Archaeal amoA Genes Research Articles

Activity and community structure of nitrifiers and denitrifiers in nitrogen-polluted rivers along a latitudinal gradient

Nitrogen (N) cycling in rivers is particularly active and dynamic due to excess nutrient inputs worldwide. However, the multidimensional spatial patterns of the activity and community structure of N-cycling microorganisms in rivers remain unclear, limiting our understanding of river ecological functions, especially N removal capacity. Here, we measured the nitrification and denitrification rates and identified nitrifying and denitrifying microorganisms using high-throughput sequencing of archaeal amoA, bacterial amoA, nirK, and nirS genes in channel sediments, riparian rhizosphere soils, and riparian bulk soils of 30 N-polluted rivers across China. Results showed that in the lateral dimension, nitrification rates in sediments did not differ significantly from those in rhizosphere and bulk soils, but denitrification rates were higher in sediments than in bulk soils. However, the archaeal amoA gene abundance in sediments was considerably lower than that in rhizosphere and bulk soils, and bacterial amoA gene abundance in sediments was greater than that in rhizosphere soils. In the vertical dimension, both nitrification and denitrification rates in riparian bulk soils decreased with soil depth, and topsoils harbored more nitrifying and denitrifying microbes than subsoils. Denitrification but not nitrification rates increased with latitude and altitude but decreased with increasing mean annual temperature and precipitation. Overall, these results provide new insights into the multidimensional spatial patterns of river N cycling at a large scale, which is crucial to evaluating the N removal function of global rivers.

Microbial ureolysis and ammonium oxidation in rice (Oryza sativa) rhizosphere: Impact of different fertilizers

Nitrogen is a crucial nutrient for rice (Oryza sativa L.) productivity, and chemical N fertilizers are often applied to enhance rice production. However, the response of soil microbial activity and corresponding functional genes to chemical fertilization remains unclear. The present study was carried out during rainy (kharif) seasons of 2019 and 2020 at the research farms of ICAR-Indian Agricultural Research Institute, New Delhi to study in the microbial responses to different concentration of nitrogen and fertilizers applied to the soil of rice fields. Study included a microcosmic experiment with 3 N concentrations (0, 10, and 100 mM), and treatment included were T1, RDF; T2, 50% N as urea and KNO3 at 75:25 with PK; T3, 50% N as urea and KNO3 at 75:25 with PK and ammonium oxidizing microbial consortium. Nitrogen addition at 10 and 100 mM increased urease activity by 19–26%, potential ammonium oxidation (PAO) by 16–49%, and ureC gene copies by 10–22%. Indeed, treated soils possessed 1.2 to 6.5 folds’ higher copies of archaeal- and bacterial amoA. In the field experiments, the rhizosphere of T1 showed the highest urease and PAO activities while having the lowest activity of ammonification. The abundance of ureC, archaeal-, and bacterial amoA genes ranged from 2.9×106 to 2.0×107, 4.6×103 to 2.4×104, and 2.3 to 9.4×106 copies/g soil, respectively. The ureC gene copies were more abundant in T1, while archaeal and bacterial amoA genes exhibited the highest copies in T3. Urease activity and ureC copies were highest during the vegetative stage, while PAO, and archaeal- and bacterial amoA gene copies were enriched during the flowering stage. The gene abundance and associated enzymatic activities showed a strong correlation, implying that structural changes in the microbial community due to different combinations of fertilizers might alter the nutrient turnover in soil. Our results showed that N-fertilizers could significantly alter the structure and activities of microbial communities, and appropriate N fertilization is necessary for improving the sustainability of rice cultivation.

