Biogeochemical Cycles Of Nitrogen Research Articles

Contribution of trimethylamine N-oxide on the growth and pressure tolerance of deep-sea bacteria

Trimethylamine N-oxide (TMAO) is widely dispersed in marine environments and plays an important role in the biogeochemical cycle of nitrogen. Diverse marine bacteria utilize TMAO as carbon and nitrogen sources or as electron acceptor in anaerobic respiration. Alteration of respiratory component according to the pressure is a common trait of deep-sea bacteria. Deep-sea bacteria from different genera harbor high hydrostatic pressure (HHP) inducible TMAO reductases that are assumed to be constitutively expressed in the deep-sea piezosphere and facilitating quick reaction to TMAO released from fish which is a potential nutrient for bacterial growth. However, whether deep-sea bacteria universally employ this strategy remains unknown. In this study, 237 bacterial strains affiliated to 23 genera of Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria were isolated from seawater, sediment or amphipods collected at different depths. The pressure tolerance and the utilization of TMAO were examined in 74 strains. The results demonstrated no apparent correlation between the depth where the bacteria inhabit and their pressure tolerance, regarding to our samples. Several deep-sea strains from the genera of Alteromonas, Halomonas, Marinobacter, Photobacterium, and Vibrio showed capacity of TMAO utilization, but none of the isolated Acinebacter, Bacillus, Brevundimonas, Muricauda, Novosphingobium, Rheinheimera, Sphingobium and Stenotrophomonas did, indicating the utilization of TMAO is a species-specific feature. Furthermore, we noticed that the ability of TMAO utilization varied among strains of the same species. TMAO has greater impact on the growth of deep-sea isolates of Vibrio neocaledonicus than shallow-water isolates. Taken together, the results describe for the first time the TMAO utilization in deep-sea bacterial strains, and expand our understanding of the physiological characteristic of marine bacteria.

Responses of soil microbial biomass, diversity and metabolic activity to biochar applications in managed poplar plantations on reclaimed coastal saline soil

AbstractWith its relatively high stability, biochar has been suggested as a means to mitigate climate change through carbon fixation and improve the physicochemical properties of soils. However, our understanding of the effects of biochar on soil microbial diversity and their metabolic activity remain unclear. In order to elucidate how the application of biochar to plantation soils influences microbial biomass and functional diversity (using Biolog EcoPlatesTM), we conducted an experiment to investigate changes in soil microbial communities at four biochar levels (0, 40, 80 and 120 Mg/ha). We found that biochar application altered the metabolic patterns of microbial communities and accelerated the utilization of amino acids, carboxylic acids, polymers and other miscellaneous plant chemical compounds by microbes. Moreover, compared to the control, soil pH increased by 0.23, 0.24, 0.28 units and microbial biomass carbon to nitrogen ratio (MBC/MBN) by 9.20, 20.99 and 17.74, respectively. Meanwhile, soil moisture decreased from 25.7 to 23.8%, 23.7 and 24.4%, and MBN declined by 42.2, 46.2 and 53.8%. Regression analysis showed that soil pH was the primary factor correlated with reduced MBN. Community physiological profiles revealed that high concentrated biochar (120 Mg/ha) elevated microbial metabolic activity, while biochar application did not alter microbial functional diversity represented by the Shannon diversity index (H′) and evenness (E). Furthermore, the application of biochar would affect biogeochemical cycling of carbon and nitrogen through the elevated microbial activity and utilization in different categories of carbon sources (polymers, carboxylic acids etc.) with the reduced MBN.

