equally accelerated reduction of nitrate to nitrite, while further nitrite reduction was primarily attributed to the abiotic reaction by Fe (II). From a bio-electrochemical point of view, this work provided new insight into the nitrate reduction of paddy soil impacted by Fe-DOC complexation.

The interplay of hematite and photic biofilm triggers the acceleration of biotic nitrate removal

The soil-water interface is replete with photic biofilm and iron minerals; however, the potential of how iron minerals promote biotic nitrate removal is still unknown. This study investigates the physiological and ecological responses of photic biofilm to hematite (Fe2O3), in order to explore a practically feasible approach for in-situ nitrate removal. The nitrate removal by photic biofilm was significantly higher in the presence of Fe2O3 (92.5%) compared to the control (82.8%). Results show that the presence of Fe2O3 changed the microbial community composition of the photic biofilm, facilitates the thriving of Magnetospirillum and Pseudomonas, and promotes the growth of photic biofilm represented by the extracellular polymeric substance (EPS) and the content of chlorophyll. The presence of Fe2O3 also induces oxidative stress (•O2-) in the photic biofilm, which was demonstrated by electron spin resonance spectrometry. However, the photic biofilm could improve the EPS productivity to prevent the entrance of Fe2O3 to cells in the biofilm matrix and mitigate oxidative stress. The Fe2O3 then promoted the relative abundance of Magnetospirillum and Pseudomonas and the activity of nitrate reductase, which accelerates nitrate reduction by the photic biofilm. This study provides an insight into the interaction between iron minerals and photic biofilm and demonstrates the possibility of combining biotic and abiotic methods to improve the in-situ nitrate removal rate.

High hydrostatic pressure stimulates microbial nitrate reduction in hadal trench sediments under oxic conditions

Hadal trenches are extreme environments situated over 6000 m below sea surface, where enormous hydrostatic pressure affects the biochemical cycling of elements. Recent studies have indicated that hadal trenches may represent a previously overlooked source of fixed nitrogen loss; however, the mechanisms and role of hydrostatic pressure in this process are still being debated. To this end, we investigate the effects of hydrostatic pressure (0.1 to 115 MPa) on the chemical profile, microbial community structure and functions of surface sediments from the Mariana Trench using a Deep Ocean Experimental Simulator supplied with nitrate and oxygen. We observe enhanced denitrification activity at high hydrostatic pressure under oxic conditions, while the anaerobic ammonium oxidation - a previously recognized dominant nitrogen loss pathway - is not detected. Additionally, we further confirm the simultaneous occurrence of nitrate reduction and aerobic respiration using a metatranscriptomic dataset from in situ RNA-fixed sediments in the Mariana Trench. Taken together, our findings demonstrate that hydrostatic pressure can influence microbial contributions to nitrogen cycling and that the hadal trenches are a potential nitrogen loss hotspot. Knowledge of the influence of hydrostatic pressure on anaerobic processes in oxygenated surface sediments can greatly broaden our understanding of element cycling in hadal trenches.

Microfluidic approaches in microbial ecology

Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.

Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics

Nitrogen (N) availability is one of the principal drivers of primary productivity across aquatic ecosystems. However, the microbial communities and emergent metabolisms that govern N cycling in tropical lakes are both distinct from and poorly understood relative to those found in temperate lakes. This latitudinal difference is largely due to the warm (>20°C) temperatures of tropical lake anoxic hypolimnions (deepest portion of a stratified water column), which result in unique anaerobic metabolisms operating without the temperature constraints found in lakes at temperate latitudes. As such, tropical hypolimnions provide a platform for exploring microbial membership and functional diversity. To better understand N metabolism in warm anoxic waters, we combined measurements of geochemistry and water column thermophysical structure with genome-resolved metatranscriptomic analyses of the water column microbiome in Lake Yojoa, Honduras. We sampled above and below the oxycline in June 2021, when the water column was stratified, and again at the same depths and locations in January 2022, when the water column was mixed. We identified 335 different lineages and significantly different microbiome membership between seasons and, when stratified, between depths. Notably, nrfA (indicative of dissimilatory nitrate reduction to ammonium) was upregulated relative to other N metabolism genes in the June hypolimnion. This work highlights the taxonomic and functional diversity of microbial communities in warm and anoxic inland waters, providing insight into the contemporary microbial ecology of tropical ecosystems as well as inland waters at higher latitudes as water columns continue to warm in the face of global change.IMPORTANCEIn aquatic ecosystems where primary productivity is limited by nitrogen (N), whether continuously, seasonally, or in concert with additional nutrient limitations, increased inorganic N availability can reshape ecosystem structure and function, potentially resulting in eutrophication and even harmful algal blooms. Whereas microbial metabolic processes such as mineralization and dissimilatory nitrate reduction to ammonium increase inorganic N availability, denitrification removes bioavailable N from the ecosystem. Therefore, understanding these key microbial mechanisms is critical to the sustainable management and environmental stewardship of inland freshwater resources. This study identifies and characterizes these crucial metabolisms in a warm, seasonally anoxic ecosystem. Results are contextualized by an ecological understanding of the study system derived from a multi-year continuous monitoring effort. This unique data set is the first of its kind in this largely understudied ecosystem (tropical lakes) and also provides insight into microbiome function and associated taxa in warm, anoxic freshwaters.

Aerobic denitrification as an N2O source from microbial communities

Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Oxic and anoxic emissions are commonly ascribed to autotrophic nitrification and heterotrophic denitrification, respectively. Beyond this established dichotomy, we quantitatively show that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed to frequent oxic/anoxic transitions. Two planktonic, nitrification-inhibited enrichment cultures were established under continuous organic carbon and nitrate feeding, and cyclic oxygen availability. Over a third of the influent organic substrate was respired with nitrate as electron acceptor at high oxygen concentrations (>6.5 mg/L). N2O accounted for up to one-quarter of the nitrate reduced under oxic conditions. The enriched microorganisms maintained a constitutive abundance of denitrifying enzymes due to the oxic/anoxic frequencies exceeding their protein turnover-a common scenario in natural and engineered ecosystems. The aerobic denitrification rates are ascribed primarily to the residual activity of anaerobically synthesised enzymes. From an ecological perspective, the selection of organisms capable of sustaining significant denitrifying activity during aeration shows their competitive advantage over other heterotrophs under varying oxygen availabilities. Ultimately, we propose that the contribution of heterotrophic denitrification to aerobic nitrogen turnover and N2O emissions is currently underestimated in dynamic environments.

Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments

The global nitrogen (N) cycle has been strongly altered by anthropogenic activities, including increased input of bioavailable N into aquatic ecosystems. Freshwater sediments are hotspots with regards to the turnover and elimination of fixed N, yet the environmental controls on the microbial pathways involved in benthic N removal are not fully understood. Here, we analyze the abundance and expression of microbial genes involved in N transformations using metagenomics and -transcriptomics across sediments of 12 Swiss lakes that differ in sedimentation rates and trophic regimes. Our results indicate that microbial N loss in these sediments is primarily driven by nitrification coupled to denitrification. N-transformation gene compositions indicated three groups of lakes: agriculture-influenced lakes characterized by rapid depletion of oxidants in the sediment porewater, pristine-alpine lakes with relatively deep sedimentary penetration of oxygen and nitrate, and large, deep lakes with intermediate porewater hydrochemical properties. Sedimentary organic matter (OM) characteristics showed the strongest correlations with the community structure of microbial N-cycling communities. Most transformation pathways were expressed, but expression deviated from gene abundance and did not correlate with benthic geochemistry. Cryptic N-cycling may maintain transcriptional activity even when substrate levels are below detection. Sediments of large, deep lakes generally showed lower in-situ N gene expression than agriculture-influenced lakes, and half of the pristine-alpine lakes. This implies that prolonged OM mineralization in the water column can lead to the suppression of benthic N gene expression.

