Aggregate-related changes in network patterns of nematodes and ammonia oxidizers in an acidic soil

Nitrification plays a central role in global nitrogen cycle, which is affected by biological interaction between soil microfauna and microorganisms. However, the complexity of soil biotic communities made it difficult to reveal organizational principles of the community and the interactions among species. Here, we used the network analysis to decipher the interactions between nematodes and ammonia oxidizers within aggregate fractions under 10-year manure application, and examine their associations with soil variables and potential nitrification activity (PNA). Three aggregate fractions included large macroaggregates (>2000 μm, LA), small macroaggregates (250–2000 μm, SA), and inter-aggregate soil and space (<250 μm, IA). Aggregate factions showed a remarkable effect on association networks of nematodes and ammonia oxidizers. The average connectivity (avgK) and the number of edges in overall networks increased with increasing aggregate sizes, while the average geodesic distance (GD) followed the opposite trend. The LA network could be viewed as a better organized or a better operational soil food web with more functional interrelated members than the SA and IA networks. The modules related to PNA were significantly correlated and clustered together as meta-modules in networks of aggregate fractions. The role-shifts prevailed among the network members such as significant module memberships (MMs) and generalist/specialist operational taxonomic units (OTUs). A half of shared nodes were further identified as shared MMs, dominated by ammonia-oxidizing bacteria (AOB) especially for Nitrosospira cluster 3a and 10. Soil pH could explain partly the shift of module hubs in different networks, while grazing by bacterivores might account for three exclusively connecters related to Nitrososphaera clusters 1.1. The strongly coupled modules correlated positively to pH and total carbon (TC), regardless of aggregate fractions. The network analysis approach provided new insights into potential importance of network interactions between nematodes and ammonia oxidizers in soil nitrogen cycling.     

Short-term population dynamics of ammonia oxidizing bacteria in an agricultural soil

Ammonia oxidizing bacteria (AOB) control the rate limiting step of nitrification, the conversion of ammonia (NH₄⁺) to nitrite (NO₂⁻). The AOB therefore have an important role to play in regulating soil nitrogen cycling. Tillage aerates the soil, stimulating rapid changes in soil N cycling and microbial communities. Here we report results of a study of the short term responses of AOB and net nitrification to simulated tillage and NH₄⁺ addition to soil. The intensively farmed vegetable soils of the Salinas Valley, California, provide the context for this study. These soils are cultivated frequently, receive large N fertilizer inputs and there are regional concerns about groundwater N concentrations. An understanding of N dynamics in these systems is therefore important. AOB population sizes were quantified using a real-time PCR approach. In a 15 day experiment AOB populations, increased rapidly following tillage and NH₄⁺ addition and persisted after the depletion of soil NH₄⁺. AOB population sizes increased to a similar degree, over a 1.5-day period, irrespective of the amount of NH₄⁺ supplied. These data suggest selection of an AOB community in this intensively farmed and C-limited soil, that rapidly uses NH₄⁺ that becomes available. These data also suggest that mineralization may play an especially important role in regulating AOB populations where NH₄⁺ pool sizes are very low. Methodological considerations in the study of soil AOB communities are also discussed.     

Subtle changes in rhizosphere microbial community structure in response to increased boron and sodium chloride concentrations