Abundance, contribution, and possible driver of ammonia-oxidizing archaea (AOA) in various types of aquatic ecosystems

In some habitats, ammonia oxidation highly depends on the activity of ammonia-oxidizing archaea (AOA), which are therefore important for studying biogeochemical nitrogen cycling. However, the behavior and distribution of AOA in aquatic ecosystems are not well characterized, especially on a global scale. We sampled 66 sites across all five continents to analyze the global abundance of AOA. Ammonium oxidation rates were measured using the dicyandiamide (DCD) and octyne inhibition method to separately evaluate the contributions of AOA to ammonium oxidation. High-throughput pyrosequencing and phylogenetic analysis were applied to study AOA community compositions, combined with DNA-stable isotope probing (DNA-SIP). The archaeal amoA gene was widespread and abundant across all aquatic ecosystem types. The average abundance was 3.59 × 108 copies g−1, with the highest values in lake samples and the lowest in river samples. The AOA abundance was influenced by pH. Archaeal ammonia oxidation rates were 0.81 ± 0.45 mg (NO3−-N) kg−1 day−1, corresponding to 63.75% of the total ammonia oxidation rate. Pyrosequencing analysis showed that the AOA community was dominated by the Group I.1b lineage (65.8%). Candidatus Nitrosocosmicus franklandus showed the highest positive correlation with archaeal ammonium oxidation rates and had the highest carbon use efficiency. Abundance, activity, and community composition of AOA were highly heterogeneous. pH negatively impacted the abundance of the archaeal amoA functional gene. AOA were the main ammonia oxidators in aquatic ecosystems. Ca. N. franklandus was found to dominate archaeal ammonium oxidation.

Spatial variability in dissolved iron concentrations in the marginal and open waters of the Indian Ocean

We analyzed 28 full vertical profiles of dissolved iron (DFe) in the Indian Ocean (i.e., between 26°S – 20°N and 72°E – 105°E) during two research expeditions (SK-304: March–May 2013, SK-311: March–April 2014) as part of the GEOTRACES-India programme. Relatively high DFe concentrations in surface waters (≤10 m) were observed in the Arabian Sea (AS: 0.68 ± 0.03 nM, n = 2) and the Bay of Bengal (BoB: 0.44 ± 0.11 nM, n = 21) compared to the stations located south of the equator (0.27 ± 0.16 nM, n = 17). Higher DFe in the coastal stations is presumably sourced from the continental shelves. Depth profiles of DFe in the AS, BoB and Andaman Sea showed sub-surface maxima, coinciding with low dissolved oxygen (DO) concentrations. High DFe concentrations in sub-surface waters of the BoB and the Andaman Sea are attributed to desorption of soluble iron from resuspended sediments of the rivers and the remineralization of sinking particulate organic matter. We also observed a significant contribution of DFe from hydrothermal vents situated at the Central Indian ridge and subduction processes along the Java trench to pelagic waters of the Indian Ocean. Fe:C remineralization ratios of 3.92 ± 0.83, 5.88 ± 2.65, 8.96 ± 3.85 and 5.74 ± 3.06 μmol/ mol were observed in the Indian Ocean, BoB, AS and Andaman Sea, respectively. To assess the surface areas and deep water masses where DFe concentrations potentially limit phytoplankton growth (when reaching the surface) we subtracted the contribution of particulate organic matter remineralization to the DFe pool using the tracer Fe* (≈DFe–RFe:P(Phosphate)). Positive Fe* values in the intermediate waters suggest an external source for DFe, whereas negative Fe* values suggest the absence of such external inputs and/or removal by scavenging processes. Our results contribute to improved understanding of DFe distributions and their coupling with the ocean biogeochemical cycling of carbon and nitrogen in this region.

