Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt.

Nitrification and denitrification are two critical processes in the global nitrogen cycle. Many microorganisms have been shown to contribute to these biological nitrogen transformation processes. However, our understanding of the nitrogen cycle is still evolving. In the recent years, novel microorganisms and metabolic pathways involved in the nitrogen cycle have been discovered.n Therefore, the overall aim of this thesis is to enrich and characterise novel microorganisms involved in the nitrogen cycle, in order to improve our understanding of the microbial nitrogen conversion processes and their interactions with other important nutrients cycles including carbon and metals.In terms of ammonium oxidation, ammonia-oxidising archaea (AOA) are critical ammonium oxidizers that regulate the nitrogen transformation in ubiquitous environments. AOA may have advantages when competing with ammonia-oxidising bacteria (AOB) in certain extreme environments such as acidic soils. Although 30% of the soils in the world are acidic soils, our understanding of the AOA living under low pH is insufficient. Therefore, the first research objective of this thesis is to enrich and identify a novel AOA under low pH. Using a fresh water reservoir sediments as inoculum, two novel microorganisms (an AOA and a NOB) were enriched in a bioreactor operated at pH 4.5, and proved to play a critical role in ammonium oxidation to nitrate. The AOA strain was assigned to the genus of Nitrosotalea and identified as a novel species Candidatus Nitrosotalea sp. GC1, while the NOB was clustered into a novel lineage within genus Nitrospira. According to the metagenomic analysis on Candidatus Nitrosotalea sp. GC1, the genes encoding enzymes for ammonium oxidation to nitrite were all identified and the Thaumarcheal HP/HB pathway was used for carbon fixation.As a member affiliating in the genus of Nitrosotalea, Candidatus Nitrosotalea sp. GC1 might have similar features to the other members, such as its acidophily, substrate affinity and nitrous oxide (N2O) production. As a critical step to help understand this novel AOA culture, the second research objective of this thesis is to characterise the effect of environmental conditions on Candidatus Nitrosotalea sp. GC1 and its N2O emission potential. With a series batch tests, the acidophily of strain GC was verified, with an optimal pH of 4.5. The Km of ammonium and O2 for Candidatus Nitrosotalea sp. GC1 are 39.7 p 3.2 and 35.2 p 3.0 mM, respectively, which were much higher than other AOA isolates, although still lower than most AOB. In addition, N2O emission from Candidatus Nitrosotalea sp. GC1 has a remarkable yield of 6.7%, which suggested the critical role of acidophilic AOA in greenhouse gas emission.In terms of nitrate reduction, dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are the main processes that convert nitrate to ammonium or inert dinitrogen gas respectively. Although organic carbon compounds are the main energy and electron sources for the most of known DNRA microorganisms, the mechanisms of methane driven DNRA process have not been investigated. Therefore, the third research objective of this thesis is to characterise the microorganisms and pathways involved in a culture performing methane driven DNRA process. In a bioreactor fed with methane and limited nitrate supply, continuous ammonium production from nitrate coupled with anaerobic oxidation of methane was observed, while an anaerobic methanotrophic archaea, Candidatus Methanoperedens nitroreducens (M. nitroreducens), dominated the microbial community. During batch tests, metagenomic and metatranscriptomic analyses showed that the DNRA related genes in Candidatus M. nitroreducens have significantly higher expression levels when the culture was producing ammonium, compared to their levels when the culture was fed with large quantity of nitrate to inhibit DNRA activity. Overall, the results confirmed that Candidatus M. nitroreducens can facilitate the methane-driven DNRA process.It has been shown that denitrification can couple to the oxidation of methane or metals (e.g. Fe or Mn), thus linking the nitrogen cycle to the methane and metal cycles, respectively. However, research works focusing on the interactions between nitrogen, methane and metal cycles in one system are rarely done. Therefore, the last research objective is to investigate interactions between anaerobic oxidation of methane and nitrate and metals reduction processes in one reactor. By setting up and incubating the bioreactor with methane, nitrate and ferrihydrite for more than 900 days, simultaneous methane oxidation and nitrate reduction were observed. Mass and electron balances suggested that in this system, nitrite/iron-dependent anaerobic oxidation of methane processes are coupled with nitrate-dependent iron (Fe) oxidation (NDFO) process. The community analysis suggested that Azospira sp. and Methylomirabiliaceae sp. may be responsible for these processes, while an unknown microorganism facilitated metal-dependent anaerobic oxidation of methane process.Overall, the discovery and characterisation of these novel microorganisms and metabolic pathways mediating ammonium oxidation and nitrate reduction will provide important insights into the understanding of the nitrogen cycle.n

Survey of dissimilatory nitrate reduction to ammonium microbial community at national wetland of Shanghai, China

DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems

Dissimilatory nitrate reduction to ammonium (DNRA) in traditional municipal wastewater treatment plants in China: Widespread but low contribution

Dissimilatory nitrate reduction to ammonium (DNRA): A unique biogeochemical cycle to improve nitrogen (N) use efficiency and reduce N-loss in rice paddy

Functional microbial inoculants affect the balance of DNRA and denitrification pathways in compost amended soil.

Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) is critical for mitigating methane emission and returning reactive nitrogen to the atmosphere. The genomes of n-DAMO archaea show that they have the potential to couple anaerobic oxidation of methane to dissimilatory nitrate reduction to ammonium (DNRA). However, physiological details of DNRA for n-DAMO archaea were not reported yet. This work demonstrated n-DAMO archaea coupling the anaerobic oxidation of methane to DNRA, which fueled Anammox in a methane-fed membrane biofilm reactor with nitrate as only electron acceptor. Microelectrode analysis revealed that ammonium accumulated where nitrite built up in the biofilm. Ammonium production and significant upregulation of gene expression for DNRA were detected in suspended n-DAMO culture with nitrite exposure, indicating that nitrite triggered DNRA by n-DAMO archaea. 15N-labeling batch experiments revealed that n-DAMO archaea produced ammonium from nitrate rather than from external nitrite. Localized gradients of nitrite produced by n-DAMO archaea in biofilms induced ammonium production via the DNRA process, which promoted nitrite consumption by Anammox bacteria and in turn helped n-DAMO archaea resist stress from nitrite. As biofilms predominate in various ecosystems, anaerobic oxidation of methane coupled with DNRA could be an important link between the global carbon and nitrogen cycles that should be investigated in future research.

Research on the impact of seawater intrusion on nitrogen (N) cycling in coastal estuarine ecosystems is crucial; however, there is still a lack of relevant research conducted under in-situ field conditions. The effects of elevated salinity on N cycling processes and microbiomes were examined in situ seawater intrusion experiments conducted from 2019 to 2021 in the Nakdong River Estuary (South Korea), where an estuarine dam regulates tidal hydrodynamics. After the opening of the Nakdong Estuary Dam (seawater intrusion event), the density difference between seawater and freshwater resulted in varying degrees of seawater trapping at topographically deep stations. Bottom-water oxygen conditions had been altered in normoxia, hypoxia, and weak hypoxia due to the different degrees of seawater trapping in 2019, 2020, and 2021, respectively. Denitrification mostly dominated the nitrate (NO3-) reduction process, except in 2020 after seawater intrusion. However, denitrification rates decreased because of reduced coupled nitrification after seawater intrusion due to the dissolved oxygen limitation in 2020. Dissimilatory nitrate reduction to ammonium (DNRA) rates immediately increased after seawater intrusion in 2020, replacing denitrification as the dominant pathway in the NO3- reduction process. The enhanced DNRA rate was mainly due to the abundant organic matter associated with seawater invasion and more reducing environment (maybe sulfide enhancement effects) under high seawater-trapping conditions. Denitrification increased in 2021 after seawater intrusion during weak hypoxia; however, DNRA did not change. Small seawater intrusion in 2019 caused no seawater trapping and overall normoxic condition, though a slight shift from denitrification to DNRA was observed. Metagenomic analysis revealed a decrease in overall denitrification-associated genes in response to seawater intrusion in 2019 and 2020, while DNRA-associated gene abundance increased. In 2021 after seawater intrusion, microbial gene abundance associated with denitrification increased, while that of DNRA did not change significantly. These changes in gene abundance align mostly with alterations in nitrogen transformation rates. In summary, ecological change effects in N cycling after the dam opening (N retention or release, that is, eutrophication deterioration or mitigation) depend on the degree of seawater intrusion and the underlying freshwater conditions, which constitute the extent of seawater-trapping.

Dissimilatory nitrate reduction to ammonium (DNRA) can save N by converting nitrate into ammonium and avoiding nitrate leaching and runoff in saltmarshes. However, little is known about the effects of invasive plants on DNRA in the upper and deeper soil layers in salt marshes. Here, we investigated DNRA rates in the soils of six different depth layers (0–5, 5–10, 10–20, 20–30, 30–50, and 50–100 cm) from the invasive Spartina alterniflora marshland, two native plants Scirpus mariqueter and Phragmites australis marshlands, and bare mudflat on Chongming Island, located in the Yangtze River Estuary, China. Our results show that S. alterniflora significantly increased DNRA rates in both the upper 50 cm soil and deeper 50–100 cm soil layers. With respect to the entire soil profile, the NO3− reduction content calculated from DNRA in S. alterniflora marshland was 502.84 g N m−2 yr−1, increased by 47.10%, 49.42%, and 38.57% compared to bare mudflat, S. mariquete, and P. australis, respectively. Moreover, NO3− reduction content from the 50–100 cm soil layers was almost identical to that in the upper 50 cm of the soil. In the month of May, DNRA is primarily regulated by SO42− and pH in the upper and deeper soil layers, respectively, whereas, in the month of October, soil pH accounted for the most variables of DNRA in both the upper and deeper soil layers. Altogether, these results from a new perspective confirm that S. alterniflora invasion increases soil N pool and may further push its invasion in salt marshes, and the importance of deeper soil in nitrogen cycling cannot be ignored.

