The Evolution Pathway of Ammonia-Oxidizing Archaea Shaped by Major Geological Events

Primordial nitrification processes have been studied extensively using geochemical approaches, but the biological origination of nitrification remains unclear. Ammonia-oxidizing archaea (AOA) are widely distributed nitrifiers and implement the rate-limiting step in nitrification. They are hypothesized to have been important players in the global nitrogen cycle in Earth’s early history. We performed systematic phylogenomic and marker gene analyses to elucidate the diversification timeline of AOA evolution. Our results suggested that the AOA ancestor experienced terrestrial geothermal environments at ∼1,165 Ma (1,928–880 Ma), and gradually evolved into mesophilic soil at ∼652 Ma (767–554 Ma) before diversifying into marine settings at ∼509 Ma (629–412 Ma) and later into shallow and deep oceans, respectively. Corroborated by geochemical evidence and modeling, the timing of key diversification nodes can be linked to the global magmatism and glaciation associated with the assembly and breakup of the supercontinent Rodinia, and the later oxygenation of the deep ocean. Results of this integrated study shed light on the geological forces that may have shaped the evolutionary pathways of the AOA, which played an important role in the ancient global nitrogen cycle.     

Cd1-型亚硝酸盐还原酶脱氮工程菌的构建与表达

目的用基因工程技术将铜绿假单胞菌PAO1中nirS基因定向克隆至表达载体pQE-30上,使nirS基因得到高效表达。方法根据GenBank公布的nirS碱基序列和表达载体pQE-30的多克隆位点设计引物,以铜绿假单胞菌PAO1的基因组DNA为模板,应用PCR技术扩增目的片段nirS;之后经过BamH I和HindⅢ双酶切,定向克隆到pQE-30上,化学转化DH5α,构建含有重组质粒的转化子pQE30-nirS-DH5α;经酶切和测序鉴定,扩增产物的碱基序列与GenBank公布的序列完全吻合,再将重组质粒pQE30-nirS转化表达菌株SG13009构建脱氮基因工程菌pQE30-nirS-SG-13009（PNS）。最后用SDS-PAGE（IPTG浓度：0．05mmol／L;诱导温度：25℃;诱导时间：2～3h）和His-tag in-gel Stain鉴定cd1-型亚硝酸盐还原酶的分子量与特异性。结果构建了高效表达cd1-型亚硝酸盐还原酶的脱氮基因工程菌PNS。结论Cd1-型亚硝酸盐还原酶能够在脱氮基因工程菌PNS中得到正确和高效的表达。     

Changes in nitrogen cycling and retention processes in soils under spruce forests along a nitrogen enrichment gradient in Germany

A network of long-term monitoring sites on nitrogen (N) input and output of forests across Germany showed that a number of Germany's forests are subject to or are experiencing N saturation and that spruce (Picea abies) stands have high risk. Our study was aimed at (1) quantifying the changes in gross rates of microbial N cycling and retention processes in forest soils along an N enrichment gradient and (2) relating the changes in soil N dynamics to N losses. We selected spruce sites representing an N enrichment gradient (indicated by leaching : throughfall N ratios) ranging from 0.04–0.13 (low N),≤0.26 (intermediate N enrichment) to≥0.42 (highly N enriched). To our knowledge, our study is the first to report on mechanistic changes in gross rates of soil N cycling and abiotic NO₃⁻ retention under ambient N enrichment gradient. Gross N mineralization, NH₄⁺ immobilization, gross nitrification, and NO₃⁻ immobilization rates increased up to intermediate N enrichment level and somewhat decreased at highly N-enriched condition. The turnover rates of NH₄⁺ and microbial N pools increased while the turnover rates of the NO₃⁻ pool decreased across the N enrichment gradient. Abiotic immobilization of NH₄⁺ did not differ across sites and was lower than that of NO₃⁻. Abiotic NO₃⁻ immobilization decreased across the N enrichment gradient. Microbial assimilation and turnover appeared to contribute largely to the retention of NH₄⁺. The increasing NO₃⁻ deposition and decreasing turnover rates of the NO₃⁻ pool, combined with decreasing abiotic NO₃⁻ retention, possibly contributed to increasing NO₃⁻ leaching and gaseous emissions across the N enrichment gradient. The empirical relationships of changes in microbial N cycling across the N enrichment gradient may be integrated in models used to predict responses of forest ecosystems (e.g. spruce) to increasing N deposition.     