Response of Chromophoric Dissolved Organic Matter Composition to Different Hydrological Scenarios in Large Eutrophic Lake Taihu

Chromophoric dissolved organic matter (CDOM) is a fraction of dissolved organic matter that can strongly absorb light in the ultraviolet and blue regions and plays an important role in the biogeochemical cycling of carbon, nitrogen, and phosphorus. Unraveling the sources, optical composition, and corresponding spatial variabilities of CDOM can improve our understanding of carbon, nitrogen, and phosphorus cycling in lakes and lake water quality management. CDOM spectral absorption and fluorescent excitation-emission matrices were measured to investigate the compositional dynamics of CDOM under different hydrological scenarios. Our results showed that the mean value of dissolved organic carbon (DOC) concentration of (8.11±1.26) mg·L-1 in the rainy season was significantly higher than that in the dry season (3.53±1.19) mg·L-1 (t-test, P<0.01), whereas the mean spectral slope S275-295 of (20.89±1.90) μm-1 in the dry season was significantly greater than that in the rainy season (19.09±1.81) μm-1 (t-test, P<0.001). Three fluorescent components were identified using parallel factor analysis, and we further found that the dynamics of the three CDOM components were strongly influenced by hydrological conditions. Fluorescence intensity (Fmax) of the terrestrial humic-rich component C2 increased with increasing water levels and rainfall. Significant negative relationships were found between all three fluorescent components and dissolved oxygen (P<0.01), suggesting that all three components served as important substrates for microbial processing. Significant positive relationships were found between the terrestrial humic-rich C2 and tryptophan-like C1 and chlorophyll-a and chemical oxygen demand, indicating that anthropogenic inputs and algal degradation contributed significantly to the CDOM pool in Lake Taihu. We further found a significant positive relationship between DOC concentration and Fmax of terrestrial humic-rich C2 (r2=0.58, P<0.001), suggesting that DOC in Lake Taihu was primarily derived from allochthonous input.

Molecular weight fractionated characterization of dissolved organic matter and its correlation with water quality in the Bahe River Basin, Northwest China

Dissolved organic matter (DOM) is one of the core carriers of organic matter decomposition and nutrient regeneration in water. It is an important link of biogeochemical cycle of carbon and nitrogen, and the key content of water environmental science research. We used liquid chromatography-organic carbon detection-organic nitrogen detection (LC-OCD-OND) to investigate the molecular weight distribution of riverine DOM in the Bahe River of Xi'an City and further analyzed its correlation with water quality. The results showed that riverine DOM was composed of biopolymers, humic substances, humus degradation products, and low molecular-weight neutrals, with the ave-rage concentration of 0.15, 1.75, 0.48, 0.36 and 0.002 mg·L-1, respectively. The DOM along the river was in order of urban＞ town＞ river source. The humic substances with molecular weight of 1000-20000 Da accounted for 49.0% of total DOM which followed the order of town＞ waste water treatment plants (WWTPs) effluents＞river estuary＞ river source. The biopolymers with the molecular weight of >20000Da accounted for 5.1% of total DOM, with the sequence of WWTPs effluents＞river estuary＞river source＞town. The allochthonous (terrigenous) DOM produced by WWTPs effluents had the greatest contribution to the riverine DOM. The fractions of DOM with different molecular weights had significant correlations with water quality parameters. The results showed that the molecular weight fractions and abundance of DOM based on LC-OCD-OND could be used as a comprehensive index for water quality monitoring, to characterize the spatial heterogeneity of river water quality, and used for quantitative identification and source apportionment of pollutant components.

Trade-offs between soil carbon sequestration and reactive nitrogen losses under straw return in global agroecosystems.

