Biogeochemical Cycles Of Nitrogen Research Articles

Phosphate Influx and Dust Deposition Create Zonal and Meridional Biogeochemical Gradients in Trichodesmium Abundance

AbstractTrichodesmium plays a key role in the biogeochemical cycling of carbon, nitrogen and phosphorus in the Tropical Atlantic Ocean. A complex interplay of physicochemical factors control the growth of Trichodesmium. However, owing to the large spatial and temporal variability, the relative influence of these factors in controlling Trichodesmium distribution and abundance remains unclear. In this study, we examined the basin‐scale distribution pattern of Trichodesmium in the upper 200 m water column of the Atlantic Ocean (25°N–30°S and 70°W–20°E) using a large data set (n = 33,235) and tried to constrain the distribution based on various physicochemical parameters. We suggest that the combined effect of warm temperatures and phosphate (PO43−) availability determines the zonal spatial extent and the abundance of Trichodesmium in the Tropical North Atlantic Ocean. However, the availability of dissolved iron, along with high sea surface temperatures and meteorological parameters such as the wind direction and precipitation, likely govern the meridional distribution of Trichodesmium across the Atlantic Ocean. Excess PO43− at the surface rules out the possibility of PO43− limitation in regulating the meridional distribution of the Trichodesmium. Depth‐integrated nitrogen fixation rates, based on a multiple linear regression, vary from 0.07 to 306 μmol N m−2 d−1. The presence of Trichodesmium colonies down to a depth of 200 m and the depth‐integrated nitrogen fixation rates reflect the pivotal role of Trichodesmium in the nitrogen budget of this region.

Anerobic ammonium oxidation coupled to iron(III) reduction catalyzed by a lithoautotrophic nitrate-reducing iron(II) oxidizing enrichment culture.

The last two decades have seen nitrogen/iron-transforming bacteria at the forefront of new biogeochemical discoveries, such as anaerobic ammonium oxidation coupled to ferric iron reduction (feammox) and lithoautotrophic nitrate-reducing ferrous iron-oxidation (NRFeOx). These emerging findings continue to expand our knowledge of the nitrogen/iron cycle in nature, and also highlight the need to re-understand the functional traits of the microorganisms involved. Here, as a proof-of-principle, we report compelling evidence for the capability of a NRFeOx enrichment culture to catalyze the feammox process. Our results demonstrate that the NRFeOx culture predominantly oxidizes NH4+ to nitrogen gas, by reducing both chelated NTA-Fe(III) and poorly soluble Fe(III)-bearing minerals (γ-FeOOH) at pH4.0 and 8.0, respectively. In the NRFeOx culture, Fe(II)-oxidizing bacteria of Rhodanobacter and Fe(III)-reducing bacteria of unclassified_Acidobacteriota coexisted. Their relative abundances were dynamically regulated by the supplemented iron sources. Metagenomic analysis revealed that the NRFeOx culture contained a complete set of denitrifying genes along with hao genes for ammonium oxidation. Additionally, numerous genes encoding extracellular electron transport-associated proteins or their homologs were identified, which facilitated the reduction of extracellular iron by this culture. More broadly, this work lightens the unexplored potential of specific microbial groups in driving nitrogen transformation through multiple pathways, and highlights the essential role of microbial iron metabolism in the integral biogeochemical nitrogen cycle.

Distinct microbial nitrogen cycling processes in the deepest part of the ocean.

The metabolic features and adaptation strategies of the nitrogen cycling microorganisms in the deepest part of the ocean are largely unknown. This study revealed that anammox bacteria might perform aerobic respiration in response to nutrient limitation or O2 fluctuations in the Mariana Trench sediments. Meanwhile, an abundant alkane-oxidizing Ketobacter species could fix N2 in hadal seawater. This study provides new insights into the roles of hadal microorganisms in global nitrogen biogeochemical cycles. It substantially expands our understanding of the microbial life in the largely unexplored deepest part of the ocean.

