A Most Probable Number method (MPN) for the estimation of cell numbers of heterotrophic nitrifying bacteria in soil

A Most Probable Number (MPN) method was developed allowing for the first time estimation of populations of bacteria capable of heterotrophic nitrification. The method was applied to an acidic soil of a coniferous forest exhibiting nitrate production. In this soil nitrate production was unlikely to be catalyzed by autotrophic nitrifiers, since autotrophic ammonia oxidizers never could be detected, and autotrophic nitrite oxidizers were usually not found in appreciable cell numbers. The developed MPN method is based on the demonstration of the presence/absence of nitrite/nitrate produced by heterotrophic nitrifying bacteria during growth in a complex medium (peptone-meat-extract softagar medium) containing low concentrations of agar (0.1%). Both the supply of the growing cultures in MPN test tubes with sufficient oxygen and the presence of low agar concentrations in the medium were found to be favourable for sustainable nitrite/nitrate production. The results demonstrate that in the acidic forest soil the microbial population capable of heterotrophic nitrifcation represents a significant part of the total aerobic heterotrophic population. By applying the developed MPN method, several bacterial strains of different genera not previously described to perform heterotrophic nitrification have been isolated from the soil and have been identified by bacterio-diagnostic tests.     

The importance of autotrophic versus heterotrophic oxidation of atmospheric ammonium in forest ecosystems with acid soil

Abstract The role of autotrophic and heterotrophic nitrifying microorganisms in the oxidation of atmospheric ammonium in two acid and one calcareous location of a Dutch woodland area was investigated. In soil slurries nitrate formation was completely inhibited by acetylene, a specific inhibitor of autotrophic ammonium-oxidizing bacteria. A survey of nitrifiers in the forest soils showed that both autotrophic ammonium- and nitrite-oxidizing bacteria were present in high numbers and evidence was obtained that autotrophic bacteria are able to nitrify below pH 4. These results show that autotrophic nitrifying bacteria may account for most of the nitrification in the examined soils. To assess the contribution of heterotrophic nitrifiers, about 200 strains of heterotrophic bacteria and 21 morphologically distinct fungal strains were isolated from the acid soil locations and tested for their ability to nitrify. Only one Penicillium strain produced nitrate in test media, but its nitrate formation when added to acid soils was poor. These findings indicate that in the investigated soil heterotrophs are of minor importance in the oxidation of atmospheric ammonium.     

Carbon losses due to soil warming: Do autotrophic and heterotrophic soil respiration respond equally?

Global warming has the potential to increase soil respiration (R_S), one of the major fluxes in the global carbon (C) cycle. R_S consists of an autotrophic (R_A) and a heterotrophic (R_H) component. We combined a soil warming experiment with a trenching experiment to assess how R_S, R_A, and R_H are affected. The experiment was conducted in a mature forest dominated by Norway spruce. The site is located in the Austrian Alps on dolomitic bedrock. We warmed the soil of undisturbed and trenched plots by means of heating cables 4 °C above ambient during the snow‐free seasons of 2005 and 2006. Soil warming increased the CO₂ efflux from control plots (R_S) by ∼45% during 2005 and ∼47% during 2006. The CO₂ efflux from trenched plots (R_H) increased by ∼39% during 2005 and ∼45% during 2006. Similar responses of R_S and R_H indicated that the autotrophic and heterotrophic components of R_S responded equally to the temperature increase. Thirty‐five to forty percent or 1 t C ha⁻¹ yr⁻¹ of the overall annual increase in R_S (2.8 t C ha⁻¹ yr⁻¹) was autotrophic. The remaining, heterotrophic part of soil respiration (1.8 t C ha⁻¹ yr⁻¹), represented the warming‐induced C loss from the soil. The autotrophic component showed a distinct seasonal pattern. Contribution of R_A to R_S was highest during summer. Seasonally derived Q₁₀ values reflected this pattern and were correspondingly high (5.3–9.3). The autotrophic CO₂ efflux increase due to the 4 °C warming implied a Q₁₀ of 2.9. Hence, seasonally derived Q₁₀ of R_A did not solely reflect the seasonal soil temperature development.     