The regulation effect of preventing soil nitrogen loss using microbial quorum sensing inhibitors

Preventing soil nitrogen (N) losses driven by microbial nitrification and denitrification contributes to improving global environmental concerns caused by NO3−-N leaching and N2O emission. Quorum sensing (QS) signals regulate nitrification and denitrification of N-cycling bacteria in pure culture and water treatment systems, and mediate the composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in activated sludge. However, whether disrupting QS could prevent soil N losses remains unclear. This study explored the feasibility of applying quorum sensing inhibitors (QSIs) as an innovative strategy to reduce N losses from agricultural soils. The two QSIs, penicillic acid and 4-iodo-N-[(3S)-tetrahydro-2-oxo-3-furanyl]-benzeneacetamide (4-iodo PHL), were more effective in reducing N losses than traditional inhibitors, including N-(n-butyl) thiophosphoric triamide and 3,4-dimethylpyrazole phosphate. After 36 days of aerobic incubation, penicillic acid and 4-iodo PHL inhibited nitrification by 39% and 68%, respectively. The inhibitory effects are attributed to the fact that 4-iodo PHL decreased the abundance of archaeal and bacterial amoA genes, as well as the relative abundance of Candidatus Nitrocosmicus (AOA), Candidatus Nitrososphaera (AOA), and Nitrospira (nitrite-oxidizing bacteria/comammox), while penicillic acid reduced archaeal amoA abundance and the relative abundance of Nitrosospira (AOB) and the microbes listed above. Penicillic acid also strongly inhibited denitrification (33%) and N2O emissions (61%) at the peak of N2O production (day 4 of anaerobic incubation) via decreasing nitrate reductase gene (narG) abundance and increasing N2O reductase gene (nosZ) abundance, respectively. Furthermore, the environmental risks of QSIs to microbial community structure and network stability, CO2 emissions, and soil animals were acceptable. Overall, QSIs have application potential in agriculture to reduce soil N losses and the associated effect on climate change. This study established a new method to mitigate N losses from the perspective of QS, and can serve as important basis of decreasing the environmental risks of agricultural non-point source pollution.

Assessing the effectiveness of 3, 4-dimethylpyrazole phosphate (DMPP) inhibitor in mitigating N2O emissions from contrasting Cd-contaminated soils

Improving nitrogen use efficiency of chemical fertilizers is essential to mitigate the negative environmental impacts of nitrogen. Nitrification, the conversion of ammonium to nitrate via nitrite by soil microbes, is a prominent source of nitrogen loss in soil systems. The effectiveness of nitrification inhibitors in reducing nitrogen loss through inhibition of nitrification is well-documented, however, their efficacy in heavy metals-contaminated soils needs thorough investigations. The current study assessed the efficacy of nitrification inhibitor 3, 4-dimethylpyrazole phosphate (DMPP) in reducing nitrous oxide (N2O) emissions in cadmium (Cd) contaminated paddy and red soils under lab-controlled environment. Obtained results indicated the substantial reduction in N2O emissions with DMPP in paddy and red soil by 48 and 35 %, respectively. However, Cd contamination resulted in reduced efficacy of DMPP, thus decreased the N2O emissions by 36 and 25 % in paddy and red soil, respectively. It was found that addition of DMPP had a significant effect on the abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA). Notably, the reduction in N2O emissions by DMPP varied with the abundance of AOB. Moreover, Cd pollution resulted in a significant (P < 0.05) reduction in the abundance of archaeal and bacterial amoA genes, as well as bacterial nirK, nirS, and nosZ genes. The combined treatment of Cd and DMPP had a detrimental impact on denitrifiers, thereby influencing the overall efficiency of DMPP. These findings provide novel insights into the application of DMPP to mitigate nitrification and its potential role in reducing N2O emissions in contaminated soils.

Nitrification and Denitrification Gene Abundances under Stable Soil Chemical Properties Established by Long-Term Compost Fertilization

Rice paddies are dynamic areas for microbe-mediated nitrogen cycling and this could be driven by the long-term alteration of paddy soil edaphic factors. The objective of this study is to evaluate the lasting impact of long-term compost fertilization on the soil chemical properties of paddy fields, determining the size of the microbial guilds involved in nitrification and denitrification. Soil sampling was done on paddy fields without fertilizer, with NPK + compost, and with compost application, and the soil chemical properties of the fields were determined from 2018 to 2021. The abundance of genes related to nitrogen cycling was measured using quantitative PCR (qPCR). Annual analyses showed that the studied soils have attained stable, baseline chemical properties with significantly increased phosphorus (P2O5), potassium (K), SOM, and total nitrogen (TN) due to decades of fertilization with NPK + compost and compost. Consequently, the genes related to bacterial amoA, nosZI, and nosZII were significantly increased in Com- and NPKCom-amended soils compared to the NF paddy field. The nirK gene abundance was unaffected after long-term amendment with compost. A positive correlation was found between the archaeal amoA gene abundance and DOC, while SOM and TN were consistently positively correlated with the abundances of bacterial amoA, nosZI, and nosZII genes, in addition to interactions with potassium and DOC. Principal component analysis (PCA) indicated soil variabilities across treatments, where the unfertilized paddy field contained lower SOM and nutrient contents with a characteristic nirK gene abundance. Similar variabilities in terms of the SOM, TN, K, nosZI, and nosZII gene abundances were observed in the Com and NPKCom paddy fields. Long-term amendment with NPK + compost and compost created soil paddy fields with stable soil chemical properties with higher SOM and nutrient contents, which established higher abundances of genes associated with denitrification and nitrification that were observed during the fallow period.

