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.     

Fate of gram-negative bacterial biomass in soil—mineralization and contribution to SOM

Soil microorganisms contribute to the formation of non-living soil organic matter (SOM) by metabolic transformation of plant-derived material. After cell death, their biomass components with a specific molecular character become incorporated into SOM imprinting its chemical properties, although this process has not yet been quantified. In order to elucidate the contribution to SOM formation, we investigated the fate of gram-negative bacterial model biomass (Escherichia coli usually introduced into soil with manure or feces) during incubation of soil with isotopically (¹³C) and genetically (lux gene) labeled cells. The decline of living cells was monitored by the loss of bioluminescence. The carbon turnover and mineralization was balanced by bulk soil stable isotope analysis, and the persistence of nucleic acids was investigated by PCR amplification of the lux gene. During incubation, the number of viable E. coli cells decreased rapidly (99.9% within the first 42 d) serving as substrate for other microorganisms or for the formation of SOM, and bioluminescent cells could only be detected during the first 56 d. However, the lux gene was still detected after 224 d, which indicates stabilization of DNA in SOM. Although the survival of E. coli in soil is limited, only about 65% of the added labeled biomass carbon was mineralized to ¹³CO₂ and 51% remained in soil after 224 d with an average ¹³C recovery of 117%. The amount of ¹³C found in the PLFA representative of living cells had decreased to 25% of the initial value, suggesting a proportional decrease of the ¹³C in the soil microbial biomass. The extent of this decrease is higher than the mineralization of the bulk E. coli C and thus the difference of around 25% has to be stabilized as metabolites, or in non-living SOM. The data provide evidence that the genetic information and a considerable part of the carbon from dying bacterial biomass were retained in both the soil microbial food web and in non-living SOM.     

Role of soil drying in nitrogen mineralization and microbial community function in semi-arid grasslands of north-west Australia

We examined effects of wetting and then progressive drying on nitrogen (N) mineralization rates and microbial community composition, biomass and activity of soils from spinifex (Triodia R. Br.) grasslands of the semi-arid Pilbara region of northern Australia. We compared soils under and between spinifex hummocks and also examined impacts of fire history on soils over a 28 d laboratory incubation. Soil water potentials were initially adjusted to −100 kPa and monitored as soils dried. We estimated N mineralization by measuring changes in amounts of nitrate (NO₃⁻-N) and ammonium (NH₄⁺-N) over time and with change in soil water potential. Microbial activity was assessed by amounts of CO₂ respired. Phospholipid fatty acid (PLFA) analyses were used to characterize shifts in microbial community composition during soil drying. Net N mineralized under hummocks was twice that of open spaces between hummocks and mineralization rates followed first-order kinetics. An initial N mineralization flush following re-wetting accounted for more than 90% of the total amount of N mineralized during the incubation. Initial microbial biomass under hummocks was twice that of open areas between hummocks, but after 28 d microbial biomass was<2 μ g⁻¹ ninhydrin N regardless of position. Respiration of CO₂ from soils under hummocks was more than double that of soils from between hummocks. N mineralization, microbial biomass and microbial activity were negligible once soils had dried to −1000 kPa. Microbial community composition was also significantly different between 0 and 28 d of the incubation but was not influenced by burning treatment or position. Regression analysis showed that soil water potential, microbial biomass N, NO₃⁻-N, % C and δ¹⁵N all explained significant proportions of the variance in microbial community composition when modelled individually. However, sequential multiple regression analysis determined only microbial biomass was significant in explaining variance of microbial community compositions. Nitrogen mineralization rates and microbial biomass did not differ between burned and unburned sites suggesting that any effects of fire are mostly short-lived. We conclude that the highly labile nature of much of soil organic N in these semi-arid grasslands provides a ready substrate for N mineralization. However, process rates are likely to be primarily limited by the amount of substrate available as well as water availability and less so by substrate quality or microbial community composition.     