Frequency of change determines effectiveness of microbial response strategies

Nature challenges microbes with change at different frequencies and demands an effective response for survival. Here, we used controlled laboratory experiments to investigate the effectiveness of different response strategies, such as post-translational modification, transcriptional regulation, and specialized versus adaptable metabolisms. For this, we inoculated replicated chemostats with an enrichment culture obtained from sulfidic stream microbiomes 16 weeks prior. The chemostats were submitted to alternatingly oxic and anoxic conditions at three frequencies, with periods of 1, 4 and 16 days. The microbial response was recorded with 16S rRNA gene amplicon sequencing, shotgun metagenomics, transcriptomics and proteomics. Metagenomics resolved provisional genomes of all abundant bacterial populations, mainly affiliated with Proteobacteria and Bacteroidetes. Almost all these populations maintained a steady growth rate under both redox conditions at all three frequencies of change. Our results supported three conclusions: (1) Oscillating oxic/anoxic conditions selected for generalistic species, rather than species specializing in only a single condition. (2) A high frequency of change selected for strong codon usage bias. (3) Alignment of transcriptomes and proteomes required multiple generations and was dependent on a low frequency of change.

Simultaneous sulfate and nitrate reduction in coastal sediments

The oscillating redox conditions that characterize coastal sandy sediments foster microbial communities capable of respiring oxygen and nitrate simultaneously, thereby increasing the potential for organic matter remineralization, nitrogen (N)-loss and emissions of the greenhouse gas nitrous oxide. It is unknown to what extent these conditions also lead to overlaps between dissimilatory nitrate and sulfate respiration. Here, we show that sulfate and nitrate respiration co-occur in the surface sediments of an intertidal sand flat. Furthermore, we found strong correlations between dissimilatory nitrite reduction to ammonium (DNRA) and sulfate reduction rates. Until now, the nitrogen and sulfur cycles were assumed to be mainly linked in marine sediments by the activity of nitrate-reducing sulfide oxidisers. However, transcriptomic analyses revealed that the functional marker gene for DNRA (nrfA) was more associated with microorganisms known to reduce sulfate rather than oxidise sulfide. Our results suggest that when nitrate is supplied to the sediment community upon tidal inundation, part of the sulfate reducing community may switch respiratory strategy to DNRA. Therefore increases in sulfate reduction rate in-situ may result in enhanced DNRA and reduced denitrification rates. Intriguingly, the shift from denitrification to DNRA did not influence the amount of N2O produced by the denitrifying community. Our results imply that microorganisms classically considered as sulfate reducers control the potential for DNRA within coastal sediments when redox conditions oscillate and therefore retain ammonium that would otherwise be removed by denitrification, exacerbating eutrophication.

Cyclohexanecarboxylic acid degradation with simultaneous nitrate removal by Marinobacter sp. SJ18

Naphthenic acid (NA) is a toxic pollutant with potential threat to human health. However, NA transformations in marine environments are still unclear. In this study, the characteristics and pathways of cyclohexanecarboxylic acid (CHCA) biodegradation were explored in the presence of nitrate. The results showed that CHCA was completely degraded with pseudo-first-order kinetic reaction under aerobic and anaerobic conditions, accompanied by nitrate removal rates exceeding 70%, which was positively correlated with CHCA degradation (P < 0.05). In the proposed CHCA degradation pathways, cyclohexane is dehydrogenated to form cyclohexene, followed by ring-opening by dioxygenase to generate fatty acid under aerobic conditions or cleavage of cyclohexene through β-oxidation under anaerobic conditions. Whole genome analysis indicated that nitrate was removed via assimilation and dissimilation pathways under aerobic conditions and via denitrification pathway under anaerobic conditions. These results provide a basis for alleviating combined pollution of NA and nitrate in marine environments with frequent anthropogenic activities.

Heterotrophic nitrification-aerobic denitrification performance of a novel strain, Pseudomonas sp. B-1, isolated from membrane aerated biofilm reactor

A heterotrophic nitrification-aerobic denitrification (HN-AD) strain isolated from membrane aerated biofilm reactor (MABR) was identified as Pseudomonas sp. B-1, which could effectively utilize multiple nitrogen sources and preferentially consume NH₄-N. The maximum degradation efficiencies of NO₃-N, NO₂-N and NH₄-N were 98.04%, 94.84% and 95.74%, respectively. The optimal incubation time, shaking speed, carbon source, pH, temperature and C/N ratio were 60 h, 180 rpm, sodium succinate, 8, 30 °C and 25, respectively. The strain preferred salinity of 1.5% and resisted heavy metals in the order of Mn²⁺ > Co²⁺ > Zn²⁺ > Cu²⁺. It can be preliminarily speculated from the results of enzyme assay that the strain removed nitrogen via full nitrification-denitrification pathway. The addition of strain into the conventional MABR significantly intensified the HN-AD performance of the reactor. The relative abundance of the functional bacteria including Flavobacterium, Pseudomonas, Paracoccus, Azoarcus and Thauera was obviously increased after the bioaugmentation. Besides, the expression of the HN-AD related genes in the biofilm was also strengthened. Thus, strain B-1 had great application potential in nitrogen removal process.

Reactive oxygen species affect the potential for mineralization processes in permeable intertidal flats

Intertidal permeable sediments are crucial sites of organic matter remineralization. These sediments likely have a large capacity to produce reactive oxygen species (ROS) because of shifting oxic-anoxic interfaces and intense iron-sulfur cycling. Here, we show that high concentrations of the ROS hydrogen peroxide are present in intertidal sediments using microsensors, and chemiluminescent analysis on extracted porewater. We furthermore investigate the effect of ROS on potential rates of microbial degradation processes in intertidal surface sediments after transient oxygenation, using slurries that transitioned from oxic to anoxic conditions. Enzymatic removal of ROS strongly increases rates of aerobic respiration, sulfate reduction and hydrogen accumulation. We conclude that ROS are formed in sediments, and subsequently moderate microbial mineralization process rates. Although sulfate reduction is completely inhibited in the oxic period, it resumes immediately upon anoxia. This study demonstrates the strong effects of ROS and transient oxygenation on the biogeochemistry of intertidal sediments.

