Differential modulation of rhizosphere dissimilatory nitrate reduction to ammonium (DNRA) by wheat cultivars under nitrogen deficiency

Nitrogen (N) deficiency reduces crop yield, but this effect may be mitigated by symbiotic interactions between crops and fungi. However, the response of wheat-fungal interactions to N deficiency remains unclear. We hypothesised that wheat cultivars with a higher reported nitrogen use efficiency (NUE), would induce shifts in the fungal community composition and functional profiles within the wheat rhizosphere to tolerate N deficiency. A glasshouse experiment was conducted to examine the effects of N deficiency on the rhizosphere fungal communities of wheat ( Triticum aestivum L.) cultivars Gladius (low N-use efficiency) and Mace (high N-use efficiency). Plants were grown until the mid-anthesis stage in a Dermosol soil treated with either 0 (Low-N) or 90 kg N ha⁻ 1 (High-N). The rhizosphere fungal communities were characterised using quantitative PCR, ITS rRNA metabarcoding, and metagenomics. The abundance and diversity of the rhizosphere fungal community were not significantly influenced by N deficiency in either Mace or Gladius cultivars ( P > 0.05). However, the fungal community composition showed significant variation across N treatments in Mace ( P < 0.05), whereas no such effect was observed in Gladius ( P > 0.05). Differential abundance analysis and fungal trait predictions indicated a reduction in fungal symbionts in both cultivars under N deficiency ( P < 0.05). Metagenomic analysis demonstrated that fungal functional profiles remained unaffected by N deficiency ( P > 0.05) but significantly differed between Mace and Gladius ( P < 0.05). This study reveals intraspecific variation in rhizosphere fungal responses to N deficiency between Mace and Gladius. The metabarcoding and metagenomic data suggest functional redundancy within the fungal community, which may enhance wheat resilience under N-deficient conditions. These findings highlight the potential of using fungal community stability in developing biofertiliser products for sustainable agriculture. • Nitrogen (N) deficiency does not alter wheat rhizosphere fungal abundance and diversity. • Fungal composition responses to N deficiency varied among wheat cultivars. • Fungal functional profiles are intraspecific but remain stable under N deficiency. • Mace rhizosphere had higher functional redundancy than Gladius under N deficiency.

Dissimilatory nitrate reduction to ammonium dominates nitrate reduction in long-term low nitrogen fertilized rice paddies

Nitrogen removal crash of denitrification in anaerobic biofilm reactor due to dissimilatory nitrate reduction to ammonium (DNRA) for tofu processing wastewater treatment: Based on microbial community and functional genes

Biogeochemical and genomic drivers of groundwater DNRA: predictability of ammonium accumulation risk.

Dissimilatory nitrate reduction to ammonium (DNRA), denitrification, anaerobic ammonium oxidation (anammox), and biological N2 fixation (BNF) can influence the nitrogen (N) use efficiency of rice production. While the effect of N application on BNF is known, little is known about its effect on NO3- partitioning between DNRA, denitrification, and anammox. Here, we investigated the effect of N application on DNRA, denitrification, anammox, and BNF and on the abundance of relevant genes in three paddy soils in Australia. Rice was grown in a glasshouse with N fertilizer (150 kg N ha-1) and without N fertilizer for 75 days, and the rhizosphere and bulk soils were collected separately for laboratory incubation and quantitative PCR analysis. Nitrogen application reduced DNRA rates by >16% in all the soils regardless of the rhizospheric zone, but it did not affect the nrfA gene abundance. Without N, the amount and proportion of NO3- reduced by DNRA (0.42 to 0.52 μg g-1 soil day-1 and 45 to 55%, respectively) were similar to or higher than the amount and proportion reduced by denitrification. However, with N the amount of NO3- reduced by DNRA (0.32 to 0.40 μg g-1 soil day-1) was 40 to 50% lower than the amount of NO3- reduced by denitrification. Denitrification loss increased by >20% with N addition and was affected by the rhizospheric zones. Nitrogen loss was minimal through anammox, while BNF added 0.02 to 0.25 μg N g-1 soil day-1 We found that DNRA plays a significant positive role in paddy soil N retention, as it accounts for up to 55% of the total NO3- reduction, but this is reduced by N application.IMPORTANCE This study provides evidence that nitrogen addition reduces nitrogen retention through DNRA and increases nitrogen loss via denitrification in a paddy soil ecosystem. DNRA is one of the major NO3- reduction processes, and it can outcompete denitrification in NO3- consumption when rice paddies are low in nitrogen. A significant level of DNRA activity in paddy soils indicates that DNRA plays an important role in retaining nitrogen by reducing NO3- availability for denitrification and leaching. Our study shows that by reducing N addition to rice paddies, there is a positive effect from reduced nitrogen loss but, more importantly, from the conversion of NO3- to NH4+, which is the favored form of mineral nitrogen for plant uptake.

Competition and interaction between DNRA and denitrification in composting ecosystems: Insights from metagenomic analysis

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

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

Straw return and low N addition modify the partitioning of dissimilatory nitrate reduction by increasing conversion to ammonium in paddy fields

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

Relationships between environmental factors and N-cycling microbes reveal the indirect effect of further eutrophication on denitrification and DNRA in shallow lakes

Fertilizer types shaped the microbial guilds driving the dissimilatory nitrate reduction to ammonia process in a Ferralic Cambisol

This research investigated spatial-temporal variation in benthic bacterial community structure, rates of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) processes and abundances of corresponding genes and transcripts at three sites—the estuary-head, mid-estuary and the estuary mouth (EM) along the nitrate gradient of the Colne estuary over an annual cycle. Denitrification rates declined down the estuary, while DNRA rates were higher at the estuary head and middle than the EM. In four out of the six 2-monthly time-points, rates of DNRA were greater than denitrification at each site. Abundance of gene markers for nitrate-reduction (nitrate reductase narG and napA), denitrification (nitrite reductase nirS) and DNRA (DNRA nitrite reductase nrfA) declined along the estuary with significant relationships between denitrification and nirS abundance, and DNRA and nrfA abundance. Spatially, rates of denitrification, DNRA and corresponding functional gene abundances decreased along the estuary. However, temporal correlations between rate processes and functional gene and transcript abundances were not observed.

Biotic factors drive distinct DNRA potential rates and contributions in typical Chinese shallow lake sediments

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