Diluted pyroligneous vinegar promoted Rhododendron growth by changing functional genes involved in N cycling in the rhizosphere

Excessive chemical fertilization in protected horticulture has caused nutrient accumulation, reduction of soil biodiversity, and subsequently soil degradation. Pyroligneous vinegar is a byproduct of pyrolysis for biochar production. While there has been an increase in interest in using pyroligneous vinegar as an amendment to improve soil quality, a paucity of data exists of its effect on the growth of acidophilous plants such as azalea (Rhododendron). To address this, we investigated the changes in the growth of azalea and soil microbial abundance, specifically those involved in nitrogen cycling in the rhizosphere with amendment of conventional inorganic NPK fertilizer (NPK) and four dilutions of pyroligneous vinegar each with matched NPK content. The results showed that the treatments of pyroligneous vinegar increased plant biomass (51%-99%), root length (29%-81%) and surface area (63%-151%), and nitrogen use efficiency (83%-299%) compared to NPK alone. The pyroligneous vinegar treatments decreased soil pH and increased the contents of rhizosphere soil dissolved organic carbon and nitrate, and changed potential denitrification activity. Compared with NPK, pyroligneous vinegar increased archaeal and bacterial amoA genes (AOA and AOB) abundances (45% − 79% and 39% − 75%, respectively) in nitrification, but inhibited the denitrification gene abundances (i.e. nirS and nirK abundance up to 21% lower). Pyroligneous vinegar increased the ratio of nosZ/(nirS + nirK), suggesting an increased potential to lower nitrous oxide emissions.Correlation analysis indicated that nitrogen use efficiency correlated positively with AOA and AOB, but negatively with nirS and nirK abundance. Therefore, our study suggests that pyroligneous vinegar could improve the growth of acidophilous plants and increase their nitrogen use efficiency by changing nitrogen cycling related functional genes, and could be a potential soil amendment in protected horticulture.

Ammonia oxidation and nitrate reduction marker genes are key indicators of nitrogen losses in temperate forest catchments.

Chronic nitrogen inputs can alleviate N limitation and potentially impose N losses in forests, indicated by soil enrichment in 15 N over 14 N. However, the complexity of the nitrogen cycle hinders accurate quantification of N fluxes. Simultaneously, soil ecologists are striving to find meaningful indicators to characterise the "openness" of the nitrogen cycle. We integrate soil δ15 N with constrained ecosystem N losses and the functional gene potential of the soil microbiome in 14 temperate forest catchments. We show that N losses are associated with soil δ15 N and that δ15 N scales with the abundance of soil bacteria. The abundance of the archaeal amoA gene, representing the first step in nitrification (ammonia oxidation to nitrite), followed by the abundance of narG and napA genes, associated with the first step in denitrification (nitrate reduction to nitrite), explains most of the variability in soil δ15 N. These genes are more informative than the denitrification genes nirS and nirK, which are directly linked to N2 O production. Nitrite formation thus appears to be the critical step associated with N losses. Furthermore, we show that the genetic potential for ammonia oxidation and nitrate reduction is representative of forest soil 15 N enrichment and thus indicative of ecosystem N losses.