Denitrification in hypersaline and coastal environments

As the association of denitrification with global warming and nitrogen removal from ecosystems has gained attention in recent decades, numerous studies have examined denitrification rates and the distribution of denitrifiers across different environments. In this minireview, reported studies focused on coastal saline environments, including estuaries, mangroves, and hypersaline ecosystems, have been analysed to identify the relationship between denitrification and saline gradients. The analyses of the literature and databases stated the direct effect of salinity on the distribution patterns of denitrifiers. However, few works do not support this hypothesis thus making this topic controversial. The specific mechanisms by which salinity influences denitrifier distribution are not fully understood. Nevertheless, several physical and chemical environmental parameters, in addition to salinity, have been shown to play a role in structuring the denitrifying microbial communities. The prevalence of nirS or nirK denitrifiers in ecosystems is a subject of debate in this work. In general terms, in mesohaline environments, the predominant nitrite reductase is NirS type and, NirK is found predominantly in hypersaline environments. Moreover, the approaches used by different researchers are quite different, resulting in a huge amount of unrelated information, making it difficult to establish comparative analysis. The main techniques used to analyse the distribution of denitrifying populations along salt gradients have been also discussed.

Nitrogen removal by Rhodococcus sp. SY24 under linear alkylbenzene sulphonate stress: Carbon source metabolism activity, kinetics, and optimum culture conditions

Artificial intervention combined with stress acclimation was used to screen a heterotrophic nitrifying-aerobic denitrifying (HN-AD) bacterial, strain Rhodococcus SY24, resistant to linear alkylbenzenesulfonic acid (LAS) stress. When LAS was<15 mg/L, strain SY24 performed better cell growth and carbon source metabolism activity. The maximum nitrification and denitrification rates of SY24 under LAS stress could reach 1.18 mg/L/h and 1.05 mg/L/h, respectively, which were 13.80 % and 8.81 % higher than those of the original strain CPZ24. Higher LAS tolerance was seen in the functional genes (amoA, nxrA, napA, narG, nirK, nirS, norB, and nosZ). Response surface modeling revealed that 2 mg/L LAS, sodium succinate as a carbon source, 190 rams, and carbon/nitrogen 11 were the ideal culture conditions for SY24 to nitrogen removal under the LAS environment. This study offered a new screening strategy for the functional species, and strain SY24 showed significant LAS tolerance and HN-AD potential.

Arable soil nitrogen dynamics reflect organic inputs via the extended composite phenotype

Achieving food security requires resilient agricultural systems with improved nutrient-use efficiency, optimized water and nutrient storage in soils, and reduced gaseous emissions. Success relies on understanding coupled nitrogen and carbon metabolism in soils, their associated influences on soil structure and the processes controlling nitrogen transformations at scales relevant to microbial activity. Here we show that the influence of organic matter on arable soil nitrogen transformations can be decoded by integrating metagenomic data with soil structural parameters. Our approach provides a mechanistic explanation of why organic matter is effective in reducing nitrous oxide losses while supporting system resilience. The relationship between organic carbon, soil-connected porosity and flow rates at scales relevant to microbes suggests that important increases in nutrient-use efficiency could be achieved at lower organic carbon stocks than currently envisaged.

Morphology and Size of Bacterial Colonies Control Anoxic Microenvironment Formation in Porous Media

Bacterial metabolisms using electron acceptors other than oxygen (e.g., methanogenesis and fermentation) largely contribute to element cycling and natural contaminant attenuation/mobilization, even in well-oxygenated porous environments, such as shallow aquifers. This paradox is commonly explained by the occurrence of small-scale anoxic microenvironments generated by the coupling of bacterial respiration and dissolved oxygen (O₂) transport by pore water. Such microenvironments allow facultative anaerobic bacteria to proliferate in oxic environments. Microenvironment dynamics are still poorly understood due to the challenge of directly observing biomass and O₂ distributions at the microscale within an opaque sediment matrix. To overcome these limitations, we integrated a microfluidic device with transparent O₂ planar optical sensors to measure the temporal behavior of dissolved O₂ concentrations and biomass distributions with time-lapse videomicroscopy. Our results reveal that bacterial colony morphology, which is highly variable in flowing porous systems, controls the formation of anoxic microenvironments. We rationalize our observations through a colony-scale Damköhler number comparing dissolved O₂ diffusion and a bacterial O₂ uptake rate. Our Damköhler number enables us to predict the pore space fraction occupied by anoxic microenvironments in our system for a given bacterial organization.

On the hidden diversity and niche specialization of the microbial realm of subterranean estuaries

Subterranean estuaries (STEs) modulate the chemical composition of continental groundwater before it reaches the coast, but their microbial community is poorly known. Here, we explored the microbial ecology of two neighbouring, yet contrasting STEs (Panxón and Ladeira STEs; Ría de Vigo, NW Iberian Peninsula). We investigated microbial composition (16S rRNA gene sequencing), abundance, heterotrophic production and their geochemical drivers. A total of 10,150 OTUs and 59 phyla were retrieved from porewater sampled during four surveys covering each STE seepage face. In both STEs, we find a very diverse microbial community composed by abundant cosmopolitans and locally restricted rare taxa. Porewater oxygen and dissolved organic matter are the main environmental predictors of microbial community composition. More importantly, the high variety of benthic microbiota links to biogeochemical processes of different elements in STEs. The oxygen-rich Panxón beach showed strong associations of the ammonium oxidizing archaea Nitrosopumilales with the heterotrophic community, thus acting as a net source of nitrogen to the coast. On the other hand, the prevailing anoxic conditions of Ladeira beach promoted the dominance of anaerobic heterotrophs related to the degradation of complex and aromatic compounds, such as Dehalococcoidia and Desulfatiglans, and the co-occurrence of methane oxidizers and methanogens.

Nitrous oxide emission in altered nitrogen cycle and implications for climate change

Natural processes and human activities play a crucial role in changing the nitrogen cycle and increasing nitrous oxide (N₂O) emissions, which are accelerating at an unprecedented rate. N₂O has serious global warming potential (GWP), about 310 times higher than that of carbon dioxide. The food production, transportation, and energy required to sustain a world population of seven billion have required dramatic increases in the consumption of synthetic nitrogen (N) fertilizers and fossil fuels, leading to increased N₂O in air and water. These changes have radically disturbed the nitrogen cycle and reactive nitrogen species, such as nitrous oxide (N₂O), and have impacted the climatic system. Yet, systematic and comprehensive studies on various underlying processes and parameters in the altered nitrogen cycle, and their implications for the climatic system are still lacking. This paper reviews how the nitrogen cycle has been disturbed and altered by anthropogenic activities, with a central focus on potential pathways of N₂O generation. The authors also estimate the N₂O-N emission mainly due to anthropogenic activities will be around 8.316 Tg N₂O-N yr^-1 in 2050. In order to minimize and tackle the N₂O emissions and its consequences on the global ecosystem and climate change, holistic mitigation strategies and diverse adaptations, policy reforms, and public awareness are suggested as vital considerations. This study concludes that rapidly increasing anthropogenic perturbations, the identification of new microbial communities, and their role in mediating biogeochemical processes now shape the modern nitrogen cycle.

