Prevalence of ammonia-oxidizing bacteria over ammonia-oxidizing archaea in sediments as related to nutrient loading in Chinese aquaculture ponds

Purpose

Nitrogen (N) application in excess of assimilatory capacity for aquaculture ponds can lead to water-quality deterioration through ammonia accumulation with toxicity to fish. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) potentially process extra ammonium, so their abundance and diversity are of great ecological significance. This study aimed to reveal variations in communities of AOA and AOB as affected by aquaculture activities.

Materials and methods

From June to September 2012, water and sediments were sampled monthly in three ponds feeding Mandarin fish in a suburb of Wuhan City, China. Molecular methods based on ammonia monooxygenase (amoA) gene were used to determine abundance and diversity of AOA and AOB in the sediments.

Results and discussion

The pond with the highest fish stock had the highest nutrient loadings in terms of different forms of N and carbon (C) in both sediment and water. The abundance and diversity of AOB were significantly higher than those of AOA in the sediment. The AOB abundance showed a significantly positive relationship to concentration of soluble reactive phosphorus (SRP) in interstitial water, and both abundance and diversity of AOA were significantly negative to concentration of ammonium in interstitial water. Furthermore, AOA species affiliated to Nitrososphaera-like and Nitrosophaera Cluster was distinguishable from those observed in other aquaculture environments.

Conclusions

Nutrients in sediment were enriched by intensive aquaculture activity, among which organic N and C, together with ammonium and SRP, shaped the communities of ammonia oxidizers, with AOB dominating over AOA in terms of abundance and diversity.

     

Effect of Organic matter application on the fate of 15N-labeled ammonium fertilizer in an upland soil

Abstract

The clay mineral composition of two “terra roxa estruturada” (TRE) soils occurring in the tropical rain forest and tropical forest/savannah transition zone, and a reddish brunizem in the savannah/semi-arid transition zone was studied comparatively in the southeast Amazon region.

Kaolin minerals were dominant in these soils, and hematite and goethite were found in the clay fraction. A small amount of 2 : 1-type clay minerals was found in two soils. The mineral composition of the clay fraction in the TRE soils was hardly influenced by the difference of the meteorological factor or their water condition in this region, and this factor should not control the influence of parent materials derived from basic rocks. The TRE soils were developed under the condition of laterite genesis, and were regarded claymineralogically as a kind of the lateritic soils.     

Availability and speciation of cadmium added to a calcareous soil under various managements

Potential risks for human health and adverse effects on soil quality caused by accumulation of cadmium (Cd) in soil at concentrations around or exceeding current European Union (EU) permitted limits have long been recognized. We have assessed availability and partitioning of Cd in a Mediterranean calcareous soil under four management regimes. Cadmium was added as a single pulse of CdSO₄ at the maximum Cd concentration established by the EU for sludge‐amended agricultural soils and concentrations exceeding the mandatory limits. Soils were treated with 0, 3, 10 and 50 mg Cd kg^?1 soil, incubated moist and analysed at selected times up to 600 days. Cadmium availability and distribution in soil were studied by neutral electrolyte and sequential extractions. During the incubation, the availability of Cd was not strictly dependent on the amount of metal added as the exchangeable fractions were similar shortly after the additions of Cd regardless of its initial concentration. Sequential extractions showed that for concentrations of 3 and 10 mg Cd kg^?1 soil Cd was evenly distributed among the soil phases, and its mobility was reduced mainly by adsorption on carbonates. At Cd concentrations exceeding 10 mg Cd kg^?1 soil a residual fraction appeared, perhaps from precipitation of Cd. Most of the Cd was associated with carbonates; land management and organic matter content had no major effects on the Cd distribution among different soil phases. The extraction protocols were effective for studying the fate of Cd in this calcareous soil as almost all of the Cd added was recovered. However, the introduction of a preliminary step with buffered NH₄NO₃ improved the determination of the most labile pools. Availability of Cd in calcareous soils estimated with reference methods appeared to be very small even when its total concentration far exceeded the current EU limits.     