It is widely recommended that crop straw be returned to croplands to maintain or increase soil carbon (C) storage in arable soils. However, because C and nitrogen (N) biogeochemical cycles are closely coupled, straw return may also affect soil reactive N (Nr) losses, but these effects remain uncertain, especially in terms of the interactions between soil C sequestration and Nr losses under straw addition. Here, we conducted a global meta-analysis using 363 publications to assess the overall effects of straw return on soil Nr losses, C sequestration and crop productivity in agroecosystems. Our results show that on average, compared to mineral N fertilization, straw return with same amount of mineral N fertilizer significantly increased soil organic C (SOC) content (14.9%), crop yield (5.1%), and crop N uptake (10.9%). Moreover, Nr losses in the form of nitrous oxide (N2 O) emissions from rice paddies (17.3%), N leaching (8.7%), and runoff (25.6%) were significantly reduced, mainly due to enhanced microbial N immobilization. However, N2 O emissions from upland fields (21.5%) and ammonia (NH3 ) emissions (17.0%) significantly increased following straw return, mainly due to the stimulation of nitrification/denitrification and soil urease activity. The increase in NH3 and N2 O emissions was significantly and negatively correlated with straw C/N ratio and soil clay content. Regarding the interactions between C sequestration and Nr losses, the increase in SOC content following straw return was significantly and positively correlated with the decrease in N leaching and runoff. However, at a global scale, straw return increased net Nr losses from both rice and upland fields due to a greater stimulation of NH3 emissions than the reduction in N leaching and runoff. The trade-offs between increased net Nr losses and soil C sequestration highlight the importance of reasonably managing straw return to soils to limit NH3 emissions without decreasing associated C sequestration potential.

The mass impacts on chemosynthetic primary producers: potential implications on anammox communities and their consequences

AbstractThe potential of a mass asteroid impact on Earth to disturb the chemosynthetic communities at global scale is discussed. Special emphasis is made on the potential influence on anammox communities and their implications in the nitrogen biogeochemical cycle. According to our preliminary estimates, anammox communities could be seriously affected as a consequence of global cooling and the large process of acidification usually associated with the occurrence of this kind of event. The scale of affectations could vary in a scenario like the Chicxulub as a function of the amount of soot, depth of the water column and the deposition rate for sulphates assumed in each case. The most severe affectations take place where the amount of soot and sulphates produced during the event is higher and the scale of time of settlements for sulphates is short, of the order of 10 h. In this extreme case, the activity of anammox is considerably reduced, a condition that may persist for several years after the impact. Furthermore, the impact of high levels of other chemical compounds like sulphates and nitrates associated with the occurrence of this kind of event are also discussed.

The Trichodesmium microbiome can modulate host N2 fixation

Abstract Trichodesmium is a marine, diazotrophic cyanobacterium that plays a central role in the biogeochemical cycling of carbon and nitrogen. Colonies ubiquitously co‐occur with a diverse microbiome of heterotrophic bacteria. We show that manipulation of the microbiome with quorum sensing acyl homoserine lactones (AHLs) significantly modulated rates of N2 fixation by Trichodesmium collected from the western North Atlantic, with positive and negative effects of varied magnitude. Changes in Trichodesmium N2 fixation did not correlate with changes in microbiome composition or geochemistry. With AHL addition, a subset of the significantly differentially expressed genes was related to known quorum sensing responses in model bacteria. However, there was little overlap in specific microbiome transcriptional responses to AHL addition between stations. Overall, these host‐microbiome interactions reflect a complex interplay of biotic and environmental factors that together form an overlooked mechanism modulating Trichodesmium N2 fixation.

Effect of ecological and conventional managements on soil enzymatic activities in coffee agroecosystems

ABSTRACT Understanding the impacts of agricultural practices on soil quality indicators, such as enzymatic activities, is of great importance, in order to advance in their diagnosis and sustainable management. This study aimed to evaluate the effect of ecological and conventional agricultural managements on enzymatic activities of a soil under coffee agroecosystems. The enzymatic activities were associated with the biogeochemical cycles of nitrogen (urease and protease), phosphorus (acid and alkaline phosphatase) and carbon (β-glucosidase), during the rainy and dry seasons. Physical-chemical soil proprieties were also assessed and related to resilience scores linked to the climatic variability reported for the areas under study. The activities of urease, alkaline and acid phosphatase and ß-glucosidase were statistically higher in ecological agroecosystems than in conventional ones. This may be attributed to the greater application of organic waste in the ecological environment, as well as to the absence of pesticides and synthetic fertilizers, which allow better conditions for the microbial activity. The resilience scores to the climate variability that showed the highest correlations with the assessed enzymatic activities were: the farmers' knowledge on soil microorganisms, non-use of pesticides and synthetic fertilizers and non-dependence on external supplies. It was concluded that the enzymatic activities are modified by the management systems, being specifically favored by the ecological management. This agroecosystem, in the long term, ensures an efficient use of the soil resources, with a lower degradation and contamination.