Two of the major constraints to grain production in large areas of South-East Australia and cropping soils worldwide are high levels of subsoil boron (B) and excessive salinity (NaCl). Although the effect of these constraints is often studied in plants, the effect on microbially mediated plant-beneficial processes is unclear. To that end, we investigated the impact of B and NaCl on soil microbial community structure (MCS) in the wheat rhizosphere using BIOLOG ecoplates and terminal restriction fragment length polymorphism (T-RFLP). In addition, the effects of B and NaCl on the nitrogen (N) cycle processes of N fixation and ammonia oxidation were assessed by the construction of clone libraries of diazotrophic (nifH) and ammonia oxidising (amoA) rhizobacteria. Analysis of BIOLOG plates using non-metric multidimensional scaling (MDS) revealed addition of both B and NaCl significantly changed MCS, the latter of which was also significant through the analysis of T-RFLP data. Utilisation of several chemical groups of BIOLOG substrates significantly changed in NaCl-amended soil; both B and NaCl affected utilisation of several individual substrates indicative of plant stress including serine and malic acid. A significant decrease in diversity and species richness was observed in high B rhizosphere soil. The community structure of ammonia-oxidising bacteria (AOB), all of which clustered with Nitrosospira-like sequences, did not significantly change in response to addition of B or NaCl, but addition of the latter resulted in a significant increase of diazotroph clones within the α-proteobacteria similar to Azospirillum sp. It appeared that the addition of B and NaCl to soil changed rhizosphere MCS indirectly through increased soil moisture and subtle changes in root exudate patterns, the addition of the latter producing a more distinct change through increased osmotic pressure, leading to a greater increase in rhizodeposition of nutrients, especially carbohydrates. The implications for the current study are that B and NaCl are more likely to affect rhizosphere MCS indirectly through root exudate quantity and/or quality than directly through microbial toxicity, and that plant health is a major determinant in rhizosphere MCS and normal N cycling.     

Fluctuations in the abundance of ammonia oxidizers and the contents of inorganic nitrogen in solarized soil

Solarization makes a great impact on the abundance of ammonia oxidizers and nitrifying activity in soil. To elucidate fluctuations in the abundance of ammonia oxidizers and nitrification in solarized soil, copy numbers of amoA gene of ammonia-oxidizing bacteria (AOB) and archaea (AOA), viable number of ammonia oxidizers and inorganic nitrogen contents were investigated in greenhouse experiments. The copy number of amoA gene and the viable number of ammonia oxidizers were determined by the quantitative polymerase chain reaction and most probable number methods, respectively. Abundance of AOB based on the estimation of amoA gene copy numbers and viable counts of ammonia oxidizers was decreased by the solarization treatment and increased during the tomato (Solanum lycopersicum L.) cultivation period following the solarization. Effect of solarization on the copy number of amoA gene of AOA was less evident than that on AOB. The proportion of nitrate in inorganic nitrogen contents was declined by the solarization and increased during the tomato cultivation period following the solarization. Positive correlations were found between the proportion of nitrate in inorganic nitrogen content and the copy number of bacterial or archaeal amoA gene or the viable number of ammonia oxidizers; the copy number of bacterial amoA gene showed a strong correlation with the viable number of ammonia oxidizers. The present study revealed influences of solarization on the fluctuation in the abundance of ammonia oxidizers and dynamics of inorganic nitrogen contents in soil and the results indicate that the determination of amoA gene of AOB is possibly a quick and useful diagnostic technique for evaluating suppression and restoration of nitrification following solarization.     

Controls on nitrification in a water-limited ecosystem: experimental inhibition of ammonia-oxidising bacteria in the Patagonian steppe

We studied controls on nitrification in an undisturbed water-limited ecosystem by inhibiting autotrophic nitrifying bacteria in soils with varying levels of vegetative cover. The activity of nitrifying bacteria was disrupted using nitrapyrin, 2-chloro-6-(trichloromethyl)-pyridine, under field conditions in three microenvironments (underneath shrubs, next to grasses and in bare soil). Ammonia-oxidising bacteria were detected by PCR analysis of DNA in soils. The inhibition of nitrification changed the concentrations of NO₃⁻ and NH₄⁺ in the soil, while the microenvironment was most important in determining the response of bacteria to the inhibitor. Nitrapyrin application resulted in a significant (p<0.05) reduction in soil NO₃⁻ concentration (39%) and a significant increase (p<0.001) in soil NH₄⁺ concentration (41%). Untreated bare-soil microenvironments had the lowest concentrations of NH₄⁺ (1.57 μg/g of dry soil) and NO₃⁻ (0.49 μg/g of dry soil) when compared to the other microenvironments, and showed the highest impacts of nitrification inhibition. For example, NH₄⁺ concentrations increased 288% and NO₃⁻ concentrations decreased 60% in inhibited bare-soil microenvironments. In contrast, untreated microenvironments underneath shrubs had the highest levels of NH₄⁺ (10.01 μg/g of dry soil) and NO₃⁻ (0.69 μg/g of dry soil), but showed no significant effects of inhibition of nitrification on soil nitrogen concentrations.     