Abstract. Over the last decades, the impact of human activities on the global nitrogen (N) cycle has drastically increased. Consequently, benthic N cycling has mainly been studied in anthropogenically impacted estuaries and coasts, while in oligotrophic systems its understanding is still scarce. Here we report on benthic solute fluxes and on rates of denitrification, anammox, and dissimilatory nitrate reduction to ammonium (DNRA) studied by in situ incubations with benthic chamber landers during two cruises to the Gulf of Bothnia (GOB), a cold, oligotrophic basin located in the northern part of the Baltic Sea. Rates of N burial were also inferred to investigate the fate of fixed N in these sediments. Most of the total dissolved fixed nitrogen (TDN) diffusing to the water column was composed of organic N. Average rates of dinitrogen (N2) production by denitrification and anammox (range: 53–360 µmol N m−2 day−1) were comparable to those from Arctic and subarctic sediments worldwide (range: 34–344 µmol N m−2 day−1). Anammox accounted for 18–26 % of the total N2 production. Absence of free hydrogen sulfide and low concentrations of dissolved iron in sediment pore water suggested that denitrification and DNRA were driven by organic matter oxidation rather than chemolithotrophy. DNRA was as important as denitrification at a shallow, coastal station situated in the northern Bothnian Bay. At this pristine and fully oxygenated site, ammonium regeneration through DNRA contributed more than one-third to the TDN efflux and accounted, on average, for 45 % of total nitrate reduction. At the offshore stations, the proportion of DNRA in relation to denitrification was lower (0–16 % of total nitrate reduction). Median value and range of benthic DNRA rates from the GOB were comparable to those from the southern and central eutrophic Baltic Sea and other temperate estuaries and coasts in Europe. Therefore, our results contrast with the view that DNRA is negligible in cold and well-oxygenated sediments with low organic carbon loading. However, the mechanisms behind the variability in DNRA rates between our sites were not resolved. The GOB sediments were a major source (237 kt yr−1, which corresponds to 184 % of the external N load) of fixed N to the water column through recycling mechanisms. To our knowledge, our study is the first to document the simultaneous contribution of denitrification, DNRA, anammox, and TDN recycling combined with in situ measurements.

Since the start of synthetic fertilizer production more than a hundred years ago, the coastal ocean has been exposed to increasing nutrient loading, which has led to eutrophication and extensive algal blooms. Such hypereutrophic waters might harbor anaerobic nitrogen (N) cycling processes due to low-oxygen microniches associated with abundant organic particles, but studies on nitrate reduction in coastal pelagic environments are scarce. Here, we report on 15N isotope-labeling experiments, metagenome, and RT-qPCR data from a large hypereutrophic lagoon indicating that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were active processes, even though the bulk water was fully oxygenated (> 224 µM O2). DNRA in the bottom water corresponded to 83% of whole-ecosystem DNRA (water + sediment), while denitrification was predominant in the sediment. Microbial taxa important for DNRA according to the metagenomic data were dominated by Bacteroidetes (genus Parabacteroides) and Proteobacteria (genus Wolinella), while denitrification was mainly associated with proteobacterial genera Pseudomonas, Achromobacter, and Brucella. The metagenomic and microscopy data suggest that these anaerobic processes were likely occurring in low-oxygen microniches related to extensive growth of filamentous cyanobacteria, including diazotrophic Dolichospermum and non-diazotrophic Planktothrix. By summing the total nitrate fluxes through DNRA and denitrification, it results that DNRA retains approximately one fifth (19%) of the fixed N that goes through the nitrate pool. This is noteworthy as DNRA represents thus a very important recycling mechanism for fixed N, which sustains algal proliferation and leads to further enhancement of eutrophication in these endangered ecosystems.

Dissimilatory nitrate reduction to ammonium (DNRA) is an essential intermediate step in the nitrogen cycle, and different sediment physicochemical properties can affect the DNRA process. But the detailed research on the environmental nitrogen cycling in urban river networks based on DNRA communities and the functional gene nrfA is lacking. In this study, the flow line of the Huangpu River in Shanghai was analyzed using isotope tracer, quantitative real-time PCR, and high-throughput sequencing techniques to evaluate the role of DNRA on the stability of the river network and marine. The significant positive correlation between the rate of DNRA and sediment organic carbon was identified. At the genus level, Anaeromyxobacter is the most dominant. Notably, both heterotrophic and autotrophic DNRA species were discovered. This study added diversity to the scope of urban freshwater river network ecosystem studies by investigating the distribution of DNRA bacteria along the Huangpu River. It provided new insights into the biological nitrogen cycle of typical urban inland rivers in eastern China.