The 'oxygen' in oxygen minimum zones

Aerobic processes require oxygen, and anaerobic processes are typically hindered by it. In many places in the global ocean, oxygen is completely removed at mid-water depths forming anoxic oxygen minimum zones (A-OMZs). Within the oxygen gradients linking oxygenated waters with A-OMZs, there is a transition from aerobic to anaerobic microbial processes. This transition is not sharp and there is an overlap between processes using oxygen and those using other electron acceptors. This review will focus on the oxygen control of aerobic and anaerobic metabolisms and will explore how this overlap impacts both the carbon and nitrogen cycles in A-OMZ environments. We will discuss new findings on non-phototrophic microbial processes that produce oxygen, and we focus on how oxygen impacts the loss of fixed nitrogen (as N₂ ) from A-OMZ waters. There are both physiological and environmental controls on the activities of microbial processes responsible for N₂ loss, and the environmental controls are active at extremely low levels of oxygen. Understanding how these controls function will be critical to understanding and predicting how fixed-nitrogen loss in the oceans will respond to future global warming.

Compound-specific stable isotope analysis of amino acid nitrogen reveals detrital support of microphytobenthos in the Dutch Wadden Sea benthic food web

The Wadden Sea is the world’s largest intertidal ecosystem and provides vital food resources for a large number of migratory bird and fish species during seasonal stopovers. Previous work using bulk stable isotope analysis of carbon found that microphytobenthos (MPB) was the dominant resource fueling the food web with particulate organic matter making up the remainder. However, this work was unable to account for the trophic structure of the food web or the considerable increase in δ15N values of bulk tissue throughout the benthic food web occurring in the Eastern regions of the Dutch Wadden Sea. Here, we combine compound-specific and bulk analytical stable isotope techniques to further resolve the trophic structure and resource use throughout the benthic food web in the Wadden Sea. Analysis of δ15N for trophic and source amino acids allowed for better identification of trophic relationships due to the integration of underlying variation in the nitrogen resources supporting the food web. Baseline-integrated trophic position estimates using glutamic acid (Glu) and phenylalanine (Phe) allow for disentanglement of baseline variations in underlying δ15N sources supporting the ecosystem and trophic shifts resulting from changes in ecological relationships. Through this application, we further confirmed the dominant ecosystem support by MPB-derived resources, although to a lesser extent than previously estimated. In addition to phytoplankton-derived particulate, organic matter and MPB supported from nutrients from the overlying water column there appears to be an additional resource supporting the benthic community. From the stable isotope mixing models, a subset of species appears to focus on MPB supported off recycled (porewater) N and/or detrital organic matter mainly driven by increased phenylalanine δ15N values. This additional resource within MPB may play a role in subsidizing the exceptional benthic productivity observed within the Wadden Sea ecosystem and reflect division in MPB support along green (herbivory) and brown (recycled/detrital) food web pathways.

Mutagenesis of high-efficiency heterotrophic nitrifying-aerobic denitrifying bacterium Rhodococcus sp. strain CPZ 24

Breeding high-efficiency heterotrophic nitrifying-aerobic denitrifying (SND) bacteria is important for the removal of biological nitrogen in wastewater treatment. In this study, a high-efficiency SND mutant strain, ΔRhodococcus sp. CPZ 24, was obtained by ultraviolet-diethyl sulfate compound mutagenesis. The maximum nitrification and denitrification rates were 3.77 and 1.37 mg·L^-1·h^-1, respectively 30.30 % and 17.10 % higher than those of wild bacteria. Biolog technology and network model analysis revealed that ΔCPZ 24 significantly improved the utilisation ability and metabolic activity of organic carbon sources. Furthermore, the expression levels of the nitrogen removal function genes nxrA, nosZ, amoA, and norB in strain ΔCPZ 24 increased significantly. In actual sewage, mutant bacteria ΔCPZ 24 have a 95.05 % ammonia-nitrogen degradation rate and a 96.67 % nitrate-nitrogen degradation rate. These results suggested that UV-DES compound mutation was a successful strategy to improve the nitrogen removal performance of SND bacteria in wastewater treatment.

Periphytic biofilms-mediated microbial interactions and their impact on the nitrogen cycle in rice paddies

Rice paddies are unique waterlogged wetlands artificially constructed for agricultural production. Periphytic biofilms (PBs) at the soil-water interface play an important role in rice paddies characterized by high nutrient input but low utilization efficiency. PBs are composed of microbial aggregates, including a wide variety of microorganisms (algae, bacteria, fungi, protozoa, and metazoa), extracellular polymeric substances and minerals (iron, aluminum, and calcium), which form an integrated food web and energy flux within a relatively stable micro-ecosystem. PBs are crucial to regulate and streamline the nitrogen cycle by neutralizing nitrogen losses and improving rice production since PBs can serve as both a sink by capturing surplus nitrogen and a source by slowly re-releasing this nitrogen for reutilization. Here the ecological advantages of PBs in regulating the nitrogen cycle in rice paddies are illustrated. We summarize the key functional importance of PBs, including the intricate and delicate community structure, microbial interactions among individual phylotypes, a wide diversity of self-produced organics, the active adaptation of PBs to constantly changing environments, and the intricate mechanisms by which PBs regulate the nitrogen cycle. We also identify the future challenges of microbial interspecific cooperation in PBs and their quantitative contributions to agricultural sustainability, optimizing nitrogen utilization and crop yields in rice paddies.

Identification of nosZ-expressing microorganisms consuming trace N2O in microaerobic chemostat consortia dominated by an uncultured Burkholderiales

Microorganisms possessing N₂O reductases (NosZ) are the only known environmental sink of N₂O. While oxygen inhibition of NosZ activity is widely known, environments where N₂O reduction occurs are often not devoid of O₂. However, little is known regarding N₂O reduction in microoxic systems. Here, 1.6-L chemostat cultures inoculated with activated sludge samples were sustained for ca. 100 days with low concentration (<2 ppmv) and feed rate (<1.44 µmoles h⁻¹) of N₂O, and the resulting microbial consortia were analyzed via quantitative PCR (qPCR) and metagenomic/metatranscriptomic analyses. Unintended but quantified intrusion of O₂ sustained dissolved oxygen concentration above 4 µM; however, complete N₂O reduction of influent N₂O persisted throughout incubation. Metagenomic investigations indicated that the microbiomes were dominated by an uncultured taxon affiliated to Burkholderiales, and, along with the qPCR results, suggested coexistence of clade I and II N₂O reducers. Contrastingly, metatranscriptomic nosZ pools were dominated by the Dechloromonas-like nosZ subclade, suggesting the importance of the microorganisms possessing this nosZ subclade in reduction of trace N₂O. Further, co-expression of nosZ and ccoNO/cydAB genes found in the metagenome-assembled genomes representing these putative N₂O-reducers implies a survival strategy to maximize utilization of scarcely available electron acceptors in microoxic environmental niches.