Insights into nitrogen biogeochemical cycling in mangrove wetland from Genome-Resolved metagenomic sequencing

The critical role of nitrogen (N) in sustaining the vitality of mangrove wetlands is widely recognized, yet research elucidating complex microbiome structures and functional genes driving N biogeochemical cycles are markedly limited. This study leverages high-throughput and metagenomic sequencing to investigate N biogeochemical cycling from the Dongzhai Harbor mangrove wetland. Results reveal that Proteobacteria (29.95–49.26%), Chloroflexi (15.68–35.33%), and Acidobacteria (5.18–12.46%) are the predominant phyla, with Deltaproteobacteria (3.71–7.95%), Gammaproteobacteria (0.83–8.73%), and Alphaproteobacteria (1.73–14.13%) leading at the order level. Microbial diversity and the prevalence of functional genes diminish with increasing sediment depth, indicating that N transformation predominantly occurs in surface sediments. The identified N metabolic pathways in mangrove sediments encompass N fixation (nifD, nifK, nifH genes), nitrification (amoA, amoB, amoC, hao, nxrA and nxrB genes), denitrification (narG, nirK, nirS, norB and nosZ genes), dissimilatory nitrate reduction to ammonium (hzo、hzsA and hzsB genes), and organic N mineralization (gdhA and ureC genes). Organic N mineralization and N fixation are most pronounced in mangrove sediments, with N fixation exhibiting greater intensity in the mangrove than mudflat zone. Salinity, TOC, TN, and SO42- predominantly foster N cycling facilitated by microbial activities, while Fe appears to impede it. These insights offer a scientific foundation for the ecological restoration and conservation of mangrove wetlands.

Unraveling the mechanism of assimilatory nitrate reduction and methane oxidation by Methylobacter sp. YHQ through dual N-O isotope analysis and kinetic modeling

Assimilatory nitrate reduction and methane (CH4) oxidation by bacteria play important roles in carbon (C) and nitrogen (N) biogeochemical cycles. Here, an investigation of enzymatic assimilatory nitrate reduction and CH4 oxidation by Methylobacter sp. YHQ from the wetlands is presented, specifically concentrating on N and oxygen (O) isotope fractionation with various initial nitrate and oxygen concentrations. The N enrichment factors (15εassimilation) increased from 4.2 ± 0.7‰ to 6.9 ±1.3‰ and the O isotope enrichment factors (18εassimilation) increased from 2.7 ± 0.9‰ to 4.7 ± 0.8‰ during nitrate assimilation when initial nitrate concentrations increased from 0.9 mM to 2 mM. Similar 18ε and 15ε values were observed at different oxygen concentrations. The values of 18ε and 15ε provided vital parameters for the assessment of assimilatory nitrate reduction via the Rayleigh equation approach. The ratios of O and N isotope enrichment factors (18ε:15ε)assimilation ranged from 0.64 ± 0.15 to 0.74 ± 0.18 during nitrate assimilation by Methylobacter sp. YHQ with Nas, which were different from (18ε:15ε)assimilation for assimilatory eukaryotic nitrate reductase (eukNR) from literature data. Thus, N and O isotope fractionation could be useful tools to distinguish eukNR from Nas during nitrate assimilation. Additionally, the rates of CH4 oxidation and nitrate reduction were evaluated with a reaction-based kinetic model, and it quantitatively described the enzymatic reactions of nitrate assimilation. Combining dual N-O isotope analysis with kinetic modeling provides new insights into the microbially driven C-N interactions.Graphical

Dissolved Nitrous Oxide and Hydroxylamine in the Northern South China Sea in Summer

AbstractNitrous oxide (N2O) is a potent greenhouse gas and a strong ozone‐depleting substance. Ocean is an important natural source of atmospheric N2O, which has attracted increasing attention recently as to understand the biogeochemical cycles of nitrogen in marine systems. Nitrification is one of the major N2O production pathways during which N2O is produced as a side product and hydroxylamine (NH2OH) is produced as an obligate intermediate. However, few studies have reported the NH2OH variability in natural seawater and its relationship between N2O remains ambiguous. In summer 2022, spatial distribution and influencing factors of N2O and NH2OH in the northern South China Sea (SCS) were investigated. Dissolved N2O varied from 5.79 to 34.80 nmol L−1 in water column and generally increased with water depth above 800 m. N2O was correlated with dissolved oxygen and nitrate, inferring that N2O was mainly produced via nitrification. NH2OH varied from below detection limit to 3.91 nmol L−1. The adoption of multiple standard additions can largely reduce the bias in NH2OH measurement. Structural equation modeling showed that NH2OH has a potential effect favoring excessive N2O. Surface N2O saturation ranged between 102% and 278%, indicating that the northern SCS was a net source of atmospheric N2O in summer.