Measurements of sediment toxicity of autotrophic and heterotrophic picoplankton by epifluorescence microscopy

Sediment toxicity from Toronto (Ontario) and Toledo (Ohio) harbours to autotrophic and heterotrophic picoplankton was evaluated simultaneously using epifluorescent microscopy. The approach is a simple, fast and effective combination of autofluorescence and fluorescence probes - 1-anilino-8-naphthalene sulfonic acid. The procedure is ideally suited for use with sediment slurries since it can differentiate fluorescent biotic material against a background of abiotic sediment particles and detritus.     

The stoichiometry of nitrogen and phosphorus spiralling in heterotrophic and autotrophic streams

1. Nutrient spiralling provides a conceptual framework and a whole‐system approach to investigate ecosystem responses to environmental changes. We use spiralling metrics to examine how the coupling of nitrogen and phosphorus uptake varies between streams dominated by either heterotrophic (i.e. bacteria‐dominated) or autotrophic (algal‐dominated) microbial communities. 2. Algae generally exhibit greater capacity to store nutrients than bacteria because of differences in cellular structures. These differences led us to hypothesise that the uptake of N and P in heterotrophic ecosystems should have reduced stoichiometric variation in response to changes in supply N : P compared to autotrophic ecosystems when assimilation dominates nutrient uptake. 3. To test this hypothesis, we used an array of serial nutrient additions in several streams in the South Fork Eel River watershed in Northern California. In one set of experiments, N and P were added alone and simultaneously in separate experiments to two small, heterotrophic streams to assess uptake rates and interactions between nutrient cycles. In a second set of experiments, N and P were added simultaneously at a range of N : P in one heterotrophic and one autotrophic stream to assess differences in uptake responses to changes in supply N : P. 4. Results of these experiments suggest two important conclusions. First, increased N supply significantly shortened P uptake lengths, while P addition had little impact on N uptake in both streams, indicating that uptake of non‐limiting nutrients is tightly coupled to the availability of the limiting element. Second, changes in P uptake and uptake ratios (U_N : U_P) with increased supply N : P supported our hypothesis that heterotrophic streams are more homeostatic in their responses to changes in nutrient supply than autotrophic streams, suggesting that physiological controls on nutrient use scale up to influence ecosystem‐scale patterns in nutrient cycling.     

Influence of tree species and ground vegetation on nitrification in an acid forest soil

Soil N transformations were studied at Ironhill, near Liphook, UK as part of a forest fumigation experiment. Nitrification potential was measured in a humoferric podzol soil, of pH 3 (in 0.01 M CaCl₂). An initial experiment into nitrogen mineralisation potential indicated that nitrification was linked strongly to the species of coniferous tree growing in the soil. Transfer of soil solution between soils had no influence on mineralisation potential and allelopathic effects of the trees were not demonstrated. The initial finding was attributed subsequently to the type of ground vegetation and its management. Attempts to reproduce soil conditions, which promoted nitrification, were partially successful.Soil, from the Ironhill site, was incubated with various nitrogenous substrates and other nutrients and sources of carbon to test whether heterotrophs were responsible for nitrification. Organic N (which was ammonified) promoted nitrification, but the addition of ammonium was inhibitory unless supplied with a readily available carbon source such as acetate. Nitrification potential was unaffected when soils were incubated with an inhibitor of autotrophic nitrification. The results of these experiments supported strongly the hypothesis that heterotrophic organisms were responsible for nitrification in this soil.     

The effect of thiosulphate and other inhibitors of autotrophic nitrification on heterotrophic nitrifiers

It has been found that heterotrophic nitrification by Thiosphaera pantotropha can be inhibited by thiosulphate in batch and chemostat cultures. Allythiourea and nitrapyrin, both classically considered to be specific inhibitors of autotrophic nitrification, inhibited nitrification by Tsa. pantotropha in short-term experiments with resting cell suspensions. Hydroxylamine inhibited ammonia oxidation in chemostat cultures, but was itself fully oxidized. Thus the total nitrification rate for the culture remained the same.Heterotrophic nitrification by another organism, a strain of Pseudomonas denitrificans has also been shown to be inhibited by thiosulphate in short term experiments and in the chemostat. During these experiments it became evident that this strain is able to grow mixotrophically (with acetate) and autotrophically in a chemostat with thiosulphate as the energy source.     