Effect of sulfamethoxazole on nitrate removal by simultaneous heterotrophic aerobic denitrification

The increase in mariculture activities worldwide has not only led to a rise of nitrogen compounds in the ecosystem but has also intensified the accumulation of antibiotics in both terrestrial and marine environments. This study focused on the effect of typical antibiotics, specifically sulfamethoxazole (SMX) on nitrate removal from mariculture wastewater by aerobic denitrification process; an aerobic denitrification system feeding with 148.2 mg/L COD, 8.59 mg/L nitrate, 0.72 mg/L nitrite, and 4.75 mg/L ammonium was set up. The hydraulic retention time (HRT) was 8 h. As the aerobic bioreactor started up successfully without SMX dosage, an excellent removal of ammonium, nitrite, and nitrate was achieved at 91.35%, 93.33%, and 88.51%, respectively; the corresponding effluent concentrations were 0.41 mg/L, 0.048 mg/L, and 0.96 mg/L. At the influent SMX doses of 0, 1, 5, and 10 mg/L, the COD removal reached 96.91%, 96.27%, 88.69%, and 85.89%, resulting in effluent concentrations of 4.53, 5.45, 17.38, and 20.6 mg/L, respectively. Nitrification was not inhibited by SMX dosage. However, aerobic denitrification was inhibited by 10 mg/L SMX. Proteobacteria was the most abundant phylum, and surprisingly its abundance increased with the increase in SMX concentration. An excellent SMX degradation was noted at initial SMX dosages of 1, 5, and 10 mg/L; the removal rate was 100%,100%, and 99.8%, respectively. The SMX degrading genera Comamonas sp., Acinetobacter sp., and Thauera sp. are of great validity to wastewater engineers because they have demonstrated efficiency in simultaneous heterotrophic aerobic denitrification and antibiotic degradation as well as COD removal. PRACTITIONER POINTS: Nitrification was not inhibited by increase in SMX dosage. An increase in SMX dosage inhibited aerobic denitrification. COD removal was not affected by increased SMX dosage. Comamonas, Acinetobacter, and Thauera had high efficiency in COD removal and SMX degradation.

Unconventional microbial mechanisms for the key factors influencing inorganic nitrogen removal in stormwater bioretention columns

Bioretention systems are environmentally friendly measures to control the amount of water and pollutants in urban stormwater runoff, and their treatment performance for inorganic N strongly depends on various microbial processes. However, microbial responses to variations of N mass reduction in bioretention systems are complex and poorly understood, which is not conducive to management designs. In the present study, a series of bioretention columns were established to monitor their fate performance for inorganic N (NH4+and NO3-) by using different configurations and by dosing with simulated stormwater events. The results showed that NH4+ was efficiently oxidized to NO3-, mainly by ammonia- and nitrite-oxidizing bacteria in the oxic media, regardless of the configurations of the bioretention systems or stormwater conditions. In contrast, NO3- removal pathways varied greatly in different columns. The presence of vegetation efficiently improved NO3-mass reduction through root assimilation and enhancement of microbial NO3- reduction in the rhizosphere. The construction of an organic-rich saturation zone can make the redox potential too low for heterotrophic denitrification to occur, so as to ensure high NO3- mass reduction mainly via stimulating chemolithotrophic NO3- reduction coupled with oxidation of reductive sulfur compounds derived from the bio-reduction of sulfate. In contrast, in the organic-poor saturation zone, multiple oligotrophic NO3- reduction pathways may be responsible for the high NO3- mass reduction. These findings highlight the necessity of considering the variation of N bio-transformation pathways for inorganic N removal in the configuration of bioretention systems.

Controlling pore-scale processes to tame subsurface biomineralization

Microorganisms capable of biomineralization can catalyze mineral precipitation by modifying local physical and chemical conditions. In porous media, such as soil and rock, these microorganisms live and function in highly heterogeneous physical, chemical and ecological microenvironments, with strong local gradients created by both microbial activity and the pore-scale structure of the subsurface. Here, we focus on extracellular bacterial biomineralization, which is sensitive to external heterogeneity, and review the pore-scale processes controlling microbial biomineralization in natural and engineered porous media. We discuss how individual physical, chemical and ecological factors integrate to affect the spatial and temporal control of biomineralization, and how each of these factors contributes to a quantitative understanding of biomineralization in porous media. We find that an improved understanding of microbial behavior in heterogeneous microenvironments would promote understanding of natural systems and output in diverse technological applications, including improved representation and control of fluid mixing from pore to field scales. We suggest a range of directions by which future work can build from existing tools to advance each of these areas to improve understanding and predictability of biomineralization science and technology.

Shift of lakeshore cropland to buffer zones greatly reduced nitrogen loss from the soil profile caused by the interaction of lake water and shallow groundwater

The interaction of lake water (LW) and shallow groundwater (SGW) accelerates nitrogen (N) loss from the soil profile in the lakeshore cropland, and cropland buffer zone (CBZ) significantly inhibits N loss in this area. Here, characteristics of N loss and transformations driven by SGW and LW interactions were explored using microcosmic experiments, and N loss was estimated using in situ monitoring data before and after the construction of the CBZ along the west bank of Erhai Lake. The results indicated that NO₃^--N, dissolved organic N and total dissolved N sustained the main N losses in the soil, and the organic N was responsible for the main N loss in the effluent. The lower total nitrogen (TN) concentrations of SGW in this area, the greater the soil N loss. Moreover, N total loss from the 100 cm soil profile in the control check was 1.8 times that in the simulated SGW treatment. We found that nitrification, denitrification and anammox driven by the microbial community and N functional genes were the key processes leading to N loss. The effluent N (3.64%) and gaseous N (0.32%) loss ratios in the cropland for continuously growing vegetables (CGV) were much higher than that in the CBZ (1.07% of effluent N and 0.25% of gaseous N loss ratios). If a 100 m wide and 48 km long area of lakeshore cropland is CGV, an increase by 47% is projected by 2030 compared with the N loss in 2020. But this region was built as a 100 m wide CBZ or 50 m wide CBZ + 50 m wide CGV after 2019, N loss will be reduced by 87% and 44% in 2030 compared with the N loss in CGV. The results implied that restoring a suitable width of CBZ can significantly reduce N loss.

OUP accepted manuscript

Oxygen (O₂) is the ultimate oxidant on Earth and its respiration confers such an energetic advantage that microorganisms have evolved the capacity to scavenge O₂ down to nanomolar concentrations. The respiration of O₂ at extremely low levels is proving to be common to diverse microbial taxa, including organisms formerly considered strict anaerobes. Motivated by recent advances in O₂ sensing and DNA/RNA sequencing technologies, we performed a systematic review of environmental metatranscriptomes revealing that microbial respiration of O₂ at nanomolar concentrations is ubiquitous and drives microbial activity in seemingly anoxic aquatic habitats. These habitats were key to the early evolution of life and are projected to become more prevalent in the near future due to anthropogenic-driven environmental change. Here, we summarize our current understanding of aerobic microbial respiration under apparent anoxia, including novel processes, their underlying biochemical pathways, the involved microorganisms, and their environmental importance and evolutionary origin.