Temporal variations of biological nitrogen fixation and diazotrophic communities associated with artificial seaweed farms

Diazotrophic communities contribute inorganic nitrogen for the primary productivity of the marine environment by biological nitrogen fixation (BNF). They play a vital role in the biogeochemical cycle of nitrogen in the marine ecological environment. However, there is still an incomplete understanding of BNF and diazotrophs in artificial seaweed farms. Therefore, this study comprehensively investigated the temporal variations of BNF associated with Gracilariopsis lemaneiformis, as well as the diazotrophic communities associated with macroalgae and its surrounding seawater. Our results revealed that a total of 13 strains belonging to Proteobacteria and Bacteroidetes were identified as N2-fixing bacteria using azotobacter selective solid medium and nifH gene cloning. Subsequently, BNF and diazotrophic communities were characterized using the acetylene reduction method and high-throughput sequencing of the nifH gene, respectively. The results showed that nitrogenase activity and nifH gene abundance of epiphytic bacteria on G. lemaneiformis varied significantly among four different cultivation periods, i.e., Cultivation Jan. (CJ), Cultivation Feb. (CF), Cultivation Mar. (CM), Cultivation Apr. (CA). Among them, the nitrogenase activity and nifH gene abundance of epiphytic bacteria on G. lemaneiformis in CM were significantly higher than those in CJ, CF, and CA, indicating that the BNF of eiphytic bacteria on G. lemaneiformis was markedly enhanced. Combined with the data on environmental factors, it was found that the low concentration of nitrogen and phosphorus in CM might considerably boost the BNF of epiphytic bacteria in G. lemaneiformis. The sequencing results of the nifH gene showed that the α-diversity of diazotrophic communities associated with G. lemaneiformis and seawater in CM was higher than that in other cultivation periods. In addition, the diazotrophic communities on G. lemaneiformis were significantly different in CJ, CF, CM, and CA, and they were significantly diverse from diazotrophic communities in seawater. LEfSe analysis indicated that Rhodobacterales, Hyphomonadaceae, Robiginitomaculum, and Robiginitomaculum antarcticum within α-proteobacteria played a remarkable role in BNF in response to nitrogen nutrient deficiency. Taken together, these results provide a unique insight into the interaction between macroalgae and its epiphytic bacteria and lay a foundation for further research on the mechanism of action of nitrogen-cycling microorganisms associated with macroalgae.

Historical development, impact mechanism and future trends of nitrogen footprint in Wuxi City, China

Human activities have changed the biogeochemical cycle of nitrogen, leading to a large amount of reactive nitrogen (Nr) into the environment, aggravating a series of environmental problems, affecting human and ecosystem health. Cities are the core areas driving nitrogen cycling in terrestrial ecosystems, however, there are numerous influencing factors and their contributions are unclear. The nitrogen footprint is an important index to understand the impact of human activities on the environment, however, the calculation of urban nitrogen footprint needs a simplified and accurate system method. Here we use a nitrogen footprint calculation model at the urban system level based on system nitrogen balance, and a multi-factor extended STIRPAT (stochastic impact by regression on population, affluence, and technology) model suitable for analyzing the impact mechanism of nitrogen footprint to estimate nitrogen footprint of Wuxi City during 1990–2050. We find that: (1) from 1990 to 2020, the total nitrogen footprint of Wuxi City was in an increasing trend, but the per capita nitrogen footprint was in a decreasing trend. The per capita nitrogen footprint of 22.36 kg capita−1 in 2020 was at a lower level globally. (2) Nr discharge from fossil fuel combustion and Haber-Bosch nitrogen fixation accounted for the main proportion of nitrogen footprint. (3) Dietary choice (Ad), GDP per capita (Ag), urbanization rate (Au), population (P), and fossil energy productivity (Te) were the key factors contributing to the increase of the nitrogen footprint, which resulted in an annual increase of 1.39 %. While nitrogen footprint productivity (Tn), nitrogen use efficiency in crop farming (Tc), and nitrogen use efficiency in animal breeding (Ta) were the key inhibit factors that inhibit the increase of nitrogen footprint, and these factors slow down the annual growth rate of nitrogen footprint by 0.39 %. (4) The continuous growth of nitrogen footprint in the baseline and population growth scenarios will bring more environmental problems and greater environmental governance pressure to Wuxi City, while the sustainable scenario that includes comprehensive means such as economic adaptation and technological improvement is more in line with the requirements of high-quality development in China. Several mitigation measures are then proposed by considering Wuxi's realities from both key impact factors and potential for nitrogen footprint reduction in different scenarios, which can provide valuable policy insights to other cities, especially lakeside cities to mitigate nitrogen footprint.