Seasonal determinations of extracellular hydrolytic activities in heterotrophic and mixed heterotrophic/autotrophic biofilms from two contrasting rivers

The temporal changes in extracellular enzyme activities in freshwater microbial biofilms were examined in two contrasting river sites in North Wales over a 12 month period. Sites were a first order, unshaded oligotrophic upland stream (Nant Waen) and a fourth order, mildly eutrophic river with riparian tree cover (River Clywedog). When algal populations were low, biofilms of the more eutrophic site supported greater enzyme activities and higher population densities than the oligotrophic site. Composition, concentration and origin of substrates available to the respective biofilm communities influenced extracellular processing patterns. Reduction in algal populations depressed total and extracellular activities in biofilms from the first order site, suggesting that biofilm communities here were maintained by in situ primary production. Biofilms from Nant Waen were often found to contain higher extracellular activities per cell than the more eutrophic River Clywedog biofilms, which might represent the enhanced ability of an oligotrophic biofilm to accumulate extracellular enzymes. In contrast, light and darkgrown River Clywedog biofilms were not enzymatically distinct, inferring a less important role for biofilm phototrophs. Some evidence was found for increased reliance on allochthonous substrates in the River Clywedog for biofilm maintenance.     

Investigation of nitrification in forest soils with soil percolation columns

Soil percolation columns in which a pF of 2 could be maintained were developed to study nitrification in soils and litter of an acid and a calcareous forest soil location. High nitrification rates were observed in the calcareous soil. In the acid soil nitrification was much slower. A column filled with leaf litter gave a low nitrification rate at the start of the experiment, but a high rate was found after 60 days of percolation with an ammonium-containing medium of pH 4. In this leaf litter high numbers of autotrophic bacteria were just present at the beginning of the experiment, whereas at the end only low numbers were detected. Results indicate that autotrophic bacteria from acid soils are sensitive to a pH increase.     

Fertilization of boreal forest reduces both autotrophic and heterotrophic soil respiration

The boreal forest is expected to experience the greatest warming of all forest biomes, raising concerns that some of the large quantities of soil carbon in these systems may be added to the atmosphere as CO₂. However, nitrogen deposition or fertilization has the potential to increase boreal forest production and retard the decomposition of soil organic matter, hence increasing both tree stand and soil C storage. The major contributors to soil‐surface CO₂ effluxes are autotrophic and heterotrophic respiration. To evaluate the effect of nutrient additions on the relative contributions from autotrophic and heterotrophic respiration, a large‐scale girdling experiment was performed in a long‐term nutrient optimization experiment in a 40‐year‐old stand of Norway spruce in northern Sweden. Trees on three nonfertilized plots and three fertilized plots were girdled in early summer 2002, and three nonfertilized and three fertilized plots were used as control plots. Each plot was 0.1 ha and contained around 230 trees. Soil‐surface CO₂ fluxes, soil moisture, and soil temperature were monitored in both girdled and nongirdled plots. In late July, the time of the seasonal maximum in soil‐surface CO₂ efflux, the total soil‐CO₂ efflux in nongirdled plots was 40% lower in the fertilized than in the nonfertilized plots, while the efflux in girdled fertilized and nonfertilized plots was 50% and 60% lower, respectively, than in the corresponding nongirdled controls. We attribute these reductions to losses of the autotrophic component of the total soil‐surface CO₂ efflux. The estimates of autotrophic respiration are conservative as root starch reserves were depleted more rapidly in roots of girdled than in nongirdled trees. Thus, heterotrophic activity was overestimated. Calculated on a unit area basis, both the heterotrophic and autotrophic soil respiration was significantly lower in fertilized plots, which is especially noteworthy given that aboveground production was around three times higher in fertilized than in nonfertilized plots.     