Spatial distribution of ammonia oxidizers in marine sediments of the Bohai, Yellow and East China Seas

Ammonia oxidation, an essential process within the global nitrogen cycle, is mainly performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). To date, the current knowledge on the biogeography of AOA and AOB in the ocean across a large geographic distance remains poorly known. In this study, the abundance, microbial composition, and diversity of AOA and AOB in marine sediments collected from the Bohai Sea, Yellow Sea, and East China Sea were characterized by employing quantitative PCR and Illumina Miseq sequencing of both archaeal and bacterial amoA genes. qPCR analysis demonstrated significantly higher abundances of archaeal amoA genes than those of bacterial amoA genes with AOA/AOB ratios varying from 1.59 to 292.88, suggesting a greater contribution of AOA to nitrification in the seas. Nitrosopumilus and Nitrosospira were the predominant clusters of AOA and AOB respectively in all sediment samples. The distribution pattern of both AOA and AOB communities revealed by PCoA (principal coordinate analysis) showed distinct geographic separation of sediment samples from the three seas. Correlation analysis indicated that ammonia (NH4+-N) and nitrate (NO3−-N) content were the main selective forces leading to the distinct biogeography of the two ammonia oxidizers in the ocean. The results are of great significance in improving our understanding of the contribution of AOA and AOB in the nitrogen transformation in the marine ecosystem and providing insights into the environmental factors that shape the assembly of aerobic ammonium oxidizers.

Seasonal timing of extreme drought regulates N2O fluxes in a semiarid grassland

Terrestrial ecosystems are important sources of nitrous oxide (N2O), a powerful greenhouse gas which can be strongly impacted by increasing droughts in association with climate change. However, detailed information on whether and how drought timing regulates N2O fluxes is still lacking. Here, we conducted a 3-year field experiment on a semiarid grassland in which extreme drought was imposed in either early-, mid-, or late-growing seasons repeatedly from 2014 to 2016. We found that early drought affected N2O emission with high interannual variability (increased, decreased and unchanged N2O emission in 2014, 2015, and 2016, respectively), coincident with changes in inorganic nitrogen (SIN), dissolve organic carbon (DOC), microbial biomass carbon (MBC), and soil functional genes (bacterial amoA, nirK, nirS, and nosZ). However, middle drought consistently suppressed N2O emissions due to simultaneous decreases in MBC, DOC and the abundances of archaeal amoA, nirK, and narG genes, causing the largest reduction in N2O emissions across the three years. In contrast, late drought had little effect on N2O fluxes, even though DOC and SIN decreased and the abundance of nirK, nirS, and nosZ increased. As a result, soil organic C and mineral N availability and functional gene abundances were not always robust factors for predicting N2O emissions under droughts across all treatments, except for abundance of AOA and nosZ. Our results highlight the vital role of seasonal timing in regulating the response of N2O emissions to extreme droughts.

N2O emissions from soils under short-term straw return in a wheat-corn rotation system are associated with changes in the abundance of functional microbes

Straw return is an effective conservation tillage measure that improves soil properties, increases crop yields, and is an efficient means of reusing agrobioenergy by-products. Straw return has been shown to affect nitrogen (N) cycling and related functional microbes in agricultural soils. However, the relationship between nitrous oxide (N2O) emissions and N-related functional genes under different straw return strategies in wheat-corn double cropping systems remains elusive. Here, we conducted a short-term field study to investigate the response of N2O emissions driven by N cycling functional genes (bacterial and archaeal amoA genes and nirS, nirK, and nosZ genes) to different straw return patterns in a wheat-corn double cropping system in the North China Plain. Three treatments were established, namely, both wheat and corn straw return (CWSR), only wheat straw mulch return (WSR), and no straw return (NSR). Over the wheat-corn season, the total N2O emissions significantly increased by 31.74% and 12.37% in CWSR and WSR-treated soils, respectively. Straw return increased nitrifying and denitrifying functional gene abundances, thus stimulating N2O emissions. Correlation analysis showed that AOA (r = 0.262, p < 0.05) and AOB (r = 0.703, p < 0.01) were strongly and positively correlated with NO3−-N concentrations, indicating that AOA and AOB were involved in nitrification under straw return. Both nirS (r = 0.287, p < 0.05) and nirK genes (r = 0.252, p < 0.05) were positively correlated with N2O emissions, while nosZ genes (r = −0.266, p < 0.05) were negatively correlated with N2O emissions. Structural equation model (SEM) analysis further revealed that straw return indirectly affected N2O emissions by influencing the abundances of AOB-amoA (r = 0.324, p < 0.05), nirK (r = 0.417, p < 0.05), and nosZ (r = −0.388, p < 0.001) genes. Overall, short-term straw return increased N2O production in a wheat-corn double cropping system, mainly through increased AOB-amoA and nirK gene abundance, which stimulated N2O production, and reduced nosZ gene abundance, which inhibited N2O reduction.