Nitrogen isotopes of marine oils in the Tarim Basin, China: Implications for the origin of organic matters and the paleoenvironment

Nitrogen isotope compositions (δ15N) of sedimentary rocks are usually used to reconstruct the paleoenvironment and nitrogen (N) biogeochemical cycle. The δ15N values of crude oils inherit the characteristics of relevant source rocks and can well reflect the information of hydrocarbon-forming organisms and environment in ancient water column. However, studies on the δ15N of crude oils are limited due to the low N content. In this study, a new efficient method is applied to the marine oils from the Bashituo (BST) and Halahatang (HLHT) areas of the Tarim Basin to obtain the nitrogenous components (i.e., nonhydrocarbons and asphaltenes) for the achievement of N concentration. The carbon and nitrogen isotopes of these components and the biomarkers of oils were measured. The δ15N values in asphaltenes (δ15NAsp) are significantly heavier than those in nonhydrocarbons (δ15NNSOs) in these oils, which are attributed to the potential directional N transfer and kinetic isotope fractionation during the thermal evolution of organic matters (OM). The δ15NAsp values have significant correlations with OM origin associated parameters and weak correlations with environmental parameters, suggesting that the difference in δ15NAsp values is mainly resulted from biological source rather than redox conditions. The δ15NNSOs values have a closer relationship with the redox condition than biological characteristics, indicating that they have a good response to paleoenvironmental variation in the water column, which is not completely overprinted by the difference of OM origin. Different redox conditions give rise to distinct nitrogen cycles, resulting in various δ15N values. Anammox occurs in the water column of the Early Cambrian dominated by physically stratified conditions with significant isotope fractionation, resulting in relatively heavier δ15N of OM in the BST area. In the Middle–Late Ordovician period, the limited suboxic zone leads to an insignificant positive bias of δ15N caused by partial denitrification in the HLHT oils. The evaluation of δ15N in nitrogenous fractions enables a more comprehensive reconstruction of N cycle for ancient oceans.

Guanidine production by plant homoarginine-6-hydroxylases.

Metabolism and biological functions of the nitrogen-rich compound guanidine have long been neglected. The discovery of four classes of guanidine-sensing riboswitches and two pathways for guanidine degradation in bacteria hint at widespread sources of unconjugated guanidine in nature. So far, only three enzymes from a narrow range of bacteria and fungi have been shown to produce guanidine, with the ethylene-forming enzyme (EFE) as the most prominent example. Here, we show that a related class of Fe2+- and 2-oxoglutarate-dependent dioxygenases (2-ODD-C23) highly conserved among plants and algae catalyze the hydroxylation of homoarginine at the C6-position. Spontaneous decay of 6-hydroxyhomoarginine yields guanidine and 2-aminoadipate-6-semialdehyde. The latter can be reduced to pipecolate by pyrroline-5-carboxylate reductase but more likely is oxidized to aminoadipate by aldehyde dehydrogenase ALDH7B in vivo. Arabidopsis has three 2-ODD-C23 isoforms, among which Din11 is unusual because it also accepted arginine as substrate, which was not the case for the other 2-ODD-C23 isoforms from Arabidopsis or other plants. In contrast to EFE, none of the three Arabidopsis enzymes produced ethylene. Guanidine contents were typically between 10 and 20 nmol*(g fresh weight)-1 in Arabidopsis but increased to 100 or 300 nmol*(g fresh weight)-1 after homoarginine feeding or treatment with Din11-inducing methyljasmonate, respectively. In 2-ODD-C23 triple mutants, the guanidine content was strongly reduced, whereas it increased in overexpression plants. We discuss the implications of the finding of widespread guanidine-producing enzymes in photosynthetic eukaryotes as a so far underestimated branch of the bio-geochemical nitrogen cycle and propose possible functions of natural guanidine production.