Soils,a sink for N2O? A review

Soils are the main sources of the greenhouse gas nitrous oxide (N₂O). The N₂O emission at the soil surface is the result of production and consumption processes. So far, research has concentrated on net N₂O production. However, in the literature, there are numerous reports of net negative fluxes of N₂O, (i.e. fluxes from the atmosphere to the soil). Such fluxes are frequent and substantial and cannot simply be dismissed as experimental noise.
Net N₂O consumption has been measured under various conditions from the tropics to temperate areas, in natural and agricultural systems. Low mineral N and large moisture contents have sometimes been found to favour N₂O consumption. This fits in with denitrification as the responsible process, reducing N₂O to N₂. However, it has also been reported that nitrifiers consume N₂O in nitrifier denitrification. A contribution of various processes could explain the wide range of conditions found to allow N₂O consumption, ranging from low to high temperatures, wet to dry soils, and fertilized to unfertilized plots. Generally, conditions interfering with N₂O diffusion in the soil seem to enhance N₂O consumption. However, the factors regulating N₂O consumption are not yet well understood and merit further study.
Frequent literature reports of net N₂O consumption suggest that a soil sink could help account for the current imbalance in estimated global budgets of N₂O. Therefore, a systematic investigation into N₂O consumption is necessary. This should concentrate on the organisms, reactions, and environmental factors involved.     

Comparison of measured and EF5-r-derived N2O fluxes from a spring-fed river

There is considerable uncertainty in the estimates of indirect N₂O emissions as defined by the Intergovernmental Panel on Climate Change's (IPCC) methodology. Direct measurements of N₂O yields and fluxes in aquatic river environments are sparse and more data are required to determine the role that rivers play in the global N₂O budget. The objectives of this research were to measure the N₂O fluxes from a spring‐fed river, relate these fluxes to the dissolved N₂O concentrations and NO₃‐N loading of the river, and to try to define the indirect emission factor (EF5‐r) for the river. Gas bubble ebullition was observed at the river source with bubbles containing 7.9 μL N₂O L^?1. River NO₃‐N and dissolved N₂O concentrations ranged from 2.5 to 5.3 mg L^?1 and 0.4 to 1.9 μg N₂O‐N L^?1, respectively, with N₂O saturation reaching 404%. Floating headspace chambers were used to sample N₂O fluxes. N₂O‐N fluxes were significantly related to dissolved N₂O‐N concentrations (r²=0.31) but not to NO₃‐N concentrations. The N₂O‐N fluxes ranged from 38 to 501 μg m^?2 h^?1, averaging 171 μg m^?2 h^?1 (±SD 85) overall. The measured N₂O‐N fluxes equated to an EF5‐r of only 6.6% of that calculated using the IPCC methodology, and this itself was considered to be an overestimate because of the degassing of antecedent dissolved N₂O present in the groundwater that fed the river.     

Nitrogen Dynamics in Ice Storm-Damaged Forest Ecosystems: Implications for Nitrogen Limitation Theory