Neonicotinoid pesticide and nitrate mixture removal and persistence in floating treatment wetlands.

Mesocosm and microcosm experiments were conducted to explore the applicability of floating treatment wetlands (FTWs), an ecologically based management technology, to remove neonicotinoid insecticides and nitrate from surface water. The mesocosm experiment evaluated three treatments in triplicate over a 21-d period. Floating treatment wetland mesocosms completely removed nitrate-N over the course of the experiment even when neonicotinoid insecticides were present. At the completion of the experiment, 79.6% of imidacloprid and degradation byproducts and 68.3% of thiamethoxam and degradation byproducts were accounted for in the water column. Approximately 3% of imidacloprid and degradation byproducts and 5.0% of thiamethoxam and degradation byproducts were observed in above-surface biomass, while ∼24% of imidacloprid and degradation byproducts, particularly desnitro imidacloprid, and<0.1% of thiamethoxam and degradation byproducts were found in the below surface biomass. Further, 1 yr after the experiments, imidacloprid, thiamethoxam, and degradation byproducts persisted in biomass but at lower concentrations in both the above- and below-surface biomass. Comparing the microbial communities of mature FTWs grown in the presence and absence of neonicotinoids, water column samples had similar low abundances of nitrifying Archaeal and bacterial amoA genes (below detection to 104 ml-1 ) and denitrifying bacterial nirK, nirS, and nosZ genes (below detection to 105 ml-1 ). Follow-up laboratory incubations found the highest denitrification potential activities in FTW plant roots compared with water column samples, and there was no effect of neonicotinoid addition (100 ng L-1 ) on potential denitrification activity. Based on these findings, (a) FTWs remove neonicotinoids from surface water through biomass incorporation, (b) neonicotinoids persist in biomass long-term(>1 yr after exposure), and (c) neonicotinoids do not adversely affect nitrate-N removal via microbial denitrification.

Potential contributions of nitrifiers and denitrifiers to nitrous oxide sources and sinks in China's estuarine and coastal areas

Abstract. Nitrous oxide (N2O) is an important ozone-depleting greenhouse gas produced and consumed by microbially mediated nitrification and denitrification pathways. Estuaries are intensive N2O emission regions in marine ecosystems. However, the potential contributions of nitrifiers and denitrifiers to N2O sources and sinks in China's estuarine and coastal areas are poorly understood. The abundance and transcription of six key microbial functional genes involved in nitrification and denitrification, as well as the clade II-type nosZ gene-bearing community composition of N2O reducers, were investigated in four estuaries spanning the Chinese coastline. The results showed that the ammonia-oxidizing archaeal amoA genes and transcripts were more dominant in the northern Bohai Sea (BS) and Yangtze River estuaries, which had low nitrogen concentrations, while the denitrifier nirS genes and transcripts were more dominant in the southern Jiulong River (JRE) and Pearl River estuaries, which had high levels of terrestrial nitrogen input. Notably, the nosZ clade II gene was more abundant than the clade I-type throughout the estuaries except for in the JRE and a few sites of the BS, while the opposite transcript distribution pattern was observed in these two estuaries. The gene and transcript distributions were significantly constrained by nitrogen and oxygen concentrations as well as by salinity, temperature, and pH. The nosZ clade II gene-bearing community composition along China's coastline had a high level of diversity and was distinctly different from that in the soil and in marine oxygen-minimum-zone waters. By comparing the gene distribution patterns across the estuaries with the distribution patterns of the N2O concentration and flux, we found that denitrification may principally control the N2O emissions pattern.