Guanidine production by plant homoarginine-6-hydroxylases

Metabolism and biological functions of the nitrogen-rich compound guanidine have long been neglected. The discovery of four classes of guanidine-sensing riboswitches and two pathways for guanidine degradation in bacteria hint at widespread sources of unconjugated guanidine in nature. So far, only three enzymes from a narrow range of bacteria and fungi have been shown to produce guanidine, with the ethylene-forming enzyme (EFE) as the most prominent example. Here, we show that a related class of Fe2+- and 2-oxoglutarate-dependent dioxygenases (2-ODD-C23) highly conserved among plants and algae catalyze the hydroxylation of homoarginine at the C6-position. Spontaneous decay of 6-hydroxyhomoarginine yields guanidine and 2-aminoadipate-6-semialdehyde. The latter can be reduced to pipecolate by pyrroline-5-carboxylate reductase but more likely is oxidized to aminoadipate by aldehyde dehydrogenase ALDH7B in vivo. Arabidopsis has three 2-ODD-C23 isoforms, among which Din11 is unusual because it also accepted arginine as substrate, which was not the case for the other 2-ODD-C23 isoforms from Arabidopsis or other plants. In contrast to EFE, none of the three Arabidopsis enzymes produced ethylene. Guanidine contents were typically between 10 and 20 nmol*(g fresh weight)-1 in Arabidopsis but increased to 100 or 300 nmol*(g fresh weight)-1 after homoarginine feeding or treatment with Din11-inducing methyljasmonate, respectively. In 2-ODD-C23 triple mutants, the guanidine content was strongly reduced, whereas it increased in overexpression plants. We discuss the implications of the finding of widespread guanidine-producing enzymes in photosynthetic eukaryotes as a so far underestimated branch of the bio-geochemical nitrogen cycle and propose possible functions of natural guanidine production.

Deciphering the functional importance of comammox vs. canonical ammonia oxidisers in nitrification and N2O emissions in acidic agricultural soils

The discovery of comammox Nitrospira has altered our perception of the nitrogen biogeochemical cycle. However, their functional importance compared to canonical ammonia oxidisers (i.e., ammonia-oxidising bacteria (AOB) and archaea (AOA)) in agricultural soils remains elusive, especially in acidic soils. Here, we assessed the functional importance of these functional guilds in nitrification and nitrous oxide (N2O) emissions in three acidic agricultural soils by using a range of nitrification inhibitors (acetylene, 3,4-dimethylpyrazole phosphate (DMPP) and different concentrations of 1-octyne) and monitored their community assemblage and population dynamics. The sensitivity of comammox Nitrospira clade A to 1-octyne varied across soils, highlighting that the inappropriate use of 1-octyne can lead to misestimation of comammox activity. AOA were key NH3 oxidisers in the three soils, while AOB also contributed significantly to nitrification in one soil. In contrast, comammox Nitrospira always played a minor role in ammonia oxidation and N2O emissions, likely due to their low abundances, restricted cellular kinetic properties and N2O production mechanisms. Together, this study demonstrates that comammox Nitrospira play a less important role in ammonia oxidation and N2O production in acidic agricultural soils than AOA and AOB, thereby providing important novel insights into the mitigation of nitrogen fertiliser loss and N2O emissions.