土地利用方式和施肥对潮棕壤氨氧化细菌活性和群落组成的影响

The effects of long-term (19 years) different land use and fertilization on activity and composition of ammonia-oxidizing bacteria (AOB) in an aquic brown soil were investigated in a field experiment in Liaoning Province, China. The 19-year experiment conducted from 1990 to 2008 involved seven treatments designed: cropping rotation of soybean-corn-corn with no fertilizer (control, CK), recycled manure (RM), fertilizer nitrogen (N), phosphorous (P) and potassium (K) (NPK), NPK+RM, and no-crop bare land, mowed fallow, and non-mowed fallow. The results showed that the potential nitrification rates of the RM, NPK+RM, mowed fallow, and non-mowed fallow treatments were significantly higher (P < 0.05) than those of the CK and NPK treatments, indicating that the long-term applications of recycled manure and return of plant residues both significantly increased the activity of AOB. Although the application of NPK did not enhance soil potential nitrification because of decreased pH, available K had an important effect on potential nitrification. Denaturing gradient gel electrophoresis (DGGE) fingerprint profiles showed that no-crop treatments had an increase in the diversity of the AOB community compared to the CK, RM, and NPK treatments, implying that agricultural practices, especially tillage, had an adverse effect on the soil AOB community. The NPK+RM treatment had the most diverse DGGE patterns possibly because of the increased available P in this treatment. A phylogenetic analysis showed that most of the DGGE bands derived belonged to Nitrosospira cluster 3, not Nitrosospira cluster 2. These demonstrated that different land use and fertilization significantly influenced the activity and composition of the AOB community by altering the soil properties, mainly including pH, total C, available K, and available P.     

Abundance and community structure of ammonia-oxidizing archaea and bacteria in an acid paddy soil

Nitrification is essential to the nitrogen cycle in paddy soils. However, it is still not clear which group of ammonia-oxidizing microorganisms plays more important roles in nitrification in the paddy soils. The changes in the abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated by real-time PCR, terminal restriction fragment length polymorphism, and clone library approaches in an acid red paddy soil subjected to long-term fertilization treatments, including treatment without fertilizers (CT); chemical fertilizer nitrogen (N); N and potassium (NK); N and phosphorus (NP); N, P, and K (NPK); and NPK plus recycled crop residues (NPK+C). The AOA population size in NPK+C was higher than those in CT, while minor changes in AOB population sizes were detected among the treatments. There were also some changes in AOA community composition responding to different fertilization treatments. Still few differences were detected in AOB community composition among the treatments. Phylogenetic analysis showed that the AOA sequences fell into two main clusters: cluster A and cluster soil/sediment. The AOB composition in this paddy soil was dominated by Nitrosospira cluster 12. These results suggested that the AOA were more sensitive than AOB to different fertilization treatments in the acid red paddy soil.     

Availability to rhodesgrass (Chloris gayana) of nitrogen in tops and roots added to soil

¹⁵N-labelled Rhodesgrass material was prepared by growing plants in sand culture with labelled ammonium sulphate as their source of nitrogen. In a greenhouse experiment the labelled plant material in various physical configurations was added to an alluvial soil (fine sandy loam) from Samford with or without added mineral nitrogen. Two crops (six harvests) of Rhodesgrass were grown in the soil and the recovery of labelled nitrogen followed with time. Its partition at the end of the experiment was also determined.In general, after 16 months about one-third was recovered in the plant and two-thirds remained in the soil (plus any undecomposed added plant material). The only indication of volatile losses was a probable deficit of up to 10 per cent where litter (above-ground material) was placed on the soil surface.A higher nitrogen concentration in litter (1.3 per cent compared with 0.8 per cent) resulted in only a slight increase in labelled nitrogen recovery. Addition of mineral nitrogen (six doses of 50 kg N/ha) increased recovery from added litter material from 22 to 28 per cent and from added root material from 23 to 30 per cent.Grinding of added root material did not affect recovery. In the litter experiment, placing on the surface, incorporating in the top 2.5 cm of soil. and grinding and mixing with the soil resulted in final recoveries of 14, 28 and 32 per cent respectively.It is pointed out that caution must be exercised in extrapolation of results from laboratory and greenhouse studies to the field because many of the treatments used in the former are not analogous to field practices.     