Season and No-Till Rice Crop Intensification Affect Soil Microbial Populations Involved in CH4 and N2O Emissions

Rice is an important source of methane (CH4) and other crops may be sources of nitrous oxide (N2O), both of which are powerful greenhouse gases. In Uruguay, irrigated rice rotates with perennial pastures and allows high productivity and low environmental impact. A long-term experiment with contrasting rice rotation intensification alternatives, including rice–soybean and continuous rice, was recently carried out in an Argialboll located in a temperate region of South America. To know if rotation systems influence soil microbial activity involved in CH4 and N2O emissions, the abundance and potential rate for gas production or consumption of microbial populations were measured during the rice crop season. CH4 was only emitted when rice was flooded and N2O emission was not detected. All rotational soils showed the highest rate for methanogenesis at tillering (30 days after rice emergence), while for methanotrophy, the maximum rate was reached at flowering. The abundance of related genes also followed a seasonal pattern with highest densities of mcrA genes being observed at rice flowering whereas pmoA genes were more abundant in dry soils after rice harvest, regardless of the rotation system. Differences were found mainly at tillering when soils with two consecutive summers under rice showed higher amounts of mcrA and pmoA gene copies. The potential denitrification rate was highest at the tillering stage, but the abundance of nirK and nirS genes was highest in winter. Regarding ammonium oxidation, bacterial amoA abundance was higher in winter while the archaeal amoA gene was similar throughout the year. A strong influence of the rice growth stage was registered for most of the parameters measured in rice paddy soils in this no-till rice intensification experiment. However, differences among rotations begin to be observed mainly at tillering when the abundance of populations of the methane and nitrous oxide cycles seemed to respond to the rice intensification.

Spatiotemporal dynamics of ammonia-oxidizing archaea and bacteria contributing to nitrification in sediments from Bohai Sea and South Yellow Sea, China

Nitrification is a central process in nitrogen cycle in the ocean. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play significant roles in ammonia oxidation which is the first and rate-limiting step in nitrification, and their differential contribution to nitrification is an important issue, attracting extensive attention. In this study, based on the quantification of archaeal and bacterial amoA gene and the measurement of potential nitrification rate (PNR), we investigated the spatiotemporal dynamics of PNRs and the amoA gene abundance and transcript abundance of aerobic ammonia oxidizers in surface sediments collected in summer and spring across ~900 km of the Bohai Sea and Yellow Sea in China. The results revealed that the contribution of AOA to nitrification was greater than that of AOB in coastal sediments, probably due to salinity and ammonia concentration. Besides, seasons had significant effect on amoA gene abundance and transcript abundance, especially for AOA, while both seasons and sea areas had significant influence on PNR of AOA and AOB. Further analysis showed complex relationships among amoA gene abundances, transcript abundances and PNRs. More importantly, both spatial (geographic distance) and environmental factors were vital in explaining the variations of ammonia-oxidizing microorganism abundances and the PNRs.

Comparative Microbial Nitrogen Functional Gene Abundances in the Topsoil vs. Subsoil of Three Grassland Habitats in Northern China.

The microbial groups of nitrogen fixers, ammonia oxidizers, and denitrifiers play vital roles in driving the nitrogen cycle in grassland ecosystems. However, the understanding of the abundance and distribution of these functional microorganisms as well as their driving factors were limited mainly to topsoil. In this study, the abundances of nitrogen functional genes (NFGs) involved in nitrogen fixation (nifH), ammonia oxidation (amoA), and denitrification (nirK, nirS, and nosZ) were investigated in both topsoil (0–10 cm, soil layer with concentrated root) and subsoil (30–40 cm, soil layer with spare root) of three grassland habitats in northern China. The abundance of NFGs decreased with soil depth except for the archaeal amoA gene and the distribution of nifH, archaeal amoA, nirK, and nirS gene was significantly impacted by grassland habitats. Moreover, the distribution of NFGs was more responsive to the vertical difference than horizontal spatial heterogeneity. Redundancy analysis revealed that the distribution pattern of overall NFGs was regulated by grassland habitats, and these regulations were more obvious in the subsoil than in the topsoil. Variance partitioning analysis further indicated that soil resource supply (e.g., organic matter) may control the vertical distribution of NFGs. Taken together, the findings in this study could fundamentally improve our understanding of the distribution of N cycling-associated microorganisms across a vertical scale, which would be useful for predicting the soil N availability and guiding the soil N management in grassland ecosystems.