Newly designed primer pair revealed dominant and diverse comammox amoA gene in full-scale wastewater treatment plants

The discovery of complete ammonia oxidizing bacteria (CAOB) capable of performing the two-step nitrification process on their own has fundamentally upended our traditional perception. However, their environmental distribution and ecological significance in driving ammonia oxidation are still urgently awaited to be assessed. In this study, the diversity and abundance of CAOB amoA gene in wastewater treatment plants (WWTPs) were presented taking advantage of a newly designed primer pair specifically targeting CAOB amoA gene. Phylogenetic results demonstrated the novel amoA gene formed a clearly distinct cluster from the canonical amoA and pmoA genes. Among the five well-supported sub-clusters, Nitrospira nitrosa cluster accounted for 94.34% of all the currently retrieved sequences from WWTPs. More importantly, qPCR results demonstrated a remarkably high abundance of CAOB amoA gene, which were up to 182.7-fold more abundant than AOB amoA gene. This study provided new dimension and fundamental basis for future researches towards biogeochemical nitrogen cycle.

Isotopic biogeochemical indicators of evapotranspiration and nitrogen flows in a check‐dam catchment in the Loess Plateau, China

AbstractThe increasingly fragile environment and associative nitrogen (N) biogeochemical cycle have become critical environmental and ecological issues in China's Loess Plateau. However, N flow and N source for typical catchments remain poorly understood in the Loess Plateau. In this study, we measured concentrations and isotopic signatures of N, hydrogen (H), and oxygen (O) in both rainfall and river water. Results showed that baseflow variation in total nitrogen (TN) concentrations ranged from 0.16 to 32.70 mg L−1. The monthly TN deposition flux and monthly TN wet deposition concentration to river water were shown significant variations between rainy and dry seasons. The range of variation in δ2H values for rainfall and baseflow was from −90.0‰ to 19.8‰ and from −67.2‰ to −38.4‰, respectively, whereas δ18O–H2O values ranged from −12.1‰ to +2.7‰ and from −9.3‰ to −3.6‰, respectively. The Local Meteoric Water Line in the check‐dam catchment was δ2H = 7.35 δ18O + 2.29 (R2 = 0.93). Furthermore, NO3− δ15N and δ18O values in baseflow ranged from −2.0‰ to +20.5‰ and from +8.0‰ to +15.6‰, respectively. The results indicated that rainfall was affected by below‐cloud secondary evaporation and caused strong isotopic kinetic fractionation to occur during the precipitation process. The NO3− in runoff was mainly derived from the nitrification of soil organic matter and manure or sewage, for which the proportion of manure or sewage was from 50.5% to 83%.

On the Properties of the Arctic Halocline and Deep Water Masses of the Canada Basin from Nitrate Isotope Ratios