氨氧化基因丰度和潜在氨氧化速率对加拿大一枝黄花入侵和土壤类型的响应

  【目的】  土壤类型和植物入侵影响土壤微生物群落结构和功能,基于此,我们研究加拿大一枝黄花 (Solidago canadensis) 入侵两种类型土壤后,土壤中氨氧化古细菌 (AOA) 和氨氧化细菌 (AOB) 的基因丰度和潜在氨氧化速率 (PAOR) 的变化规律及影响机理。  【方法】  云南和浙江是加拿大一枝黄花入侵的重点地区,本研究在云南省滇池周边的海东湿地公园、捞鱼河湿地公园和安乐村 (土壤类型均为冲积土) 以及浙江省东部的杭州湾湿地公园、临海上盘镇和路桥镇峰江村 (土壤类型均为黄泥田土),分别选择一块采样地,面积为100～150 m2。在每块采样地加拿大一枝黄花入侵 (Mono) 和未入侵 (Nat) 之处,划出0.5 m × 0.5 m,采集土壤和植物样品。Mono和Nat地块相距10～20 m,每个地块重复3次。采用qPCR和室内培养技术分析土壤中AOA、AOB基因丰度和PAOR,用植物生态和土壤化学方法分析植物生物量和土壤化学性状。  【结果】  加拿大一枝黄花入侵后,冲积土中AOA丰度和PAOR显著下降,黄泥田土中AOA丰度和PAOR却显著提高,而AOB丰度在两种类型土壤中均显著提高。Nat冲积土中AOA丰度和PAOR大于黄泥田土,而Mono条件下冲积土中AOA丰度和PAOR小于黄泥田土,AOB丰度在两种土壤类型中均变化较小。Mono样地植被地上部分和地下部分生物量、土壤有机质含量和pH是影响冲积土和黄泥田土AOA丰度和PAOR的重要因素。与AOA不同,冲积土AOB丰度仅受植物地下部分生物量的影响,而黄泥田土AOB丰度同时受植物地下部分生物量、土壤总磷含量和pH影响。  【结论】  加拿大一枝黄花入侵大大增加了植被地上部和地下部生物量,进而为微生物提供了大量的碳源,同时提高了土壤pH,因此,氨氧化细菌AOB的丰度显著增加。土壤类型仅影响AOA的丰度,对AOB和氨氧化潜力没有显著影响,而加拿大一枝黄花入侵显著影响两类土壤中的AOA、AOB丰度以及氨氧化潜力。     

Fate of nitrogen derived from 15N-labeled plant residues and composts in rice-planted paddy soil

Pot experiments that lasted for 3 y were conducted to investigate the dynamics of nitrogen derived from plant residues (rice root, hull, straw, corn root, and rapeseed pod-wall), and composts (rice straw compost, cattle manure compost, and cattle manure sawdust compost), which were labeled with ¹⁵N. The rates of nitrogen uptake by rice (=N efficiency), denitrification, and immobilization derived from the organic materials incorporated before the first year of cultivation were investigated throughout 3 y of cultivation. At the end of the first year of cultivation, relatively high rates of N efficiency were obtained for rapeseed pod-wall (24.6%), rice straw (19.1%), and rice hull (18.6%), while corn root and cattle manure sawdust compost displayed a noticeably high denitrification rate. Corn root, cattle manure sawdust compost, rice hull, and rapeseed pod-wall exhibited remarkably high N mineralization rates ranging from 60 to 75% of the organic materials N applied. Cumulative rates of N efficiencies from the organic materials applied before the first year of cultivation fitted well to a first-order kinetic model and their asymptotes were compared among the organic materials. The asymptotic rates of N efficiency tended to depend on the rates at the end of the first year of cultivation.     