Short-term increases in relative nitrification rates due to trenching in forest floor and mineral soil horizons of different forest types

The representation of NO₃ ^– dynamics within forest growth simulation models could improve forest management. An extensive literature review revealed an 88% probability of measuring a higher relative nitrification index (i.e. RNI = [NO₃ ^–] ÷ [NO₃ ^– + NH₄ ⁺]) in mineral soil horizons than in forest floors, across a wide range of conifer and hardwood ecosystems. We then hypothesised that humus form and fine root density could be used as two crude variables to predict changes in in situ, potential and relative nitrification rates. Twenty-seven trench plots were established in 1999, across nine contrasting hardwood and coniferous stands in the Eastern Townships of Québec. Forest floor and mineral soil samples were collected from each plot, and from a 1 m radius surrounding each plot, on three dates during summer 2000. In situRNI values increased significantly in trench plots as the season progressed. Potential nitrification rates (i.e. NO₃ ^– concentrations following incubation) were two orders of magnitude higher in forest floor than in mineral soil samples. RNI was significantly higher in mineral soil than in forest floor samples after incubations, but the relative increase in RNI due to trenching was higher in forest floor samples. Indices of available C were significantly higher in forest floor than mineral soil samples, and decreased only in forest floor samples during incubations. Likewise, trenching significantly reduced available C in forest floor samples only. Seasonal changes in soil temperature and fine root growth were the most plausible explanations for seasonal changes in NO₃ ^– dynamics, whereas other factors such soil acidity and moisture appeared less important in determining NO₃ ^– dynamics in this study. We conclude that crude assessments of humus form and fine root density have the potential to be used as calibration parameters for the simulation of NO₃ ^– dynamics in forest growth and yield models.     

基于BP神经网络模型的全球森林土壤异养硝化过程N2O排放通量估算

N₂O作为重要的温室气体之一,对地球和人类都有很大的影响。为了深入探究对有机氮异养硝化作用及其产生N₂O过程的影响机制,完善全球N₂O通量估算模型,本研究采用Pearson相关性分析与广义可加模型(GAM)对全球135个样点有机氮异养硝化速率及其产生N₂O速率的影响因子进行分析,然后将主要影响因子作为BP神经网络的输入层来模拟全球森林土壤有机氮异养硝化速率及其产生N₂O速率的空间分布。结果显示,土壤pH和土壤C/N是影响有机氮异养硝化速率的主要因素,土壤C/N、土壤孔隙含水量(WFPS)以及土壤温度是影响有机氮异养硝化产生N₂O速率的主要因素。全球森林土壤异养硝化速率平均为0.4241(0.0014～0.689)μg N·g^-1·d^-1,异养硝化产生N₂O速率平均为0.2936(0.21～1.103)μg N₂O·kg^-1·d^-1     

The use of mean pool abundances to interpret 15N tracer experiments

A pulse dilution ¹⁵N technique was used in the field to determine the effect of the ammonium to nitrate ratio in a fertilizer application on the uptake of ammonium and nitrate by ryegrass and on gross rates of mineralization and nitrification. Two experiments were performed, corresponding approximately to the first and second cuts of grass. Where no substantial recent immobilization of inorganic nitrogen had occurred, mineralization was insensitive to the form of nitrogen applied, ranging from 2.1–2.6 kg N ha^-1 d^-1. The immobilization of ammonium increased as the proportion of ammonium in the application increased. In the second experiment there was evidence that high rates of immobilization in the first experiment were associated with high rates of mineralization in the second. The implication was that some nitrogen immobilized in the first experiment was re-mineralized during the second. Whether this was nitrogen taken up, stored in roots and released following defoliation was not clear. Nitrification rates in this soil were low (0.1–0.63 kg N ha^-1 d^-1), and as a result, varying the ratio of ammonium to nitrate applied markedly altered the relative uptake of ammonium and nitrate. In the first experiment, where temperatures were low, preferential uptake of ammonium occurred, but where >90% of the uptake was as ammonium, a reduction in yield and nitrogen uptake was observed. In the second experiment, where temperatures and growth rates were higher, the proportion of ammonium to nitrate taken up had no effect on yield or nitrogen uptake.     