Despite the widely recognized importance of disturbance in accelerating the loss of elements from land, there have been few empirical studies of the effects of natural disturbances on nitrogen (N) dynamics in forest ecosystems. We were provided the unusual opportunity for such study, partly because the intensively monitored watersheds at the Hubbard Brook Experimental Forest (HBEF), New Hampshire, experienced severe canopy damage following an ice storm. Here we report the effects of this disturbance on internal N cycling and loss for watershed 1 (W1) and watershed 6 (W6) at the HBEF and patterns of N loss from nine other severely damaged watersheds across the southern White Mountains. This approach allowed us to test one component of N limitation theory, which suggests that N losses accompanying natural disturbances can lead to the maintenance of N limitation in temperate zone forest ecosystems. Prior to the ice storm, fluxes of nitrate (NO₃ ^–) at the base of W1 and W6 were similar and were much lower than N inputs in atmospheric deposition. Following the ice storm, drainage water NO₃ ^– concentrations increased to levels that were seven to ten times greater than predisturbance values. We observed no significant differences in N mineralization, nitrification, or denitrification between damaged and undamaged areas in the HBEF watersheds, however. This result suggests that elevated NO₃ ^- concentrations were not necessarily due to accelerated rates of N cycling by soil microbes but likely resulted from decreased plant uptake of NO₃ ^-. At the regional scale, we observed high variability in the magnitude of NO₃ ^- losses: while six of the surveyed watersheds showed accelerated rates of NO₃ ^– loss, three did not. Moreover, in contrast to the strong linear relationship between NO₃ ^– loss and crown damage within HBEF watersheds [r ²: (W1 = 0.91, W6 = 0.85)], stream water NO₃ ^– concentrations were weakly related to crown damage (r ² = 0.17) across our regional sites. The efflux of NO₃ ^– associated with the ice storm was slightly higher than values reported for soil freezing and insect defoliation episodes, but was approximately two to ten times lower than NO₃ ^– fluxes associated with forest harvesting. Because over one half of the entire years worth of N deposition was lost following the ice storm, we conclude that catastrophic disturbances contribute synergistically to the maintenance of N limitation and widely observed delays of N saturation in northern, temperate zone forest ecosystems. Present address: Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, New Jersey 08544, USA.     

A comparison of ammonia-oxidiser populations in eutrophic and oligotrophic basins of a large freshwater lake

A combination of PCR amplification and oligonucleotide probing was used to investigate the populations of ammonia-oxidisers of the -Proteobacteria in the eutrophic and oligotrophic basins of Lake Windermere, a large temperate lake in the English Lake District. Numbers of ammonia-oxidisers (MPN) in the Windermere lakewater were low (< 100 cells ml^–1) throughout the year with the exception of peaks in August, which coincided with stratification, and November in the South Basin where overturn may have introduced ammonia-oxidising bacteria into the water column. Sediment samples contained larger populations of ammonia oxidisers, usually ca. 10⁴ per g. dry weight, which remained relatively constant throughout the seasonal cycle in both Basins. DNA was recovered from lakewater and sediment samples and Nitrosospiraand N. europaea-eutrophalineage16S rRNA genes amplified in a nested PCR reaction, with confirmation of identity by oligonucleotide hybridisation. Nitrosospira 16S rDNA was readily detected in all samples and therefore found to be ubiquitous. In contrast, nitrosomonad DNA of the N. europaea-eutropha lineage could only be detected in the oligotrophic North Basin. Enrichment cultures of lakewater samples only exhibited nitrification at low (0.67 mM) and medium (5 mM) ammonium concentrations, whilst sediment enrichments nitrified at all concentrations tested including high (12.5 mM) ammonium medium. These data suggest that ammonia-oxidiser populations may be physiologically distinguished between lakewater and sediment, and that species distribution in a single lake is non-uniform.     

Nitrogen uptake and transformation in a midwestern U.S. stream: A stable isotope enrichment study