The abundance of nitrogen cycle genes amoA and nifH depends on land-uses and soil types in South-Eastern Australia

Nitrogen is a critical nutrient in plant-based primary production systems, therefore measurements of N cycling by microorganisms may add value to agricultural soil monitoring programs. Bacterial-mediated nitrogen cycling was investigated in soils from two broad land-uses (managed and remnant vegetation) across different Soil Orders from three geomorphic zones in Victoria, Australia, by examining the abundance of the genes amoA and nifH using quantitative polymerase chain reaction (qPCR). The aim of the study was to identify parameters influencing bacterial populations possessing the genes nifH and amoA, and examine their distribution at a regional scale across different management treatments. The gene amoA was most abundant in the neutral to slightly alkaline surface soils from Calcarosols in North-West Victoria. There was a highly significant (P < 0.001) interaction between land-use and geomorphic zones in terms of the abundance of amoA. Detection of the gene nifH was site specific with low copy number (less than 100 copies per nanogram of DNA) observed for some strongly acidic surface soil sites in North-East Victoria (Dermosols) and South-West Victoria (Sodosols/Chromosols), while nifH was more abundant in selected Calcarosols of North-West Victoria. The gene amoA was detected across more sites than nifH and was strongly influenced by land-use, with almost consistently greater abundance in managed compared to remnant sites, particularly for North-West and South-West Victoria. The abundance of nifH was not related to land-use, with similar copy numbers observed for both managed and remnant sites at some locations. For the gene nifH, there was no significant interaction between land-use and geomorphic zones, between managed and remnant sites or between the three geomorphic zones. Regression tree analysis revealed a number of likely soil chemical and microbial variables which may act as drivers of gene abundance of amoA and nifH. Variables identified as drivers for amoA included pH, Olsen P, microbial biomass carbon, nitrate and total nitrogen while for nifH the variables were microbial biomass carbon, electrical conductivity, microbial biomass nitrogen, total nitrogen and total potassium. Measures of N cycling genes could be used as an additional indicator of soil health to assess potential ecosystem functions. The spatial scale of the current study demonstrates that a landscape approach may assist soil health monitoring programs by evaluating N cycle gene abundance in the context of the different microbial and chemical conditions related to Soil Order and land-use management.     

Impacts of different N management regimes on nitrifier and denitrifier communities and N cycling in soil microenvironments