Population size and specific nitrification potential of soil ammonia-oxidizing bacteria under long-term fertilizer management

Population size of soil ammonia-oxidizing bacteria (AOB) was quantified by real-time PCR in a long-term (16 years) field experiment under different fertilizer managements. AOB population sizes in mineral nitrogen-fertilized soils and organic manure-fertilized soil were 10.3 and 3.1 times, respectively, that of the control, while phosphorus and potassium fertilization had no significant effect. On the other hand, the AOB specific nitrification potential (soil nitrification potential per AOB cell) was significantly higher (P < 0.05) in organic manure-fertilized soil than in mineral-fertilized soils and the control, indicating that AOB was likely more metabolically active in organic manure-fertilized soils than in mineral nitrogen-fertilized soils after long-term application.     

Effects of urease and nitrification inhibitors added to urea on nitrous oxide emissions from a loess soil

Urea fertilizer‐induced N₂O emissions from soils might be reduced by the addition of urease and nitrification inhibitors. Here, we investigated the effect of urea granule (2–3 mm) added with a new urease inhibitor, a nitrification inhibitor, and with a combined urease inhibitor and nitrification inhibitor on N₂O emissions. For comparison, the urea granules supplied with or without inhibitors were also used to prepare corresponding supergranules. The pot experiments without vegetation were conducted with a loess soil at (20 ± 2)°C and 67% water‐filled pore space. Urea was added at a dose of 86 kg N ha^–1 by surface application, by soil mixing of prills (<1 mm) and granules, and by point‐placement of supergranules (10 mm) at 5 cm soil depth. A second experiment was conducted with spring wheat grown for 70 d in a greenhouse. The second experiment included the application of urea prills and granules mixed with soil, the point‐placement of supergranules and the addition of the urease inhibitor, and the combined urease plus nitrification inhibitors at 88 kg N ha^–1. In both experiments, maximum emissions of N₂O appeared within 2 weeks after fertilization. In the pot experiments, N₂O emissions after surface application of urea were less (0.45% to 0.48% of total fertilization) than from the application followed by mixing of the soil (0.54% to 1.14%). The N₂O emissions from the point‐placed‐supergranule treatment amounted to 0.64% of total fertilization. In the pot experiment, the addition of the combined urease plus nitrification inhibitors, nitrification inhibitor, and urease inhibitor reduced N₂O emissions by 79% to 87%, 81% to 83%, and 15% to 46%, respectively, at any size of urea application. Also, the N₂O emissions from the surface application of the urease‐inhibitor treatment exceeded those of the granules mixed with soil and the point‐placed‐supergranule treatments receiving no inhibitors by 32% to 40%. In the wheat growth experiment, the N₂O losses were generally smaller, ranging from 0.16% to 0.27% of the total fertilization, than in the pot experiment, and the application of the urease inhibitor and the combined urease plus nitrification inhibitors decreased N₂O emissions by 23% to 59%. The point‐placed urea supergranule without inhibitors delayed N₂O emissions up to 7 weeks but resulted in slightly higher emissions than application of the urease inhibitor and the urease plus nitrification inhibitors under cropped conditions. Our results imply that the application of urea fertilizer added with the combined urease and nitrification inhibitors can substantially reduce N₂O emissions.     

Distinct responses of ammonia-oxidizing bacteria and archaea to green manure combined with reduced chemical fertilizer in a paddy soil

Journal of Soils and Sediments - Ammonia oxidation is the rate-limiting step in nitrification. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the key drivers of the nitrogen cycle. Chinese...     