This study presents a comprehensive analysis ofnitrogen (N) cycling in a second-order forestedstream in southern Michigan that has moderatelyhigh concentrations of ammonium (mean,16 g N/L) and nitrate (17 g N/L). Awhole-stream ¹⁵NH₄ ⁺ addition wasperformed for 6 weeks in June and July, and thetracer ¹⁵N was measured downstream inammonium, nitrate, and detrital and livingbiomass. Ancillary measurements includedbiomass of organic matter, algae, bacteria andfungi, nutrient concentrations, hydrauliccharacteristics, whole-stream metabolism, andnutrient limitation assays. The resultsprovide insights into the heterotrophic natureof woodland streams and reveal the rates atwhich biological processes alter nitrogentransport through stream systems.Ammonium uptake lengths were 766–1349 m anduptake rates were 41–60 g N m^–2min^–1. Nitrate uptake could not bedetected. Nitrification rates were estimatedfrom the downstream increase in¹⁵N-enriched nitrate using a simulationmodel. The ammonium was removed bynitrification (57% of total uptake),heterotrophic bacteria and fungi associatedwith detritus (29%), and epilithic algae(14%). Growth of algae was likely limited bylight rather than nutrients, and dissolvedO₂ revealed that the stream metabolism washeterotrophic overall (P:R = 0.2). Incubationsof detritus in darkened chambers showed thatuptake of ¹⁵N was mostly heterotrophic.Microbial N in detritus and algal N inepilithon appeared to reach isotopic steadystate with the dissolved ammonium, but theisotopic enrichment of the bulk detritus andepilithon did not approach that of ammonium,probably due to a large fraction of organic Nin the bulk samples that was not turning over. The actively cycling fraction of total N inorganic compartments was estimated from theisotopic enrichment, assuming uptake ofammonium but not nitrate, to be 23% forepilithon, 1% for fine benthic organic matter,5% for small woody debris, and 7% for leaves. These percentages agree with independentestimates of epilithic algal biomass, whichwere based on carbon:chlorophyll ratios in bulksamples and in algal fractions separated bydensity-gradient centrifugation in colloidalsilica, and of microbial N in the detritus,which were based on N released by chloroformfumigations.     

Control of nitrification of fertilizer nitrogen: Effect of inhibitors,banding and nesting

Laboratory incubation and field experiments were conducted to evaluate thiourea, ATC (4-amino-1, 2, 4 triazole hydrochloride) and N-Serve 24 E (2-chloro-6-trichloromethyl-pyridine) as inhibitors of nitrification of fertilizer N. In the incubation experiment, most of the added aqueous NH₃ or urea was nitrified at 14 days on both soils, but addition of the inhibitors to fertilizer N decreased the conversion of NH₄−N to NO₃−N markedly. There was less nitrification for ATC and thiourea but not for N-Serve 24 E when the fertilizers and the inhibitors were placed at a point as opposed to when mixed into soil. After 28 days, ATC and N-Serve 24 E were more effective in inhibiting nitrification than thiourea. ATC and N-Serve 24 E also inhibited release of mineral N (NH₄−N+NO₃−N) from native soil N. In the uncropped field experiment, which received N fertilizers in the fall, nitrification of fall-applied N placed in the 15-cm bands was almost complete by early May in the Malmo soil, but not in the Breton soil. When ATC or thiourea had been applied with urea, nitrification of fall-applied N was depressed by May and the recovery of applied N as NH₄−N was greater with increasing band spacing to 60 cm or placing N fertilizer in nests (a method of application where urea prills were placed at a point in the soil in the center of 60×60 cm area). In late June, the percentage recovery of fall-applied N in soil as NH₄−N or mineral N increased with wide band spacing, or nest placement, or by adding ATC to fertilizer N on both soils. These results indicate that placing ammonium-based N fertilizers in widely-spaced bands or in nests with low rates of inhibitors slows nitrification enough to prevent much of the losses from fall-applied N. Scientific Paper No. 552, Lacombe Research Station, Research Branch, Agric, Can.     

Soil N mineralization and nitrification in relation to nitrogen solution chemistry in a small forested watershed

Spatial variations in soil processes regulating mineral N losses to streams were studied in a small watershed near Toronto, Ontario. Annual net N mineralization in the 0–8 cm soil was measured in adjacent upland and riparian forest stands using in situ soil incubations from April 1985 to 1987. Mean annual rates of soil N mineralization and nitrification were higher in a maple soil (93.8 and 87.0 kg.ha^–1) than in a pine soil (23.3 and 8.2 kg.ha^–1 ). Very low mean rates of mineralization (3.3 kg.ha^–1) and nitrification (3.4 kg.ha^–1) were found in a riparian hemlock stand. Average NO₃-N concentrations in soil solutions were 0.3–1.0 mg.L^–1 in the maple stand and >0.06mg.L^–1 in the pine stand. Concentrations of NO₃–N in shallow ground water and stream water were 3–4× greater in a maple subwatershed than in a pine subwatershed. Rapid N uptake by vegetation was an important mechanism reducing solution losses of NO₃–N in the maple stand. Low rates of nitrification were mainly responsible for negligible NO₃–N solution losses in the pine stand.