Real-time quantitative PCR assays, targeting part of the ammonia monooxygenase (amoA), nitrous oxide reductase (nosZ), and 16S rRNA genes were coupled with ¹⁵N pool dilution techniques to investigate the effects of long-term agricultural management practices on potential gross N mineralization and nitrification rates, as well as ammonia-oxidizing bacteria (AOB), denitrifier, and total bacterial community sizes within different soil microenvironments. Three soil microenvironments [coarse particulate organic matter (cPOM; >250 μm), microaggregate (53-250 μm), and silt-and-clay fraction (<53 μm)] were physically isolated from soil samples collected across the cropping season from conventional, low-input, and organic maize-tomato systems (Zea mays L.-Lycopersicum esculentum L.). We hypothesized that (i) the higher N inputs and soil N content of the organic system foster larger AOB and denitrifier communities than in the conventional and low-input systems, (ii) differences in potential gross N mineralization and nitrification rates across the systems correspond with AOB and denitrifier abundances, and (iii) amoA, nosZ, and 16S rRNA gene abundances are higher in the microaggregates than in the cPOM and silt-and-clay microenvironments. Despite 13 years of different soil management and greater soil C and N content in the organic compared to the conventional and low-input systems, total bacterial communities within the whole soil were similar in size across the three systems (∼5.15 × 10⁸ copies g⁻¹ soil). However, amoA gene densities were ∼2 times higher in the organic (1.75 × 10⁸ copies g⁻¹ soil) than the other systems at the start of the season and nosZ gene abundances were ∼2 times greater in the conventional (7.65 × 10⁷ copies g⁻¹ soil) than in the other systems by the end of the season. Because organic management did not consistently lead to larger AOB and denitrifier communities than the other two systems, our first hypothesis was not corroborated. Our second hypothesis was also not corroborated because canonical correspondence analyses revealed that AOB and denitrifier abundances were decoupled from potential gross N mineralization and nitrification rates and from inorganic N concentrations. Our third hypothesis was supported by the overall larger nitrifier, denitrifier, and total bacterial communities measured in the soil microaggregates compared to the cPOM and silt-and-clay. These results suggest that the microaggregates are microenvironments that preferentially stabilize C, and concomitantly promote the growth of nitrifier and denitrifier communities, thereby serving as potential hotspots for N₂O losses.     

Cause and duration of mustard incorporation effects on soil-borne plant pathogenic fungi

Two fungal plant pathogens, Rhizoctonia solani AG 2-2 and Fusarium oxysporum f.sp. lini, were studied in relation to general responses of soil fungi and bacteria following incorporation of Brassica juncea. Our aim was to understand to what extent the changes in the biological and physicochemical characteristics of the soil could explain the effects on the studied pathogens and diseases, and to determine the temporal nature of the responses. Short-term effects of mustard incorporation (up to 4 months) were investigated in a microcosm experiment, and compared with a treatment where composted plant material was incorporated. In a field experiment, the responses were followed up to 11 months after removal or incorporation of a mustard crop. In general, responses in the variables measured changed more after incorporation of fresh mustard material than after addition of similar amounts of composted plant material (microcosms) or after removal of the mustard crop (field). The soil inoculum potential of R. solani AG 2-2 decreased directly after incorporation of mustard, but increased later to disease levels above those in the untreated soil. Neither of these effects could be explained by changes in the population density of R. solani AG 2-2. Fusarium spp. were less influenced, although an increase in the suppressiveness to Fusarium wilt was observed after mustard incorporation as compared with the treatment where mustard was removed. The microbial responses to mustard incorporation were more pronounced for bacteria than for fungi. After an initial substantial increase, the bacterial density decreased but remained above the levels in the control treatment throughout the experimental periods. The bacterial community structure was modified up to 8 months after mustard incorporation. We conclude that incorporation of fresh mustard influences soil microbial communities, especially the bacteria, and has a potential to control the pathogenic activity of R. solani 2-2 on a short-term perspective. The time dependency in microbial responses is important and should be taken into consideration for the evaluation of the potential of Brassicas to control plant disease on a field scale.     

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     

Hydraulic lift may buffer rhizosphere hyphae against the negative effects of severe soil drying in a California Oak savanna