Simultaneous Nitrogen Removal and Plant Growth Promotion Using Salt-‍tolerant Denitrifying Bacteria in Agricultural Wastewater

Excess nitrate (NO3-) and nitrite (NO2-) in surface waters adversely affect human and environmental health. Bacteria with the ability to remove nitrogen (N) have been isolated to reduce water pollution caused by the excessive use of N fertilizer. To obtain plant growth-promoting rhizobacteria (PGPR) with salt tolerance and NO3--N removal abilities, bacterial strains were isolated from plant rhizosphere soils, their plant growth-promoting effects were evaluated using tomato in plate assays, and their NO3--N removal abilities were tested under different salinity, initial pH, carbon source, and agriculture wastewater conditions. The results obtained showed that among the seven strains examined, five significantly increased the dry weight of tomato plants. Two strains, Pseudomonas stutzeri NRCB010 and Bacillus velezensis NRCB026, showed good plant growth-promoting effects, salinity resistance, and NO3--N removal abilities. The maximum NO3--N removal rates from denitrifying medium were recorded by NRCB010 (90.6%) and NRCB026 (92.0%) at pH 7.0. Higher NO3--N removal rates were achieved using glucose or glycerin as the sole carbon source. The total N (TN) removal rates of NRCB010 and NRCB026 were 90.6 and 66.7% in farmland effluents, respectively, and 79.9 and 81.6% in aquaculture water, respectively. These results demonstrate the potential of NRCB010 and NRCB026 in the development of novel biofertilizers and their use in reducing N pollution in water.

Anthropogenic-estuarine interactions cause disproportionate greenhouse gas production: A review of the evidence base

Biologically productive regions such as estuaries and coastal areas, even though they only cover a small percentage of the world's oceans, contribute significantly to methane and nitrous oxide emissions. This paper synthesises greenhouse gas data measured in UK estuary studies, highlighting that urban wastewater loading is significantly correlated with both methane (P < 0.001) and nitrous oxide (P < 0.005) concentrations. It demonstrates that specific estuary typologies render them more sensitive to anthropogenic influences on greenhouse gas production, particularly estuaries that experience low oxygen levels due to reduced mixing and stratification or high sediment oxygen demand. Significantly, we find that estuaries with high urban wastewater loading may be hidden sources of greenhouse gases globally. Synthesising available information, a conceptual model for greenhouse gas concentrations in estuaries with different morphologies and mixing regimes is presented. Applications of this model should help identification of estuaries susceptible to anthropogenic impacts and potential hotspots for greenhouse gas emissions.

Cryptic niche differentiation of novel sediment ecotypes of Rugeria pomeroyi correlates with nitrate respiration

Marine intertidal sediments fluctuate in redox conditions and nutrient availability, and they are also known as an important sink of nitrogen mainly through denitrification, yet how denitrifying bacteria adapt to this dynamic habitat remains largely untapped. Here, we investigated novel intertidal benthic ecotypes of the model pelagic marine bacterium Ruegeria pomeroyi DSS-3 with a population genomic approach. While differing by only 1.3% at the 16S rRNA gene level, members of the intertidal benthic ecotypes are complete denitrifiers whereas the pelagic ecotype representative (DSS-3) is a partial denitrifier lacking a nitrate reductase. The intertidal benthic ecotypes are further differentiated by using non-homologous nitrate reductases and a different set of genes that allow alleviating oxidative stress and acquiring organic substrates. In the presence of nitrate, the two ecotypes showed contrasting growth patterns under initial oxygen concentrations at 1 vol% versus 7 vol% and supplemented with different carbon sources abundant in intertidal sediments. Collectively, this combination of evidence indicates that there are cryptic niches in coastal intertidal sediments that support divergent evolution of denitrifying bacteria. This knowledge will in turn help understand how these benthic environments operate to effectively remove nitrogen.

A Review on the Application of Isotopic Techniques to Trace Groundwater Pollution Sources within Developing Countries

Owing to a lack of efficient solid waste management (SWM) systems, groundwater in most developing countries is found to be contaminated and tends to pose significant environmental health risks. This review paper proffers guidelines on the application of isotopic techniques to trace groundwater pollution sources from data spanning from 2010 to 2020 within developing countries. Earlier groundwater studies in those countries were mainly focused on using hydrochemical and geophysical techniques. The limitation of these techniques is that they can only monitor the concentration of pollutants in the water bodies and possible leachate infiltration but cannot determine the specific sources of the pollution. Stable isotopes of δ18O, δ2H and δ13C can confirm leachate migration to water bodies due to methanogenesis. The high tritium in landfill leachates is useful to identify leachate percolation in groundwater. The δ15N technique has been used to distinguish between synthetic and organic nitrogen sources but its application is limited to differentiating between atmospheric vs. inorganic nitrogen sources. The use of a dual isotope of δ15N–NO3− and δ18O–NO3− is beneficial in terms of identifying various sources of nitrogen such as atmospheric and inorganic fertilizers but is yet to be used to differentiate between nitrogen pollution sources from dumpsites, sewage and animal manure. The coupling of the 11B isotope with δ15N–NO3− and δ18O–NO3− and other hydrochemical parameters has proven to be effective in distinguishing between nitrate fertilizer, animal manure, seawater contamination and sewage. Therefore, in areas affected by agricultural activities, landfill leachates, domestic or sewage effluent and seawater intrusion, it is incumbent to couple hydrochemical (Cl−, NO3−, B, DO) and isotope techniques (δ18O, 2H, δ13C, δ18O–NO3−, δ15N–NO3−, δ11B and 3H) to effectively determine pollution sources of groundwater in developing countries. The foregoing review will provide guidelines for studies that may aim to critically distinguish between seawater intrusion, dumpsites, sewage and septic leachates.

Mix-cultured aerobic denitrifying bacterial communities reduce nitrate: Novel insights in micro-polluted water treatment at lower temperature

Three mix-cultured aerobic denitrifiers were screened from a source water reservoir and named HE1, HE3 and SU4. Approximately 72.9%, 68.6% and 66.2% of nitrate were effectively removed from basal medium, respectively, after 120 h of cultivation at 8 °C. The nitrogen balance analysis revealed about one-fifth of the initial nitrogen was converted into gaseous denitrification products. According to the results of Biolog, the three microfloras had high metabolic capacity to carbon sources. The dominant genera were Pseudomonas and Paracoccus in these bacterial communities based on nirS gene sequencing. Response surface methodology elucidated that the denitrification rates of identified bacteria reached the maximum under the following optimal parameters: C/N ratio of 7.51-8.34, pH of 8.03-8.09, temperature of 18.03-20.19 °C, and shaking speed of 67.04-120 rpm. All results suggested that screened aerobic denitrifiers could potentially be applied to improve the source water quality at low temperature.

Simultaneous ammonium and sulfate biotransformation driven by aeration: Nitrogen/sulfur metabolism and metagenome-based microbial ecology

The present study aimed to clarify the effect of oxygen respiration on biotransformation of alternative electron acceptors (e.g., nitrate and sulfate) underlying the simultaneous removal of ammonium and sulfate in a single aerated sequencing batch reactor. Complete nitrification was achieved in feast condition, while denitrification was carried out in both feast and famine conditions when aeration intensity (AI) was higher than 0.22 L/(L·min). Reactors R1 [0.56 L/(L·min)], R2 [0.22 L/(L·min)], and R3 [0.08 L/(L·min)] achieved 72.39% sulfate removal efficiency in feast condition, but H₂S release occurred in R3. Following exogenous substrate depletion, sulfate concentration increased again and exceeded the influent value in R1, indicating that sulfate transformation was affected by oxygen intrusion. Metagenomic analysis showed that a higher AI promoted sulfate reduction by switching from dissimilatory to assimilatory pathway. Lower AI-acclimated microorganisms (R3) produced H₂S and ammonium, while higher AI-acclimated microorganisms (R1) accumulated nitrite, which confirmed that biotransformation of N and S was strongly regulated by redox imbalance driven by aeration. This implied that respiration control, a microbial self-regulation mechanism, was linked to the dynamic imbalance between electron donors and electron acceptors. Aerobic nitrate (sulfate) reduction, as one of the effects of respiration control, could be used as an alternative strategy to compensate for dynamic imbalance, when supported by efficient endogenous metabolism. Moderate aeration induced microorganisms to change their energy conservation and survival strategy through respiration control and inter-genus protection of respiratory activity among keystone taxa (including Azoarcus in R1, Thauera in R2, and Thiobacillus, Ottowia, and Geoalkalibacter in R3) to form an optimal niche in response to oxygen intrusion and achieve benign biotransformation of C, N, and S without toxic intermediate accumulation. This study clarified the biotransformation mechanism of ammonium and sulfate driven by aeration and provided theoretical guidance for optimizing existing aeration-based techniques.

MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes

Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites-HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)-where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species of Octadecabacter is among the hybrid MAGs produced, containing the genus's only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment.

Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments

The microbial community composition and biogeochemical dynamics of coastal permeable (sand) sediments differs from cohesive (mud) sediments. Tide- and wave-driven hydrodynamic disturbance causes spatiotemporal variations in oxygen levels, which select for microbial generalists and disrupt redox cascades. In this work, we profiled microbial communities and biogeochemical dynamics in sediment profiles from three sites varying in their exposure to hydrodynamic disturbance. Strong variations in sediment geochemistry, biogeochemical activities, and microbial abundance, composition, and capabilities were observed between the sites. Most of these variations, except for microbial abundance and diversity, significantly correlated with the relative disturbance level of each sample. In line with previous findings, metabolically flexible habitat generalists (e.g., Flavobacteriaceae, Woeseaiceae, Rhodobacteraceae) dominated in all samples. However, we present evidence that aerobic specialists such as ammonia-oxidizing archaea (Nitrosopumilaceae) were more abundant and active in more disturbed samples, whereas bacteria capable of sulfate reduction (e.g., uncultured Desulfobacterales), dissimilatory nitrate reduction to ammonium (DNRA; e.g., Ignavibacteriaceae), and sulfide-dependent chemolithoautotrophy (e.g., Sulfurovaceae) were enriched and active in less disturbed samples. These findings are supported by insights from nine deeply sequenced metagenomes and 169 derived metagenome-assembled genomes. Altogether, these findings suggest that hydrodynamic disturbance is a critical factor controlling microbial community assembly and biogeochemical processes in coastal sediments. Moreover, they strengthen our understanding of the relationships between microbial composition and biogeochemical processes in these unique environments.

Ammonia-oxidizing archaea have similar power requirements in diverse marine oxic sediments

Energy/power availability is regarded as one of the ultimate controlling factors of microbial abundance in the deep biosphere, where fewer cells are found in habitats of lower energy availability. A critical assumption driving the proportional relationship between total cell abundance and power availability is that the cell-specific power requirement keeps constant or varies over smaller ranges than other variables, which has yet to be validated. Here we present a quantitative framework to determine the cell-specific power requirement of the omnipresent ammonia-oxidizing archaea (AOA) in eight sediment cores with 3-4 orders of magnitude variations of organic matter flux and oxygen penetration depth. Our results show that despite the six orders of magnitude variations in the rates and power supply of nitrification and AOA abundances across these eight cores, the cell-specific power requirement of AOA from different cores and depths overlaps within the narrow range of 10^-19-10^-17 W cell^-1, where the lower end may represent the basal power requirement of microorganisms persisting in subseafloor sediments. In individual cores, AOA also exhibit similar cell-specific power requirements, regardless of the AOA population size or sediment depth/age. Such quantitative insights establish a relationship between the power supply and the total abundance of AOA, and therefore lay a foundation for a first-order estimate of the standing stock of AOA in global marine oxic sediments.

Advection Drives Nitrate Past the Microphytobenthos in Intertidal Sands, Fueling Deeper Denitrification

Nitrification rates are low in permeable intertidal sand flats such that the water column is the primary source of nitrate to the sediment. During tidal inundation, nitrate is supplied to the pore space by advection rather than diffusion, relieving the microorganisms that reside in the sand from nitrate limitation and supporting higher denitrification rates than those observed under diffusive transport. Sand flats are also home to an abundant community of benthic photosynthetic microorganisms, the microphytobenthos (MPB). Diatoms are an important component of the MPB that can take up and store high concentrations of nitrate within their cells, giving them the potential to alter nitrate availability in the surrounding porewater. We tested whether nitrate uptake by the MPB near the sediment surface decreases its availability to denitrifiers along deeper porewater flow paths. In laboratory experiments, we used NO_x (nitrate + nitrite) microbiosensors to confirm that, in the spring, net NO_x consumption in the zone of MPB photosynthetic activity was stimulated by light. The maximum potential denitrification rate, measured at high spatial resolution using microsensors with acetylene and nitrate added, occurred below 1.4 cm, much deeper than light-induced NO_x uptake (0.13 cm). Therefore, the shallower MPB had the potential to decrease NO_x supply to the deeper sediments and limit denitrification. However, when applying a realistic downward advective flow to sediment from our study site, NO_x always reached the depths of maximum denitrification potential, regardless of light availability or season. We conclude that during tidal inundation porewater advection overwhelms any influence of shallow NO_x uptake by the MPB and drives water column NO_x to the depths of maximum denitrification potential.

A distinct growth physiology enhances bacterial growth under rapid nutrient fluctuations

It has long been known that bacteria coordinate their physiology with their nutrient environment, yet our current understanding offers little intuition for how bacteria respond to the second-to-minute scale fluctuations in nutrient concentration characteristic of many microbial habitats. To investigate the effects of rapid nutrient fluctuations on bacterial growth, we couple custom microfluidics with single-cell microscopy to quantify the growth rate of E. coli experiencing 30 s to 60 min nutrient fluctuations. Compared to steady environments of equal average concentration, fluctuating environments reduce growth rate by up to 50%. However, measured reductions in growth rate are only 38% of the growth loss predicted from single nutrient shifts. This enhancement derives from the distinct growth response of cells grown in environments that fluctuate rather than shift once. We report an unexpected physiology adapted for growth in nutrient fluctuations and implicate nutrient timescale as a critical environmental parameter beyond nutrient identity and concentration.

Here the authors use microfluidics and single-cell microscopy to quantify the growth dynamics of individual E. coli cells exposed to nutrient fluctuations with periods as short as 30 seconds, finding that nutrient fluctuations reduce growth rates up to 50% compared to a steady nutrient delivery of equal average concentration, implying that temporal variability is an important parameter in bacterial growth.