Distribution of large soil invertebrates as related to soil parameters

The study of three types of forest soils has shown virtually no reliable relationships between the distribution of large soil invertebrates and the soil parameters (the stone content, pH, litter thickness, etc.) when the sample area has a size of 76 cm². However, an increase in the size of the observation plots by two to four times (depending on the particular soil type) makes it possible to find statistically significant coefficients of correlation between the studied parameters. Thus, the size of the sample area influences our assessment of the relationships between the abundance of large invertebrates and the soil parameters. In each of the studied types of forest soils, the heterogeneity of the soil structure is manifested at different scales. A correct forecast of the effect of the factors of the soil on the population of large invertebrates depends on the spatial distribution of these factors.     

Dynamics of 15N-labeled ammonium sulfate in various inorganic and organic soil fractions of wetland rice soils

Summary The dynamics of basally applied ¹⁵N-labeled ammonium sulfate in inorganic and organic soil fractions of five wetland rice soils of the Philippines was studied in a greenhouse experiment. Soil and plant samples were collected and analyzed for ¹⁵N at various growth stages. Exchangeable NH₄ ⁺ depletion continued after 40 days after transplanting (DAT) and corresponded with increased nitrogen uptake by rice plants. Part of the applied fertilizer was fixed by 2:1 clay minerals, especially in Maligaya silty clay loam, which contained beidellite as the dominant clay mineral. After the initial fixation, nonexchangeable ¹⁵N was released from 20 DAT in Maligaya silty clay loam, but fixation delayed fertilizer N uptake from the soil. Part of the applied N was immobilized into the organic fraction. In Guadalupe clay and Maligaya silty clay loam, immobilization increased with time while the three other soils showed significant release of fertilizer N from the organic fraction during crop growth. Most of the immobilized fertilizer N was recovered in the nondistillable acid soluble (alpha-amino acid + hydrolyzable unknown-N) fraction at crop maturity. Between 61% and 66% of applied N was recovered from the plant in four soils while 52% of fertilizer N was recovered from the plant in Maligaya silty loam. Only 20% – 30% of the total N uptake at maturity was derived from fertilizer N. Nmin (mineral N) content of the soil before transplanting significantly correlated with N uptake. Twenty-two to 34% of applied N was unaccounted for possibly due to denitrification and ammonia volatilization.     

The isotopic composition of the soil microbial biomass and of adenine and guanine isolated from soil incubated with 14C- and 15N-labelled plant material: Comparison with fumigation method

Adenine and guanine were extracted from a calcareous soil by a new method and shown to be pure by C-to-N ratio, optical density and mass spectrometry. The soil had been incubated with ¹⁴C-and ¹⁵N-labelled maize leaves. The specific activity and atom% excess ¹⁵N of the soil microbial biomass were determined by the fumigation method and also in the isolated adenine and guanine. The specific activity of the microbial biomass was very similar to that of the adenine and guanine (taking both bases together). In contrast, the atom% excess of the microbial biomass N was 5–6 times that in the isolated adenine and guanine. The authors put forward an hypothesis to explain this difference.     

Contributions of ammonia-oxidizing archaea and bacteria to nitrification in Oregon forest soils