Many studies have shown that the total abundance of hyphae in the soil covaries seasonally with soil moisture. We investigated the extent to which soil hyphal abundance varies as a function of depth and moisture availability within the soil profile during the dry season, and determined whether soil moisture compensation via hydraulic lift (HL) buffers rhizosphere fungi from the effects of severe soil drying. We measured soil water potential, isotopic composition of soil water and total hyphal length in a California coast live oak stand and adjacent grassland at the beginning and end of the 5-month summer drought period. Throughout the summer, oaks maintained predawn water potential values (−0.4±0.1 MPa) that were significantly above those recorded in the 0-200 cm soil depth interval, strongly suggesting root access to groundwater. Direct evaporation of soil water was much more intense and affected deeper layers of the profile in the grassland compared to the oak stand, as indicated by extremely negative water potential values and very enriched isotopic composition of soil water near the surface. Significantly higher soil water potential and less isotopically enriched soil water at 15-40 cm depth in the oak stand were consistent with oak root exudation of isotopically depleted groundwater or deep soil water not exposed to evaporation. Hyphal length in the soil profile declined markedly during the summer drought period in the grassland, particularly in upper layers (41-75% decrease at 0-40 cm depth), indicating rapid turnover of the arbuscular mycorrhizae (AMF) dominated hyphal carbon pool after grass senescence. By contrast, soil hyphal length in the ectomycorrhizal (EM)/AM oak stand remained remarkably constant throughout the summer drought period, with the only exception of the topsoil layer exposed to direct evaporation (49% decrease at 5 cm depth). The sustained exudation of water from roots to soil through HL may have buffered rhizosphere hyphae against the negative effects of extreme soil desiccation in the oak stand. These data suggest that HL by deep-rooted trees may influence the biogeochemical cycling of carbon and nutrients in seasonally dry ecosystems through effects on rhizosphere fungi.     

Long term effects of a brown coal-based amendment on the properties of soil humic acids

In this study a typical grey-brown podzolic soil was amended with different doses of a brown coal-based preparation called Rekulter (R) largely used in Poland. After seven years, soils were analyzed and humic acids (HAs) were extracted both from the control soil and from the amended soils. All HAs were characterized by Fourier transform infrared spectroscopy and fluorescence spectroscopy both in emission, excitation and synchronous-scan mode and as Excitation-Emission-Matrix (EEM) contour maps. A higher carbon content was observed in the amended soils whereas significant differences were highlighted between the unamended and the amended soil HAs. HAs from amended soils showed a higher content of carboxyl groups and a more aromatic character, particularly HA extracted from the soil amended with the highest dose of R.     

Assessing the potential of ammonia oxidizing bacteria to produce nitrous oxide in soils of a high arctic lowland ecosystem on Devon Island, Canada

The contribution of nitrifiers (ammonia-oxidizing bacteria (AOB)) and denitrifiers to nitrous oxide (N₂O) emission from arctic soils remains inconclusive. Based on preliminary experiments, we hypothesized that AOB are the primary producers of N₂O in a high arctic lowland ecosystem on Devon Island, Nunavut, Canada. In part 1 of the study, flux chambers were installed in a catena to determine in situ fluxes of gases (N₂O and carbon dioxide (CO₂)) from 16 June to 13 July 2004. Although fluxes were low, N₂O production occurred in the wettest area of the landscape when ammonium levels were high. As ammonium, but not nitrate, levels declined in the wet sedge meadow, N₂O emissions correspondingly decreased. In part 2, the contribution of nitrification and denitrification to N₂O production was assessed by Acetylene Inhibition Assay and ¹⁵N isotopically enriched incubations. Ammonium fertilization stimulated N₂O emissions to a greater extent than nitrate, and acetylene had a greater impact on N₂O emissions in ammonium-fertilized soils than in nitrate-amended soils. Stable isotope analysis indicated that at 50-55% water filled pore space, nitrification was the dominant (>80%) N₂O emitting process. In part 3, molecular analyses of the two N₂O producing groups indicated the both nitrifiers and denitrifiers did not differ between landforms. Our results suggest nitrifier denitrification is the dominant process occurring in these arctic soils and that the role of denitrifiers in N₂O release from arctic soils needs to be re-evaluated.     