Dynamic stratification and biogeochemical cycling response of microbial communities in east indian ocean ridge

Marine harbors a diverse and intricate microbial ecosystem crucial for driving biogeochemical and nutrient cycles. To gain insights into the ecological functions of microbial communities in deep-sea sediments and their responses to biogeochemical cycling, this study investigated microbial dynamics within the East Indian Ocean (EIO) ridge, focusing on vertical stratification of sediment communities. Notably, depth-related microbial patterns surpassed regional stratification effects. Environmental factors, such as TN and NO2–-N, significantly shaped community structures, while stochastic processes, particularly homogenizing dispersal, contributed to spatial similarity and structural stability. In this challenging environment, bacterial and archaeal communities established symbiotic relationships for enhanced survival, and dominated carbon and nitrogen biogeochemical cycling processes, respectively. Key bacterial genera acted as bridging agents, orchestrating intricate interactions, while archaeal communities displayed greater dispersion. Metabolic pathways analyses revealed that bacterial community was characterized by denitrification and DNRA processes, while archaea were dominated by the nirK-encoded denitrification pathway. Ultimately, this study shed light on nuanced interactions and ecological roles of microbial communities, contributed to broader understanding of biogeochemical processes and global carbon/nitrogen sinks.

Life cycle assessment of ammonium sulfate recovery from urban wastewater

ABSTRACT Anthropogenic nitrogen fluxes are profoundly altering the global biogeochemical nitrogen cycle. Better management of these nitrogen fluxes is essential. Recovering nitrogen from urban wastewater reduces both the energy and resources required to produce nitrogen-based fertilizer and to remove nitrogen from wastewater collected. Nitrogen can be recovered from wastewater in the form of ammonium sulfate, a common nitrogen-based fertilizer. In the urban setting, the technology can be applied to target source-separated urine or municipal wastewater. To assess the environmental sustainability of this approach, this study compared the life cycle environmental impacts of ammonium sulfate recovered from urban wastewater (through eight different recovery technology trains) and ammonium sulfate produced by six different industrial processes. The results show that wastewater-derived ammonium sulfate generally has lower potential environmental impacts than industrially produced ammonium sulfate in most of the impact categories assessed. The impact for the source-separated urine centralized recovery train is the smallest. The contribution analysis shows that energy, sulfuric acid and sodium hydroxide use are the major contributors, while the background inventory analysis shows that the results can be sensitive to the choice of region-specific background inventory. In the future, nitrogen recovery from urban wastewater is promising for the circular economy in cities.

Effects of biodegradable microplastics on arsenic migration and transformation in paddy soils: a comparative analysis with conventional microplastics

The combined pollution of microplastics (MPs) and arsenic (As) in paddy soils has attracted more attention worldwide. However, there are few comparative studies on the effects of biodegradable and conventional MPs on As migration and transformation. Therefore, conventional (polystyrene, polyethylene, polyvinyl chloride) and biodegradable (polybutadiene styrene, polylactic acid, polybutylene adipate terephthalate) MPs were selected to explore and demonstrate their influences and mechanism on As migration from paddy soils to overlying water and As speciation transformation through microcosmic experiment with measuring the changes of As chemical distribution, physicochemical indexes and microbial community in paddy soils. The results showed that biodegradable MPs enhanced As migration and transformation more effective than conventional MPs during 60 d. Biodegradable MPs indirectly increased the content of As(Ⅲ) and bioavailable As by changing the microbial community structure and affecting the biogeochemical cycles of carbon, nitrogen, sulfur and iron in soils, and promoted the As migration and transformation. PBS showed the strongest promoting effect, transforming to more As(Ⅲ) (11.43%) and bioavailable As (4.28%) than control. This helps to a better understanding of the effects of MPs on As biogeochemical cycle and to clarify the ecological and food safety risks of their combined pollution in soils.

Experimental simulation of thermal evolution of nitrogen content and isotopes in source rocks: Implications for nitrogen cycling characterization and oil-source correlation