Assimilation and oxidation of urea‐derived nitrogen in the summer Arctic Ocean

AbstractUrea sinks are mainly associated with assimilation by phytoplankton. However, recent studies have shown that there is a process by which nitrifiers convert urea‐derived nitrogen (urea‐N) into nitrate. We examined these two processes in the shelf and off‐shelf regions of the Arctic Ocean. Urea concentration was high near the bottom in the shelf region, while it was depleted throughout the water column in the off‐shelf region. Urea‐N assimilation was generally higher in the upper euphotic zone than the lower euphotic zone. By contrast, urea‐N oxidation was low in the upper euphotic zone and increased with depth. These results indicate that urea sinks consist of a two‐layer system. We further examined the organisms involved in urea‐N oxidation and found a dominance of shallow clade ammonia‐oxidizing archaea, whose abundance was low in the upper euphotic zone and increased with depth. The abundances of archaeal ureC and amoA genes of shallow clade ammonia‐oxidizing archaea were well correlated (ρ = 0.96, Spearman's correlation), suggesting that most of shallow clade ammonia‐oxidizing archaea could use urea as a source of ammonia oxidation. However, we found that the urea‐N oxidation rate often exceeded the ammonia oxidation rate while kinetics experiments suggested that ammonia oxidizers use urea less actively than ammonia. Network analyses indicated that ammonia oxidizers were closely related to other prokaryotes with the ability to decompose urea. These results suggested that ammonia‐oxidizing archaea may not necessarily use urea‐N directly.

Soil microbial community responding to moderately elevated nitrogen deposition in a Japanese cool temperate forest surrounded by fertilized grasslands

ABSTRACT To examine the hypothesis that the soil microbial community in a nitrogen (N) limited forest responds to moderately elevated N deposition (< 10 kg ha−1 yr−1), correlations between N deposition and soil microbial properties were analyzed in a cool temperate forest surrounded by normally fertilized pasture grasslands in northern Japan. Three experimental plots were established in forest edges adjacent to the grasslands, and the other three plots were in forest interiors at least 700 m away from the grasslands. N deposition in each plot was measured from May to November 2018. In August 2018, we collected litter and surface soil samples from all plots to measure net N mineralization and nitrification rates as indicators of microbial activity, and microbial biomass and various gene abundances (i.e., bacterial 16S rRNA gene, fungal ITS region, and bacterial and archaeal amoA genes) as indicators of microbial abundance. N deposition in forest edges was 1.4-fold greater than that in forest interiors, whereas maximum N deposition was 3.7 kg ha−1. N deposition was significantly correlated with net N mineralization and nitrification rates and 16S rRNA and bacterial amoA gene abundances. Microbial community structures analyzed for bacterial 16S rRNA gene and fungal ITS region amplicons were different between litter and soil samples but were similar between the forest edge and interior, although this analysis was made only for single pair of the two plots in the forest edge and interior. N deposition was also correlated with the soil C/N ratio and nitrate and ammonium contents. Thus, it was suggested that some soil microbial activities and abundances in an N limited forest likely responded to moderately elevated N deposition. These findings provide primary information on soil microbial response to moderately elevated N deposition.

Linking 16S rRNA Gene Classification to amoA Gene Taxonomy Reveals Environmental Distribution of Ammonia-Oxidizing Archaeal Clades in Peatland Soils.