Dissimilatory nitrate reduction to ammonium (DNRA) plays an important role in keeping nitrate retention as a more bioavailable form (ammonium) in estuarine and intertidal environments. However, the effects of soil abiotic and biotic characteristics on DNRA in Spartina alterniflora ecotones of estuarine and intertidal wetlands remain unclear. In this study, we used nitrogen isotope tracing and molecular approaches to investigate DNRA activity, and abiotic and biotic factors of both rhizosphere and non-rhizosphere soils in Spartina alterniflora ecotones of the Yangtze estuarine and intertidal wetlands. DNRA varied significantly throughout the sampling sites, with potential rates of 0.53–3.57 nmol N g−1 h−1. The rates of DNRA were significantly higher in rhizosphere than non-rhizosphere soils at the oligohaline sites. Salinity had more influence on DNRA activity than Spartina alterniflora at the brackish sites. Total organic carbon, nitrate, Fe (II) and sulfide were significantly correlated with DNRA rates and nrfA gene abundance. Soil substrates strongly affected DNRA activity in rhizosphere soil, while nrfA gene abundance was the predominant factor mediating DNRA activity in non-rhizosphere soil. DNRA contributed more to the total nitrate reduction at the brackish than oligohaline sites, suggesting that DNRA plays an important role in nitrate reduction in estuarine and intertidal wetlands. This study suggests that soil substrates rather than nrfA gene dominate DNRA activity in estuarine and intertidal wetlands after Spartina alterniflora invasion. Our results are helpful to understand the importance of soil characteristics changes induced by the exotic plant invasion to nitrogen cycling in estuarine and intertidal wetlands.

Electron shuttle potential of biochar promotes dissimilatory nitrate reduction to ammonium in paddy soil

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 220:33-46 (2001) - doi:10.3354/meps220033 A diagenetic model discriminating denitrification and dissimilatory nitrate reduction to ammonium in a temperate estuarine sediment B. A. Kelly-Gerreyn1,*, M. Trimmer2, D. J. Hydes1 1Southampton Oceanography Centre, Waterfront Campus, European Way, Southampton SO14 3ZH, United Kingdom 2School of Biological Sciences, Queen Mary College, University of London, London E1 4NS, United Kingdom *E-mail: b.kelly-gerreyn@soc.soton.ac.uk ABSTRACT: A diagenetic model is presented which considers nitrate reduction by both denitrification and Dissimilatory Nitrate Reduction to Ammonium (DNRA). This work builds on an existing model (Kelly-Gerreyn et al. 1999; Mar Ecol Prog Ser 177:37-50). Previous models have assumed nitrate reduction to be solely due to denitrification. This paper questions the reliability of this assumption in coastal areas and suggests that DNRA can account for a high proportion of nitrate reduction. Data from a North Sea estuary (the lower Gt. Ouse, Norfolk, UK) containing high nutrient concentrations (mean 406 µM NO3-) are used to derive a relationship between temperature and the proportioning of nitrate reduction driven by nitrate from the overlying water into denitrification and DNRA. The relationship is assumed to apply to total nitrate reduction. The result is a function which shows that DNRA and denitrification occur at all temperatures but that DNRA is the favoured pathway at the extremes of the observed temperatures (<14 and >17°C) while denitrification is favoured only in a narrow range of temperatures (14 to 17°C). The mechanism is probably an adaptive response of different nitrate-reducing bacteria to temperature. This temperature relationship is implemented in the model and used to successfully simulate both observed rates of uncoupled denitrification (4 to 228 µmolN m-2 h-1), denitrification fuelled by nitrate in the overlying water (Dw), and calculated rates of DNRA fuelled by nitrate in the overlying water (DNRAw) (measured nitrate flux - measured Dw rate). In contrast, standard diagenetic formulae for nitrate reduction (i.e. by denitrification only) cannot satisfactorily reproduce the Dw rates observed in these sediments. It is concluded that temperature is an important controlling factor for partitioning nitrate reduction into DNRA and denitrification in the lower Gt. Ouse sediments. This temperature effect implies that during an extended warm summer in temperate estuaries receiving high nitrate inputs, nitrate reduction may contribute to, rather than counteract, a eutrophication event. Diagenetic models of the nitrogen cycle in coastal areas should include DNRA. KEY WORDS: Diagenesis model · Denitrification · Dissimilatory nitrate reduction to ammonium · Temperature Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 220. Online publication date: September 27, 2001 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2001 Inter-Research.