Sedimentary nitrogen isotopes have been widely used to reconstruct the nitrogen cycling and redox characteristics of ancient oceans, but they also have important value in the study of oil genesis, such as oil classification. However, the thermal evolution of nitrogen isotopes in the source rock and associated oil is currently unclear. In this study, the thermal evolution (from the oil generation to the dry gas stage) of three types of low-maturity source rock was simulated. And the content and isotope composition of total organic carbon (TOC) and total nitrogen (TN) of the pyrolyzed source rock, expelled oil and retained oil were measured. In combination with weight-quantitative analyses, the following conclusions can be drawn: (1) During the main oil and gas generation stage, the pyrolyzed source rocks lost 15.1–28.3% of TN, which is much lower than the loss of TOC (26.2–46.1%). This difference may be related to the fact that the TOC content of the generated oil and gas is two orders of magnitude higher than the TN. In addition, TOC loss occurred mainly within the oil generation-expulsion stage, whereas TN loss occurred mainly in the dry gas stage and higher maturity stage. (2) The nitrogen isotope compositions of three types of source rocks and associated kerogens became heavier by 0.5–1.5‰ as thermal maturity increased, which is similar to the change of organic carbon isotope compositions. The δ15N values of pyrolyzed source rocks generally have poor relationships with either the amount of expelled oil and gas or the TN loss, which is different from the δ13Corg values. The δ15N fluctuations may be attributed to three processes: oil generation-expulsion, N2 gas generation-expulsion, and inorganic N (like NH4+) expulsion. The bulk nitrogen isotope composition of source rocks is only slightly affected by thermal maturity and can be used to indicate the nitrogen biogeochemical cycle and water redox conditions during the deposition. (3) Similar to δ13Corg values, δ15N values of both expelled oil and retained oil increased gradually with enhanced thermal maturity, implying a control of kinetic isotope effect. Among the three types of source rock, two of them having relatively light nitrogen isotope compositions (δ15N value of ∼2.5‰) generated and expelled oils with similar nitrogen isotope compositions, while the third type, which has heavy nitrogen isotope composition (δ15N value of ∼13.0‰), generated and expelled oils with much lighter nitrogen isotope compositions (by 3–6‰). This finding shows that there may be significant nitrogen isotope fractionation during the generation and primary migration of oil from source rocks. The nitrogen isotopes should be used in oil-source correlation with caution, even though related mechanisms need to be further studied. Nevertheless, using a combination of organic carbon and nitrogen isotopes, the oil generated and expelled by the three types of source rocks could be distinguished. Therefore, the use of nitrogen isotopes for oil-source correlation under geological conditions should be combined with other isotope and molecular indicators.

Uptake patterns for nitrogen and sulfur source by aquatic plants and various nitrogen acquisition strategies: Affected by mining activities

Understanding the nitrogen and sulfur uptake strategies of mine plants, including sources and preferences for nitrogen forms (ammonium nitrogen (NH4+) vs nitrate nitrogen (NO3−)), is critical to improving understanding of the role of plants in participating in the biogeochemical cycles of nitrogen and sulfur in mining areas. In this study, the stable N and S isotopic compositions of two species of aquatic plants (calamus and reed) in Linhuan mining area were analyzed to determine their absorption strategies for different nitrogen and sulfur sources. The results showed that river water was the largest source of nitrogen and sulfur, contributing 54.6% and 53.9% respectively. NO3− is the main form of nitrogen uptake by reed and calamus, followed by NH4+. In order to adapt to the change of nitrogen form in the environment, reed and calamus tend to absorb and utilize NO3− to maintain their absorption of nitrogen. Mine effluents from mining activities provide at least 12.9% and 16.8% sulfate to reed and calamus respectively, and the effect of mine effluents on reed and calamus sulfur has been underestimated. This study reveals the key factors controlling plant isotope composition, and the use of nitrogen and sulfur isotope composition of aquatic plants can help quantify the level of influence of mining activities, and understand the biogeochemical cycle of nitrogen and sulfur in mining areas.