Estuarine microbial diversity and nitrogen cycling increase along sand-mud gradients independent of salinity and distance

Estuaries are depositional environments prone to terrigenous mud sedimentation. While macrofaunal diversity and nitrogen retention are greatly affected by changes in sedimentary mud content, its impact on prokaryotic diversity and nitrogen cycling activity remains understudied. We characterized the composition of estuarine tidal flat prokaryotic communities spanning a habitat range from sandy to muddy sediments, while controlling for salinity and distance. We also determined the diversity, abundance and expression of ammonia oxidizers and N₂ O-reducers within these communities by amoA and clade I nosZ gene and transcript analysis. Results show that prokaryotic communities and nitrogen cycling fractions were sensitive to changes in sedimentary mud content, and that changes in the overall community were driven by a small number of phyla. Significant changes occurred in prokaryotic communities and N₂ O-reducing fractions with only a 3% increase in mud, while thresholds for ammonia oxidizers were less distinct, suggesting other factors are also important for structuring these guilds. Expression of nitrogen cycling genes was substantially higher in muddier sediments, and results indicate that the potential for coupled nitrification-denitrification became increasingly prevalent as mud content increased. Altogether, results demonstrate that mud content is a strong environmental driver of diversity and N-cycling dynamics in estuarine microbial communities.

Quantifying potential N turnover rates in hypersaline microbial mats by 15N tracer techniques

Microbial mats, due to stratification of the redox zones, have a potential to include a complete N cycle, however an attempt to evaluate a complete N cycle in these ecosystems has not been yet made. In this study, occurrence and rates of major N cycle processes were evaluated in intact microbial mats from Elkhorn Slough, Monterey Bay, CA, USA, and Baja California Sur, Mexico under oxic and anoxic conditions using ¹⁵N-labeling techniques. All of the major N transformation pathways, with the exception of anammox, were detected in both microbial mats. Nitrification rates were found to be low at both sites for both seasons investigated. The highest rates of ammonium assimilation were measured in Elkhorn Slough mats in April and corresponded to high in situ ammonium concentration in the overlying water. Baja mats featured higher ammonification than ammonium assimilation rates and this, along with their higher affinity for nitrate compared to ammonium and low dissimilatory nitrate reduction to ammonium rates, characterized their differences from Elkhorn Slough mats. Nitrogen fixation rates in Elkhorn Slough microbial mats were found to be low implying that other processes such as recycling and assimilation from water are main sources of N for these mats at the times sampled. Denitrification in all of the mats was incomplete with nitrous oxide as end product and not dinitrogen. Our findings highlight N cycling features not previously quantified in microbial mats and indicate a need of further investigations in these microbial ecosystems.Importance: Nitrogen is essential for life. The nitrogen cycle on Earth is mediated by microbial activity and has had a profound impact on both the atmosphere and the biosphere throughout geologic time. Microbial mats, present in many modern environments, have been regarded as living records of the organisms, genes, and phylogenies of microbes, as they are one of the most ancient ecosystems on Earth. While rates of major nitrogen metabolic pathways have been evaluated in a number of ecosystems, it remains elusive in microbial mats. In particular it is unclear what factors affect nitrogen cycling in these ecosystems and how morphological differences between mats impact nitrogen transformations. In this study we investigate nitrogen cycling in two microbial mats having morphological differences. Our findings provide insight for further understanding of biogeochemistry and microbial ecology of microbial mats.

A fungus-bacterium co-culture synergistically promoted nitrogen removal by enhancing enzyme activity and electron transfer

The fungus Penicillium citrinum WXP-2 and the bacterium Citrobacter freundii WXP-9 were isolated and found to have poor denitrification performance. Surprisingly, co-culture of the two strains which formed fungus-bacterium pellets (FBPs) promoted the removal efficiency of nitrate (NO₃^--N; 95.78%) and total nitrogen (TN; 81.73%). Nitrogen balance analysis showed that excess degraded NO₃^--N was primarily converted to N₂ (77.53%). Moreover, co-culture increased the dry weight to 0.74 g/L. The diameter of pellets and cell viability also increased by 1.49 and 1.78 times, respectively, indicating that the co-culture exerted a synergistic effect to promote growth. The increase in electron-transmission system activity [99.01 mg iodonitrotetrazolium formazan/(g·L)] and nitrate reductase activity [8.65 mg N/(min·mg protein)] were responsible for denitrification promotion. The FBPs also exhibited the highest degradation rate at 2:1 inoculation ratio and 36 h delayed inoculation of strain WXP-9. Finally, recycling experiments of FBP demonstrated that the high steady TN removal rate could be maintained for five cycles.

Learning from microorganisms: using new insights in microbial physiology for sustainable nitrogen management

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To reduce nitrate to N₂ distinct nitrogen-oxide-reducing microorganisms function together.

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Detecting nirS, nirK or narG genes cannot be directly linked to NO and N₂O emission.

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Nitrogen-oxide-reducing specialists can be exploited to reduce NO and N₂O emission from wwtp.

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Aerobic methanotrophs and methane stripping must be considered for the application of N-DAMO.

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Ammonium recovery could be a more sustainable alternative to nitrogen removal.

Diverse nitrogen-transforming microorganisms with a wide variety of physiological properties are employed for biological nitrogen removal from wastewater. There are many technologies that achieve the required nitrogen discharge standards; however, greenhouse gas emissions and energy consumption constitute the bulk of the environmental footprint of wastewater treatment plants. In this review, we highlight current and proposed approaches aiming to achieve more energy-efficient and environment-friendly biological nitrogen removal, discuss whether new discoveries in microbial physiology of nitrogen-transforming microorganisms could be used to reduce greenhouse gas emissions, and summarize recent advances in ammonium recovery from wastewater.

Temperature and oxygen level determine N2 O respiration activities of heterotrophic N2 O-reducing bacteria: Biokinetic study

Nitrous oxide (N₂ O), a potent greenhouse gas, is reduced to N₂ gas by N₂ O-reducing bacteria (N₂ ORB), a process which represents an N₂ O sink in natural and engineered ecosystems. The N₂ O sink activity by N₂ ORB depends on temperature and O₂ exposure, yet the specifics are not yet understood. This study explores the effects of temperature and oxygen exposure on biokinetics of pure culture N₂ ORB. Four N₂ ORB, representing either clade I type nosZ (Pseudomonas stutzeri JCM5965 and Paracoccus denitrificans NBRC102528) or clade II type nosZ (Azospira sp. strains I09 and I13), were individually tested. The higher activation energy for N₂ O by Azospira sp. strain I13 (114.0 ± 22.6 kJ mol^-1 ) compared with the other tested N₂ ORB (38.3-60.1 kJ mol^-1 ) indicates that N₂ ORB can adapt to different temperatures. The O₂ inhibition constants (K_I ) of Azospira sp. strain I09 and Ps. stutzeri JCM5965 increased from 0.06 ± 0.05 and 0.05 ± 0.02 μmol L^-1 to 0.92 ± 0.24 and 0.84 ± 0.31 μmol L^-1 , respectively, as the temperature increased from 15°C to 35°C, while that of Azospira sp. strain I13 was temperature-independent (p = 0.106). Within the range of temperatures examined, Azospira sp. strain I13 had a faster recovery after O₂ exposure compared with Azospira sp. strain I09 and Ps. stutzeri JCM5965 (p < 0.05). These results suggest that temperature and O₂ exposure result in the growth of ecophysiologically distinct N₂ ORB as N₂ O sinks. This knowledge can help develop a suitable N₂ O mitigation strategy according to the physiologies of the predominant N₂ ORB.