AbstractNitrogen is a limiting nutrient for primary production in the western Arctic Ocean. Measurements of the nitrogen (15N/14N) and oxygen (18O/16O) isotope ratios of nitrate in the southeastern Beaufort Sea provide insight into biogeochemical cycling of nitrogen in the western Arctic Ocean. Nitrate O isotope ratios in the Pacific halocline evidence a highly regenerated reservoir. Coincident peaks in nutrient concentrations and reduced dissolved oxygen concentrations suggest that nitrate accrues from organic matter remineralization in bottom waters of the Chukchi shelf and that these ventilate the basin predominantly in summer, when isolated from the atmosphere. Preformed nitrate in Pacific Winter Water lacks 18O/16O elevation from nitrate assimilation, contrasting with preformed nitrate in other ocean regions. A reactive N deficit and elevated nitrate N isotope ratios in the Pacific halocline further indicate substantial N loss to coupled nitrification‐denitrification in shelf sediments upstream. In the Atlantic Water below, nitrate isotope ratios identify two distinct waters entering the Arctic at Fram Strait, from (1) the surface West Spitsbergen Current, bearing isotopic signatures akin to North Atlantic waters, and (2) deeper inflows of waters ventilated in the Nordic Seas, transporting nitrate O isotope ratios indicative of regenerated nitrate. Poorly ventilated Canada Basin Deep Water shows evidence of nominal accrual of remineralized products, and nitrate isotope ratios suggest an influence of slow benthic denitrification on the sea floor. The observations reveal that shelf processes have a disproportionate influence on tracer properties of the Pacific halocline, while those in Atlantic Water are dominated by processes in the Nordic Seas.

Effect of Soil pH on Composition and Abundance of Nitrite-oxidising Bacteria

Nitrification, the microbial oxidation of ammonia to nitrate (NO3-) via nitrite (NO2-) is a vital process in the biogeochemical nitrogen cycle and is performed by two distinct functional groups; ammonia oxidisers [comprised of ammonia oxidising bacteria (AOB) and ammonia oxidising archaea (AOA)] and nitrite oxidising bacteria. Autotrophic nitrification is said to occur in acidic soils, even though most laboratory cultures of isolated ammonia and nitrite oxidising bacteria fail to grow below neutral pH. Published studies revealed that soil pH is a major driver for determining the distribution and abundance of AOB and AOA. To determine whether distinct populations of nitrite oxidising bacteria within the lineages of Nitrospira and Nitrobacter are adapted to a particular range of pH as observed in ammonia oxidising organisms, the community structure of Nitrospira-like and Nitrobacter-like NOB were determined across a pH gradient (4.5 – 7.5) by amplifying nitrite oxidoreductase (nxrA) and 16S rRNA genes followed by denaturing gradient gel electrophoresis (DGGE). The community structure of both Nitrospira and Nitrobacter changed with soil pH, with distinct populations observed in acidic and neutral soils. The abundance of Nitrospira-like 16S rRNA and Nitrobacter-like nxrA gene copies contrasted across the pH gradient. Nitrobacter-like nxrA gene abundance decreased with increasing soil pH, whereas Nitrospira-like 16S rRNA gene abundance increased with increasing pH. Nitrification activity of both Nitrospira-like and Nitrobacter-like NOB in acidic and neutral pH soil was investigated in a microcosm experiment incubated at 30 oC for 21 days, with high rates of nitrification observed in both soils. Findings indicated that abundance and distributions of soil NOB is influence by soil pH.

Agulhas Current properties shape microbial community diversity and potential functionality

Understanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas Current system and the Subtropical Front in the South Indian Ocean (SIO). Samples collected from the epipelagic, oxygen minimum and bathypelagic zones were analysed by 16S rRNA gene amplicon and metagenomic sequencing. In contrast to previous studies, we found high taxonomic richness in surface and deep water samples, but generally low richness for OMZ communities. Beta-diversity analysis revealed significant dissimilarity between the three water depths. Most microbial communities were dominated by marine Gammaproteobacteria, with strikingly low levels of picocyanobacteria. Community composition was strongly influenced by specific environmental factors including depth, salinity, and the availability of both oxygen and light. Carbon, nitrogen and sulfur cycling capacity in the SIO was linked to several autotrophic and copiotrophic Alphaproteobacteria and Gammaproteobacteria. Taken together, our data suggest that the environmental conditions in the Agulhas Current system, particularly depth-related parameters, substantially influence microbial community structure. In addition, the capacity for biogeochemical cycling of nitrogen and sulfur is linked primarily to the dominant Gammaproteobacteria taxa, whereas ecologically rare taxa drive carbon cycling.