A highly resolved taxonomy for ammonia-oxidizing archaea (AOA) based on the alpha subunit of ammonia monooxygenase (amoA) was recently established, which uncovered novel environmental patterns of AOA, challenging previous generalizations. However, many microbiome studies target the 16S rRNA gene as a marker; thus, the usage of this novel taxonomy is currently limited. Here, we exploited the phylogenetic congruence of archaeal amoA and 16S rRNA genes to link 16S rRNA gene classification to the novel amoA taxonomy. We screened publicly available archaeal genomes and contigs for the co-occurring amoA and 16S rRNA genes and constructed a 16S rRNA gene database with the corresponding amoA clade taxonomy. Phylogenetic trees of both marker genes confirmed congruence, enabling the identification of clades. We validated this approach with 16S rRNA gene amplicon data from peatland soils. We succeeded in linking 16S rRNA gene amplicon sequence variants belonging to the class Nitrososphaeria to seven different AOA (amoA) clades, including two of the most frequently detected clades (Nitrososphaerales γ and δ clades) for which no pure culture is currently available. Water status significantly impacted the distribution of the AOA clades as well as the whole AOA community structure, which was correlated with pH, nitrate, and ammonium, consistent with previous clade predictions. Our study emphasizes the need to distinguish among AOA clades with distinct ecophysiologies and environmental preferences, for a better understanding of the ecology of the globally abundant AOA. IMPORTANCE The recently established phylogeny of amoA provides a finer resolution than previous studies, allowing clustering of AOA beyond the order level and thus revealing novel clades. While the 16S rRNA gene is mostly appreciated in microbiome studies, this novel phylogeny is in limited use. Here, we provide an alternative path to identifying AOA with this novel and highly resolved amoA taxonomy by using 16S rRNA gene sequencing data. We constructed a 16S rRNA gene database with the associated amoA clade taxonomy based on their phylogenetic congruence. With this database, we were able to assign 16S rRNA gene amplicons from peatland soils to different AOA clades, with a level of resolution provided previously only by amoA phylogeny. As 16S rRNA gene amplicon sequencing is still widely employed in microbiome studies, our database may have a broad application for interpreting the ecology of globally abundant AOA.

Distribution and Activity of Ammonia-Oxidizers on the Size-Fractionated Particles in the Pearl River Estuary

To distinguish between the distribution and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in the Pearl River estuary (PRE), we investigated the DNA- and cDNA-based β-proteobacterial and archaeal amoA genes on three size-fractionated particles of &amp;gt;3.0 μm, 0.45–3.0 μm, and 0.22–0.45 μm. Results showed that AOB were more abundant in the freshwater with high concentrations of ammonium (NH4+) and low dissolved oxygen, whereas AOA were dominant in the NH4+-depleted seawater and sensitive to temperature. Obvious shifts in ammonia-oxidizing communities were found along the salinity gradient in the PRE. AOB clearly presented a particle-associated nature, as evidenced by higher relative abundance of amoA genes attached to the large particles (&amp;gt;3.0 μm) and their transcripts exclusively detected on this fraction. Moreover, higher transcriptional activity (indicated by the cDNA/DNA ratio) of AOB on the large particles, suggesting AOB were actively involved in ammonia oxidation despite their lower abundance in the mid- and lower estuarine regions. In contrast, AOA exhibited higher transcriptional activity on the 0.45–3.0 μm and 0.22–0.45 μm particles, implying the free-living strategy of these microbes. Together, these findings from field observations provide useful information on the ecological strategies of ammonia-oxidizing communities in response to different environmental conditions.

Microbial functions and soil nitrogen mineralisation processes in the soil of a cool temperate forest in northern Japan

There is little knowledge about microbial functional community structures and the relationships between microbial communities and nitrogen transformation processes. Here, we investigated the relationships between soil microbial communities and nitrogen mineralisation potentials in a cool temperate forest throughout the growing season. Microbial communities were assessed by quantification of the total bacterial, archaeal, and fungal gene abundances and the bacterial and archaeal amoA gene abundances, functional predictions of bacteria and fungi, and analysis of the bacterial-fungal co-occurrence network. In mid-summer, ectomycorrhizal fungal abundance was significantly higher, whereas the total bacterial abundance was significantly lower. Bacterial and archaeal amoA gene abundances were also significantly higher in mid-summer. However, regardless of the seasonal fluctuation of microbial gene abundances, the net nitrification and nitrogen mineralisation potential did not show clear seasonality. In the network analysis, the microbial community was divided into 13 modules, which were subgroups assumed to have similar niches. Furthermore, two modules that mainly consisted of microbial species of Proteobacteria and Bacteroidetes were significantly and positively correlated with the net nitrification and mineralisation potentials. Our results indicated that microbial subgroups sharing similar niches, instead of total microbial abundances and functional gene abundances, could be important factors affecting the net nitrogen mineralisation potential.