转基因水稻秸秆还田对土壤硝化反硝化微生物群落的影响

转基因作物可能通过根系分泌物和植株残体组成的改变及外源基因的转移释放令土壤微生物群落产生变化,影响土壤微生物的生态功能。氨氧化细菌和反硝化细菌是驱动土壤硝化和反硝化过程的关键微生物,其群落结构的变化直接关系土壤氮素的转化与利用。本研究利用荧光定量PCR和PCR-DGGE技术分析了转cry1Ac/cpti双价抗虫基因水稻‘Kf8’秸秆还田降解过程中,土壤氨氧化细菌和反硝化细菌群落丰度与组成的变化,探讨转基因水稻是否存在影响稻田土壤氮素转化与N2O排放的可能。结果显示:无论是氨氧化细菌amo A基因还是反硝化细菌nirS基因,其丰度在转基因水稻‘Kf8’与非转基因水稻‘Mh86’的秸秆还田土壤中都没有显著差异;转基因水稻‘Kf8’和非转基因水稻‘Mh86’秸秆还田降解过程中0~10 cm土层中的amo A基因丰度均显著高于10~20 cm及20~30 cm土层(P0.05);各深度土层中的nirS基因丰度均存在随秸秆还田时间延长而增加的趋势。水稻秸秆还田降解过程中,转基因水稻‘Kf8’的土壤氨氧化细菌和反硝化细菌的群落多样性指数及组成,均与非转基因水稻‘Mh86’没有显著差异。相关分析结果表明土壤氨氧化细菌和反硝化细菌群落组成均与水稻秸秆还田时间存在显著相关性(P=0.002),反硝化细菌群落组成还与土层深度显著相关(P=0.024)。本研究表明转cry1Ac/cpti抗虫基因水稻秸秆还田对稻田土壤硝化和反硝化关键微生物群落不会产生明显影响。就土壤微生物群落而言,转cry1Ac/cpti抗虫基因水稻秸秆还田不存在影响土壤氮素转化与N2O排放的可能。     

Soil feedback effects to the foredune grass Ammophila arenaria by endoparasitic root-feeding nematodes and whole soil communities

In coastal foredunes, the grass Ammophila arenaria develops a soil community that contributes to die-back and replacement by later successional plant species. Root-feeding nematodes and pathogenic soil microorganisms are involved in this negative feedback. Regular burial by wind-blown beach sand results in vigorous growth of A. arenaria, probably because of enabling a temporary escape from negative soil feedback. Here, we examine the role of root-feeding nematodes as compared to the whole soil community in causing negative feedback to A. arenaria. We performed a 3-year sand burial experiment in the field and every year we determined the feedback of different soil communities to plant growth in growth chamber bioassays.In the field, we established A. arenaria in tubes with beach sand, added three endoparasitic root-feeding nematode species (Meloidogyne maritima, Heterodera arenaria and Pratylenchus penetrans) or root zone soil to the plants, and created series of ceased and continued sand burial. During three subsequent years, plant biomass was measured and numbers of nematodes were counted. Every year, bioassays were performed with the field soils and biomass of seed-grown A. arenaria plants was measured to determine the strength of feedback of the established soil communities to the plant.In the field, addition of root zone soil had a negative effect on biomass of buried plants. In the bioassays, addition of root zone soil also reduced the biomass of newly planted seedlings, however, only in the case when the field plants had not been buried with beach sand. Addition of the three endoparasitic root-feeding nematodes did not influence plant biomass in the field and in the bioassays. Our results strongly suggest that the negative feedback to A. arenaria is not due to the combination of the three endoparasitic nematodes, but to other components in the soil community, or their interactions with the nematodes.     

Crude extract of Astragalus mongholicus root inhibits crop seed germination and soil nitrifying activity