Improved Method for Extracting Nitrites in Soil

Soil nitrite (NO2−) is an important reactive intermediate in many nitrogen transformation processes, but it is unstable under acidic conditions and may be lost as gaseous N. The canonical extraction method of soil NO2− using a potassium chloride (KCl) solution greatly underestimates its concentration. To reflect the concentration more accurately, we optimized the extraction method of soil NO2− for three agricultural soils differing in soil texture and pH, an alkalic fluvo-aquic soil and acidic Mollisol and Ultisol soils, respectively. Both extractable soil ammonium (NH4+) and nitrate (NO3−) were systematically investigated to optimize the simultaneous extraction of soil inorganic nitrogen. The effects of different extractants (deionized water (DIW), un-buffered 2 mol L−1 KCl, and pH-buffered 2 mol L−1 KCl), shaking time (10 and 30 min), and storage duration of the extracts (stored at −20 °C for 1 day, and at 4 °C for 1, 3, and 6 days) on the determination of soil inorganic nitrogen were investigated. The results showed that the un-buffered KCl extractant significantly underestimated soil NO2− concentration compared to DIW. The highest recovery of NO2− was obtained by extracting with DIW at 10 min of shaking for all three soils. Compared with DIW, the concentration of NH4+ and NO3− in soil extracted from the KCl solution increased significantly. Furthermore, the soil inorganic nitrogen content of extracts stored at 4 °C for one day was closer to the direct measurements of fresh samples than with the other storage methods. Overall, the recommended analysis method for soil NO2− was extraction by DIW, shaking for 10 min, and filtering with a 0.45 µm filter, while soil NH4+ and NO3− were extracted with a KCl solution and shaken for 30 min. The extract should be stored at 4 °C and analyzed within 24 h. Our study provides an efficient extraction method for soil NO2− and supports studies on the biogeochemical nitrogen cycle, e.g., in the investigation of soil nitrous acid (HONO) and nitric oxide (NO) emissions.

Pontiella agarivorans sp. nov., a novel marine anaerobic bacterium capable of degrading macroalgal polysaccharides and fixing nitrogen.

Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2T from microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2T represents a novel species within the Pontiella genus in the Kiritimatiellota phylum (within the PVC superphylum). Strain NLcol2T is able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases (nifDKH) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2T (= DSM 113125T = MCCC 1K08672T) is proposed to be the type strain of a novel species in the Pontiella genus, and the name Pontiella agarivorans sp. nov. is proposed.IMPORTANCEGrowth and intentional burial of marine macroalgae is being considered as a carbon dioxide reduction strategy but elicits concerns as to the fate and impacts of this macroalgal carbon in the ocean. Diverse heterotrophic microbial communities in the ocean specialize in these complex polymers such as carrageenan and fucoidan, for example, members of the Kiritimatiellota phylum. However, only four type strains within the phylum have been cultivated and characterized to date, and there is limited knowledge about the metabolic capabilities and functional roles of related organisms in the environment. The new isolate strain NLcol2T expands the known substrate range of this phylum and further reveals the ability to fix nitrogen during anaerobic growth on macroalgal polysaccharides, thereby informing the issue of macroalgal carbon disposal.

Activity-based labelling of ammonia- and alkane-oxidizing microorganisms including ammonia-oxidizing archaea.

Recently, an activity-based labelling protocol for the in vivo detection of ammonia- and alkane-oxidizing bacteria became available. This functional tagging technique enabled targeted studies of these environmentally widespread functional groups, but it failed to capture ammonia-oxidizing archaea (AOA). Since their first discovery, AOA have emerged as key players within the biogeochemical nitrogen cycle, but our knowledge regarding their distribution and abundance in natural and engineered ecosystems is mainly derived from PCR-based and metagenomic studies. Furthermore, the archaeal ammonia monooxygenase is distinctly different from its bacterial counterparts and remains poorly understood. Here, we report on the development of an activity-based labelling protocol for the fluorescent detection of all ammonia- and alkane-oxidizing prokaryotes, including AOA. In this protocol, 1,5-hexadiyne is used as inhibitor of ammonia and alkane oxidation and as bifunctional enzyme probe for the fluorescent labelling of cells via the Cu(I)-catalyzed alkyne-azide cycloaddition reaction. Besides efficient activity-based labelling of ammonia- and alkane-oxidizing microorganisms, this method can also be employed in combination with deconvolution microscopy for determining the subcellular localization of their ammonia- and alkane-oxidizing enzyme systems. Labelling of these enzymes in diverse ammonia- and alkane-oxidizing microorganisms allowed their visualization on the cytoplasmic membranes, the intracytoplasmic membrane stacks of ammonia- and methane-oxidizing bacteria, and, fascinatingly, on vesicle-like structures in one AOA species. The development of this novel activity-based labelling method for ammonia- and alkane-oxidizers will be a valuable addition to the expanding molecular toolbox available for research of nitrifying and alkane-oxidizing microorganisms.