Characterization of the First "Candidatus Nitrotoga" Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria.

ABSTRACTNitrification is a key process of the biogeochemical nitrogen cycle and of biological wastewater treatment. The second step, nitrite oxidation to nitrate, is catalyzed by phylogenetically diverse, chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Uncultured NOB from the genus “Candidatus Nitrotoga” are widespread in natural and engineered ecosystems. Knowledge about their biology is sparse, because no genomic information and no pure “Ca. Nitrotoga” culture was available. Here we obtained the first “Ca. Nitrotoga” isolate from activated sludge. This organism, “Candidatus Nitrotoga fabula,” prefers higher temperatures (>20°C; optimum, 24 to 28°C) than previous “Ca. Nitrotoga” enrichments, which were described as cold-adapted NOB. “Ca. Nitrotoga fabula” also showed an unusually high tolerance to nitrite (activity at 30 mM NO2−) and nitrate (up to 25 mM NO3−). Nitrite oxidation followed Michaelis-Menten kinetics, with an apparent Km (Km(app)) of ~89 µM nitrite and a Vmax of ~28 µmol of nitrite per mg of protein per h. Key metabolic pathways of “Ca. Nitrotoga fabula” were reconstructed from the closed genome. “Ca. Nitrotoga fabula” possesses a new type of periplasmic nitrite oxidoreductase belonging to a lineage of mostly uncharacterized proteins. This novel enzyme indicates (i) separate evolution of nitrite oxidation in “Ca. Nitrotoga” and other NOB, (ii) the possible existence of phylogenetically diverse, unrecognized NOB, and (iii) together with new metagenomic data, the potential existence of nitrite-oxidizing archaea. For carbon fixation, “Ca. Nitrotoga fabula” uses the Calvin-Benson-Bassham cycle. It also carries genes encoding complete pathways for hydrogen and sulfite oxidation, suggesting that alternative energy metabolisms enable “Ca. Nitrotoga fabula” to survive nitrite depletion and colonize new niches.

Microbially mediated nitrate-reducing Fe(II) oxidation: Quantification of chemodenitrification and biological reactions

Abstract Redox reactions between iron and nitrogen drive the global biogeochemical cycles of these two elements and, concomitantly, change the fate of nutrients in and the mineralogy of the cycles. The microbially mediated NO3−-reducing Fe(II) oxidation process (NRFO) plays a key role in Fe/N interactions under neutral-anoxic conditions. Microbially mediated NRFO was considered a biological process, yet recently it has been documented that chemical mechanisms are also at play. However, the relative contributions of biological processes and chemical processes to Fe(II) oxidation remain largely unquantified owing to the co-occurrence of the reactions. Herein, the kinetics and secondary minerals of microbially mediated NRFO by Pseudogulbenkiania sp. strain 2002 and Acidovorax sp. strain BoFeN1 were investigated with acetate as electron donor unless otherwise stated. The results of Cells + NO3− suggested the two strains could biologically reduce NO3− to NO3−/NOx/N2O/N2 and concomitantly oxidize acetate and result in cell growth. Fe(II) oxidation and NO3− reduction occurred simultaneously in the presence of Fe(II) (Cells + Fe(II) + NO3−). For strain BoFeN1, the presence of Fe(II) slightly enhanced the NO3− reduction, acetate consumption, and cell growth, all of which were substantially retarded by Fe(II) for strain 2002. When compared with the microbial nitrite reduction, the relatively higher rate of chemical reaction between NO2− and dissolved Fe(II) confirmed the occurrence of chemodenitrification in the microbially mediated NRFO processes. After 5 days’ incubation, no green rust was observed, and lepidocrocite, goethite, and magnetite were observed with the Cells + Fe(II) + NO3− treatment, but only goethite was found with the Fe(II) + NO2−. The spectra for the EPSs + Fe(II) treatment suggested that the oxidized c-Cyts in the EPSs could oxidize Fe(II), which show the theoretical capability of taking electrons from Fe(II) into the cells via c-Cyts. A brief model was established by combining the verified reactions of (1) biological reduction of NO3− to NO2−/NOx/N2O/N2, (2) Fe(II) oxidation by NO2−, and (3) Fe(II) oxidation by c-Cyts in EPSs. Based on the model, the rate constant of Fe(II) oxidation by c-Cyts in EPSs was derived. For nitrite reduction, the relative contribution of biological processes to the nitrite reduction was higher than that of chemodenitrification. For Fe(II) oxidation, the relative contribution of the chemical process via nitrite to Fe(II) oxidation was higher than that of biological processes. These findings provide a quantitative interpretation of the chemodenitrification and biological reactions in the microbially mediated NRFO processes, which could assist the mechanistic understanding of the global biogeochemical cycles of iron and nitrogen in subsurface environments.