Astragalus mongholicus has been of medicinal use within the traditional Chinese system for centuries. However, little information is available on its allelopathic effects on other crop plants and soil biochemical properties. Field experiment showed that the extracted residues of A. mongholicus root inhibited seed germination of wheat. Inhibition of seed germination was further confirmed in laboratory using the same crude extract. When the crude extract was applied to soil at various rates and incubated for 30 days, soil urease activity and denitrifying enzyme activity were significantly increased while soil nitrification rate was significantly decreased at 10% amendment rate as compared to the control. Soil respiration rate was significantly increased by the crude extract when measured at the start of incubation but returned to basal levels after 30 days of incubation. The crude extract supplemented to NB medium significantly decreased the colony numbers of Agrobacterium tumefaciens C58, Paraccocus denitrificans and soil bacteria. The stimulating effects of crude extract observed in the amended soil was attributed to the easily-available carbohydrates in the extract, which might served as external energy sources for heterotrophic microbial activities. It was concluded that A. mongholicus contained some compounds that inhibited seed germination, soil nitrification and bacterial growth in general. Possible links between allelochemicals responsible for the inhibitory effects observed in the present study and the medically bioactive compounds are discussed based on information reported in other fields. Further work is needed to specify and verify the allelochemicals produced by this herbal plant.     

Fate, tree growth effect and potential impact on soil microbial communities of mycorrhizal and bacterial inoculation in a forest plantation

The knowledge of the survival of inoculated beneficial fungal and bacterial strains in the field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developing. The aim of this study was to monitor, 4 years after plantation into the field site, the effects of Douglas fir (Pseudotsuga menziesii) co-inoculation with the mycorrhiza helper bacterial strain Pseudomonas fluorescens BBc6R8 and/or the fungal strain Laccaria bicolor S238N on seedling growth and on the indigenous bacterial and ectomycorrhizal communities using quantitative and qualitative approaches. The field persistence of the inoculated strains was also monitored. The seedling shoot volume estimate was statistically significantly higher in the fungal inoculated plots in comparison to the non-inoculated plots but no treatment-related changes in the quantitave or qualitative microbial measurements were observed and the inoculated strains could not be detected after 4 years.     

Influence of urea on the cherry leaf spot pathogen, Blumeriella jaapii, and on microorganisms in decomposing cherry leaves

Growth chamber and orchard experiments were carried out to clarify the response of the cherry leaf spot pathogen, Blumeriella jaapii, and microorganisms in the leaf litter to two levels of urea (2.5% or 5%) applied post leaf fall to sour cherry leaves. In general, urea application reduced the development of B. jaapii measured as biomass by quantitative PTA-ELISA in the leaf litter and spore counting in the spring and increased the overall microbial biomass (measured with biomarker phospholipid fatty acids (PLFAs)) and fungal activity (assessed as β-N-acetylglucosaminidase activity). The biomass increase of all groups of microorganisms in the litter generally began immediately after application of urea and, with the notable excepts of B. jaapii and Gram-negative bacteria containing the biomarker PLFA cyclo17:0, continued after the ammonia and pH levels had stabilized to levels similar to the control leaves approximately 10 days later. Application of 2.5% urea increased the biomass of most groups of saprotrophic microorganisms and accelerated litter decomposition to a higher extent than application of 5% urea and during the first week after treatment applications the 5% urea level inhibited the total microbial biomass. This may be ascribed to ammonia toxicity as 5% urea resulted in a markedly higher ammonia elevation than 2.5% urea, the first week after application. From then onwards in both the 2.5% and 5% treatments the fungal and Gram-positive communities benefited from a lowered C:N ratio, increasing their activities approximately 2 times compared to a water-treated control. Inhibition of B. jaapii coincided with the period of urea breakdown in which elevated levels of ammonia and leaf pH were measured in the treated leaves. This period lasted for approximately 10 days after which the biomass of B. jaapii in the treated leaves continued to decrease at a slow but faster rate than in the untreated leaves. Our results indicate that the urea application caused an elevation in leaf pH and ammonia levels, which together with an acceleration in litter decomposition, adversely affected the saprotrophic growth of B. jaapii, leading to reduced production of ascospores and winter-conidia the following spring.     