Ammonia oxidation, the first step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB); however, the relative contributions of AOA and AOB to soil nitrification are not well understood. In this study we used 1-octyne to discriminate between AOA- and AOB-supported nitrification determined both in soil-water slurries and in unsaturated whole soil at field moisture. Soils were collected from stands of red alder (Alnus rubra Bong.) and Douglas-fir (Pseudotsuga menziesii Mirb. Franco) at three sites (Cascade Head, the H.J. Andrews, and McDonald Forest) on acidic soils (pH 3.9–5.7) in Oregon, USA. The abundances of AOA and AOB were measured using quantitative PCR by targeting the amoA gene, which encodes subunit A of ammonia monooxygenase. Total and AOA-specific (octyne-resistant) nitrification activities in soil slurries were significantly higher at Cascade Head (the most acidic soils, pH < 5) than at either the H.J. Andrews or McDonald Forest, and greater in red alder compared with Douglas-fir soils. The fraction of octyne-resistant nitrification varied among sites (21–74%) and was highest at Cascade Head than at the other two locations. Net nitrification rates of whole soil without NH₄⁺ amendment ranged from 0.4 to 3.3 mg N kg⁻¹ soil d⁻¹. Overall, net nitrification rates of whole soil were stimulated 2- to 8-fold by addition of 140 mg NH₄⁺-N kg⁻¹ soil; this was significant for red alder at Cascade Head and the H.J. Andrews. Red alder at Cascade Head was unique in that the majority of NH₄⁺-stimulated nitrifying activity was octyne-resistant (73%). At all other sites, NH₄⁺-stimulated nitrification was octyne-sensitive (68–90%). The octyne-sensitive activity—presumably AOB—was affected more by soil pH whereas the octyne-resistant (AOA) activity was more strongly related to N availability.     

Concentrations of 60 elements in the soil solution as related to the soil acidity

Little is known about solubility and soil solution concentrations of most elements occurring in the solid phase of soils. This study reports changes in solution concentrations of 60 mineral elements following CaCO₃ addition to a moderately acid semi‐natural soil, and possible mechanisms accounting for the differing solubility patterns as related to soil acidity are discussed. Soil solutions were obtained by high‐speed centrifuging and ultrafiltration (0.2 μm) of samples at 60% water‐holding capacity of the A horizon of a Cambisol developed from a shale–gneiss moraine and supplied with CaCO₃ at 20 rates to yield a soil solution pH range of 5.2–7.8. Concentrations of elements were determined in the solutions by ICP‐AES or (for most elements) ICP‐MS. Several distinct patterns of soil solution concentrations as a function of soil solution pH were demonstrated. Positively related to pH and CaCO₃ supply were soil solution concentrations of As, Br, Mo, S, Sb, Se, U, and W, and to a lesser degree, Co, Cr, Hg, Mg, and Sr. Inversely related to pH were concentrations of Al, B, Ba, Bi, Cs, Ce, Eu, Ga, Ge, Fe, Li, K, Rb, Na, Th, and Ti; less distinctly inversely rated were Dy, Er, Gd, Hf, La, Lu, Mn, Nd, Pr, Sm, Sc, Si, Tl, Tm, and Yb. ‘U‐shaped’ relationships to pH were demonstrated for the concentrations of Ag, Cd, Nb, Ni, P, V, and Zr. There were no or irregular relations between pH and concentrations of Be, Cu, Ho, Pb, Ta, and Tb. Differences between elements in their soil solution concentrations as related to total (HNO₃‐digestible) concentrations and the solubility of organic C were also treated. Increasing the pH of a soil by adding CaCO₃ changes the solubility of most mineral elements substantially, the several distinct patterns observed being governed by, for example, ionic properties and charge, affinity for organic compounds, and pH‐dependent formation and solubility of complexes.     

Humic acids stimulate growth and activity of in vitro tested axenic cultures of soil autotrophic nitrifying bacteria

In the present study, the effect of humic acids on activity and growth of Nitrosomonas europaea and Nitrobacter agilis was investigated in vitro under axenic conditions. Humates from compost-stabilized vegetable waste or leonardite were added to the chemolithotrophic culturing medium at concentrations of 0, 5, 50 and 100 mg l^–1. It was found that both types of humic acids increased either NH₄ ⁺ or NO₂ ^– oxidation and cell growth of nitrifying bacteria in a dose-independent manner. By combining these results with data from a comparative growth evaluation of N. agilis based on possible utilization of humates or pyruvate in heterotrophic conditions, evidence was obtained that nitrifiers cannot use humic acids as an alternative carbon and energy source. Thus, the stimulating effect of this fraction of soil organic matter on chemolithotrophic ammonia and nitrite oxidizers might be attributed to an increase in microbial membrane permeability favouring a better utilization of nutrients. Received: 15 April 1996