Inhibition of nitrification in forest soil by monoterpenes

Nitrate production was detected in untreated soil of a Norway spruce (Picea abies L.) stand only after clear-cutting the stand. The aim of this study was to determine whether allelochemical inhibition of nitrification by monoterpenes played any role in inhibiting nitrification in the stand. Therefore, soils from a clear-cut plot and from a forest plot were studied. In the field, monoterpenes (mostly - and -pinenes), measured by soil microair diffusive samplers, were intensively produced in the forest plot, but not in the clear-cut plot. In the laboratory, soil samples taken from the forest plot produced only small amounts of monoterpenes, indicating that monoterpenes were mainly produced by the roots and not to great extent by the soil microbial population. The effect of a mixture of monoterpenes (seven major monoterpenes detected in the field) on net nitrification, net N mineralization and denitrification activities of soil from the clear cut plot, and on carbon mineralization of soils from both the forest and clear-cut plots, was studied in the laboratory. In both aerobic incubation experiments and in soil suspensions with excess NH4-N, nitrification was inhibited by exposure to the vapours of monoterpenes at similar concentrations at which they had been detected in forest plot. This indicates direct inhibition of nitrification by monoterpenes. Exposure to monoterpenes did not affect denitrification. However, it increased respiration activity of both soils. This could also indicate indirect inhibition of nitrification by monoterpenes, due to immobilization of mineral N. Thus it seems that monoterpenes could play a role in inhibiting nitrification in the forest soil.     

Effects of wildfire on soil respiration and its heterotrophic and autotrophic components in a montane coniferous forest

Aims Episodic wildfires are expected to occur more frequently under future climate change scenarios, with substantial effects on CO₂exchange between terrestrial ecosystems and the atmosphere. This study examined the effects of wildfire on soil respiration (R_S) and its heterotrophic (R_H) and autotrophic (R_A) components, as well as their temperature responses (temperature sensitivity,Q₁₀).     

Decadal warming causes a consistent and persistent shift from heterotrophic to autotrophic respiration in contrasting permafrost ecosystems

Soil carbon in permafrost ecosystems has the potential to become a major positive feedback to climate change if permafrost thaw increases heterotrophic decomposition. However, warming can also stimulate autotrophic production leading to increased ecosystem carbon storage—a negative climate change feedback. Few studies partitioning ecosystem respiration examine decadal warming effects or compare responses among ecosystems. Here, we first examined how 11 years of warming during different seasons affected autotrophic and heterotrophic respiration in a bryophyte‐dominated peatland in Abisko, Sweden. We used natural abundance radiocarbon to partition ecosystem respiration into autotrophic respiration, associated with production, and heterotrophic decomposition. Summertime warming decreased the age of carbon respired by the ecosystem due to increased proportional contributions from autotrophic and young soil respiration and decreased proportional contributions from old soil. Summertime warming's large effect was due to not only warmer air temperatures during the growing season, but also to warmer deep soils year‐round. Second, we compared ecosystem respiration responses between two contrasting ecosystems, the Abisko peatland and a tussock‐dominated tundra in Healy, Alaska. Each ecosystem had two different timescales of warming (<5 years and over a decade). Despite the Abisko peatland having greater ecosystem respiration and larger contributions from heterotrophic respiration than the Healy tundra, both systems responded consistently to short‐ and long‐term warming with increased respiration, increased autotrophic contributions to ecosystem respiration, and increased ratios of autotrophic to heterotrophic respiration. We did not detect an increase in old soil carbon losses with warming at either site. If increased autotrophic respiration is balanced by increased primary production, as is the case in the Healy tundra, warming will not cause these ecosystems to become growing season carbon sources. Warming instead causes a persistent shift from heterotrophic to more autotrophic control of the growing season carbon cycle in these carbon‐rich permafrost ecosystems.     