Impacts of silver nanoparticles on enzymatic activities, nitrifying bacteria, and nitrogen transformation in soil amended with ammonium and nitrate

Silver nanoparticles (AgNPs) are effective antimicrobial compounds that are used in a myriad of applications. Soil microorganisms play crucial roles in nitrogen cycling, but there is a lack of comprehensive understanding of the effects of AgNPs on enzymatic activity in the nitrogen cycle, nitrifying bacteria, and nitrogen transformation in soil. Herein, enzyme activities were determined following the addition of different forms of nitrogen, ammonium nitrogen ((NH₄)₂SO₄), nitrate nitrogen (KNO₃), and amide nitrogen (urea, CO(NH₂)₂) at 200 mg N kg^-1, into the soil amended with AgNPs at 0, 10, 50, and 100 mg kg^-1. After 7 d of incubation with 10 mg kg^-1 AgNPs, the activities of urease, nitrite reductase (NiR), nitrate reductase (NaR), and hydroxylamine reductase (HyR) were reduced by 12.5%, 25.0%, 12.2%, and 24.2%, respectively. Of particular note, more than 53.5%, 61.7%, and 34.7% of NaR, NiR, and HyR activities, respectively, were inhibited at 100 mg kg^-1AgNPs. The abundance (most probable number) of ammonia- and nitrite-oxidizing bacteria (AOB and NOB, respectively) was measured using real-time quantitative polymerase chain reaction (qPCR) and the Cochran method. The abundance of AOB and NOB decreased when AgNPs were present in the soil. The NH₄NO₃ amendment increased copy numbers of bacterial and archaeal amoA nitrification functional genes, by 38.3% and 12.4%, respectively, but AgNPs at 50 mg kg^-1 decreased these values by 70% and 56.4%, respectively. The results of ¹⁵N enrichment (atom% excess) of NH₄⁺ and NO₃^- experiments illustrated the influence of AgNPs on soil nitrogen transformation. According to the ¹⁵N atom% excess detected, the conversion of ¹⁵N-labeled NH₄⁺ to NO₃^- was significantly inhibited by the different levels of AgNPs in soil. The reduced gross nitrification rate further confirmed this finding. Overall, this study revealed considerable evidence that AgNPs inhibited nitrogen cycle enzyme activity, the number of nitrifying bacteria, the abundance of the amoA gene, and the gross nitrification rate. Silver nanoparticles inhibited nitrogen transformation, and the rate of nitrification was also negatively correlated with AgNP levels.     

Rhizosphere activity, grass species and N availability effects on the soil C and N cycles

We examined whether grass species and soil nitrogen (N) availability could enhance Carbon (C) and N turnover during root litter decay in grassland. Three species with increasing competitiveness (Festuca ovina, Dactylis glomerata and Lolium perenne) were grown at two N fertiliser levels in an undisturbed grassland soil, in which soil organic fractions derived for the last 9 years from Lolium root litter which was ¹³C-depleted. During the subsequent experimental year, the C turnover was calculated using the respective δ¹³C values of the old and new C in the root phytomass, in two Particulate Organic Matter (POM) fractions above 200 μm and in the lightest part of the aggregated soil fraction between 50 and 200 μm. Soil N availability was monitored during the regrowth periods with ion exchange resins (IER). The C decay rates of each particle size fraction were calculated with a simple mechanistic model of C dynamics. The N mineralisation immobilisation turnover (MIT) was characterised by dilution of ¹⁵N-labelled fertiliser in the N harvestThe C:N ratio and the residence time of C in the fractions decreased with particle size. The presence of a grass rhizosphere increased the decay rate of old C. Accumulation of new C in particle size fractions increased with species competitiveness and with N supply. Species competitiveness increased C turnover in the aggregated fraction, as a result of greater accumulation of new C and faster decay of old C. Fertiliser N increased N turnover and C mineralisation in the SOM. Species competitiveness decreased soil -N exchanged with the IER and increased dissolved organic C (DOC) content. The nature of the current rhizosphere is thus an important factor driving C and N transformations of the old root litter, in relation with grass species strategy. Plant competitiveness may stimulate the C and N turnover in the more evolved SOM fractions in a similar way to the mineral N supply.