Response of Atmospheric Nitrogen Deposition to Different Ecosystems

Atmospheric nitrogen deposition is one of the most important elements in nitrogen biogeochemical cycles. It is not only one of the major processes for removing nitrogenous pollutants in the air, but also an important way for the ecosystem to obtain nitrogen from the atmosphere. In recent years, due to the combustion of minerals, the use of chemical fertilizers and the rapid development of livestock husbandry, human activities have led to the continuous increase of atmospheric active nitrogen concentration, which has aroused widespread concern of all parties. This paper introduces the types and sources of atmospheric nitrogen deposition and focuses on the response of atmospheric nitrogen deposition to different ecosystems.

Possible nitrogen fertilization of the early Earth Ocean by microbial continental ecosystems

While significant efforts have been invested in reconstructing the early evolution of the Earth’s atmosphere–ocean–biosphere biogeochemical nitrogen cycle, the potential role of an early continental contribution by a terrestrial, microbial phototrophic biosphere has been largely overlooked. By transposing to the Archean nitrogen fluxes of modern topsoil communities known as biological soil crusts (terrestrial analogs of microbial mats), whose ancestors might have existed as far back as 3.2 Ga ago, we show that they could have impacted the evolution of the nitrogen cycle early on. We calculate that the net output of inorganic nitrogen reaching the Precambrian hydrogeological system could have been of the same order of magnitude as that of modern continents for a range of inhabited area as small as a few percent of that of present day continents. This contradicts the assumption that before the Great Oxidation Event, marine and continental biogeochemical nitrogen cycles were disconnected.

Improvement of Ni phytoextraction by Alyssum murale and its rhizosphere microbial activities by applying nitrogen fertilizer

AbstractPhytoextraction represents an innovative approach in the management of nickel (Ni) rich soils whether natural (ultramafic) or anthropogenic (contaminated sites). However, its success depends both on the production of a high plant biomass and the ability of plants to accumulate metals. The application of nitrogen (N) fertilizer can improve the biological and chemical soil fertility and thus agricultural yields. Moreover, soil microorganisms play a key role by influencing nutrient flows, which are the main limiting factors of plant growth in degraded soils. In this work, we investigated the effects of two levels of both Ni and mineral N soil applications on the microbial activities and Ni phytoextraction efficiency by Alyssum murale growing in a pot experiment during 5 months. Plant growth, nutrients and Ni uptake, soil microbial populations and their enzymatic activities involved in the biogeochemical cycles of nitrogen, phosphorus, carbon and sulfur (urease, alkaline phosphatase, β‐glucosidase and arylsulfatase, respectively) were determined. The results showed that plant dry mass was unsurprisingly not affected when the soil Ni concentration was increased. However, it led to an increase of the amount of Ni extracted per pot. A negative effect of Ni addition was observed on both total bacteria and urease activity, without any effect on other enzymes. On the contrary, N fertilizer played a significant positive role by promoting both plant growth and Ni phytoextraction, partly as a result of the stimulation and flourishing of bacterial populations.