Contrasting responses of heterotrophic and autotrophic respiration to experimental warming in a winter annual‐dominated prairie

Understanding how soil respiration (Rs) and its source components respond to climate warming is crucial to improve model prediction of climate‐carbon (C) feedback. We conducted a manipulation experiment by warming and clipping in a prairie dominated by invasive winter annual Bromus japonicas in Southern Great Plains, USA. Infrared radiators were used to simulate climate warming by 3 °C and clipping was used to mimic yearly hay mowing. Heterotrophic respiration (Rh) was measured inside deep collars (70 cm deep) that excluded root growth, while total soil respiration (Rs) was measured inside surface collars (2–3 cm deep). Autotrophic respiration (Ra) was calculated by subtracting Rh from Rs. During 3 years of experiment from January 2010 to December 2012, warming had no significant effect on Rs. The neutral response of Rs to warming was due to compensatory effects of warming on Rh and Ra. Warming significantly (P < 0.05) stimulated Rh but decreased Ra. Clipping only marginally (P < 0.1) increased Ra in 2010 but had no effect on Rh. There were no significant interactive effects of warming and clipping on Rs or its components. Warming stimulated annual Rh by 22.0%, but decreased annual Ra by 29.0% across the 3 years. The decreased Ra was primarily associated with the warming‐induced decline of the winter annual productivity. Across the 3 years, warming increased Rh/Rs by 29.1% but clipping did not affect Rh/Rs. Our study highlights that climate warming may have contrasting effects on Rh and Ra in association with responses of plant productivity to warming.     

A field study on the fate of 15N-ammonium to demonstrate nitrification of atmospheric ammonium in an acid forest soil

To demonstrate the contribution of atmospheric ammonium to soil acidification in acid forest soils, a field study with¹³N-ammonium as tracer was performed in an oak-birch forest soil. Monitoring and analysis of soil solutions from various depths on the¹³N-ammonium and¹⁵N-nitrate contents, showed that about 54% of the applied¹⁵N-ammonium was oxidized to nitrate in the forest floor. Over a period of one year about 20% of the¹⁵N remained as organic nitrogen in this layer. The percentage¹⁵N enrichment in ammonium and nitrate were in the same range in all the forest floor percolates, indicating that even in extremely acid forest soils (pH < 4) nitrate formation from ammonium can occur. Clearly, atmospheric ammonium can contribute to soil acidification even at low soil pH.     

应用小波多尺度分析亚热带森林土壤异养呼吸特征

土壤异养呼吸是森林生态系统碳循环的重要组成部分,其时间变化规律和影响因子一直是碳循环研究的难点和重点。利用全自动连续观测系统对亚热带米槠常绿阔叶次生林土壤异养呼吸进行高频率观测,采用连续小波变换技术对高频率实测值与模型估测值间的差值进行分析,探讨亚热带森林土壤异养呼吸的变化机制。结果发现,土壤异养呼吸速率年变化范围在0.82—7.11μmol CO_2 m~(-2)s~(-1)之间,全年平均值为2.66μmol CO_2 m~(-2)s~(-1),在7月份达到全年最高值。虽然土壤温度和水分双因素模型能够较好地解释土壤异养呼吸的年变化,但土壤温度和土壤异养呼吸速率在时间序列上未出现同步变化模式,同时双因素模型估测值与高频率实测值年均值相差18%,其中4—7月模型值低估12%,而8—9月模型值高估15%。进一步利用连续小波变换对模型误差分析发现,模型值与实测值差异在4—7月主要分布在短周期(32—64 h)和长周期(≥85 d),这可能与生长季节土壤底物有效性提高,大量的易变化碳输入激发原有土壤有机碳分解有关。8—9月差异主要分布在长周期(≥85 d),这可能是干旱造成底物有效性降低,微生物只能利用原有难分解有机碳进行维持代谢。因此亚热带森林土壤异养呼吸会不仅受到温度、土壤水分等环境因素影响,而且底物有效性变化也可能是影响亚热带常绿阔叶林土壤异养呼吸变化的重要因素。     

Fine root mass in relation to soil N supply in a cool temperate forest

Soil inorganic nitrogen supply and fine root mass in the top layers of mineral soil (0–5 and 5–10cm) were investigated at upper and lower sites of a cool temperate forest where Fagus crenata and Quercus crispula dominate. At both sites, soil inorganic nitrogen supply was greatest in the 0–5cm layer. The predominant forms of soil inorganic nitrogen supply were NH₄⁺-N at the upper site and NO₃^–-N at the lower site. Fine roots were concentrated in the 0–5cm layer at the upper site, but not at the lower site. The form of supplied soil inorganic nitrogen supply can be important in determining the vertical distribution of fine roots.