Effects of trifluralin and metabolites on the decomposition of selected substrates by soil microorganisms

Summary The effects of trifluralin and 12 of its soil-formed metabolites on the decomposition of radio-labelled glucose, protein and cellulose were determined, using ¹⁴CO₂ evolution from soil as a measure of decomposition. Trifluralin increased ¹⁴C-glucose mineralization rates, but these increases could be eliminated by adding N. Trifluralin had no inhibitory effect on the mineralization of protein or cellulose, but five of the metabolites inhibited glucose mineralization. None of the trifluralin metabolites affected protein mineralization. Seven trifluralin metabolites increased the rate of cellulose mineralization when applied at rates exceeding those that would be expected in soil. After considering the rate of metabolite application and the magnitude of the responses observed these compounds are expected to have no major effects on the microbial decomposition processes in soil.     

Transformation of C-labelled lignin and humic substances in forest soil by the saprobic basidiomycetes Gymnopus erythropus and Hypholoma fasciculare

Litter decomposing basidiomycetous fungi produce ligninolytic oxidases and peroxidases which are involved in the transformation of lignin, as well as humic and fulvic acids. The aim of this work was to evaluate their importance in lignin transformation in forest litter. Two litter decomposing basidiomycete species differing in their abilities to degrade lignin - Hypholoma fasciculare, and Gymnopus erythropus - were cultured on sterile or non-sterile oak litter and their transformation of a ¹⁴C-labelled synthetic lignin (dehydrogenation polymer ¹⁴C-DHP) was compared with that of the indigenous litter microflora. Both in sterile and non-sterile litter, colonisation by basidiomycetes led to higher titres of lignocellulose-degrading enzymes, in particular of laccase and Mn-peroxidase (MnP). The titres of the latter were 6 to 40-fold increased in the presence of basidiomycetes compared to non-sterile litter. During 10 weeks, G. erythropus mineralised over 31% of ¹⁴C-DHP in sterile litter and 23% in non-sterile litter compared to 14% in the non-sterile control. Lignin mineralization by H. fasciculare was comparable to the non-sterile control, 12% in sterile litter and 16% in the non-sterile litter. The largest part of ¹⁴C from ¹⁴C-DHP was transformed into humic compounds during litter treatment with both fungi as well as in the control. In addition to the fast lignin mineralization, microcosms containing G. erythropus also showed a lower final content of unaltered lignin and 23-28% of the lignin was converted into water-soluble compounds with relatively low molecular mass (<5 kDa). Both G. erythropus and H. fasciculare were also able to further mineralise humic compounds. During a 10-week fungal treatment of an artificial ¹⁴C-humic acid (¹⁴C-HA) supplemented to the natural humic material of a forest soil, the fungi mineralised 42% and 19% of the labelled material, respectively, under sterile conditions. The ¹⁴C-HA mineralization by introduced basidiomycetes in microcosms containing non-sterile humic material, however, did not significantly differ from that of a non-sterile control and was around 12%. Altogether the results show that saprobic basidiomycetes can considerably differ in their rates of lignin and humic substance conversion. Furthermore, lignin degradation in forest soil can rather slow down by interspecific competition than it is accelerated by cooperation of different microorganisms occupying specific nutritional niches. Therefore, the overall contribution of saprobic basidiomycetes depends on their particular eco-physiological status and the competitive pressure, and may be often lower than initially expected. Significant lignin transformation including partial mineralization is seemingly not exclusively dependent on exceptional high titres of ligninolytic enzymes but also on so far unknown factors. Higher endocellulase production and subsequent weight loss was found in microcosms where saprobic basidiomycetes were combined with indigenous microbes. Potentially, lignin degradation by the basidiomycetes may have increased cellulose availability to the indigenous microbes.     

Nitrogen dynamics and microbial response in soil amended with either olive pulp or its by-products after biogas production

Olive pulp (OP), the residual material of a two-phase olive oil extraction system, and effluents from hydrogen (EH₂) and methane (ECH₄) production, have been evaluated as soil amendments particularly for their impact on soil mineral nitrogen (N) dynamics, gross N mineralization, and soil microbial biomass N (N_mic). Both N transformation and microbial growth were mainly influenced by the amount and quality of added organic carbon (C). Both OP and EH₂, which contain more carbohydrates and lipids than polyphenolic compounds, stimulated NO₃ ⁻ immobilization during the early incubation period and increased N_mic, saprophytic fungi, and N mineralization. On the contrary, soil amended with ECH₄, which is characterized by the lowest C content but the highest content of polyphenolic compounds, behaved as the control; neither NO₃ ⁻ immobilization nor microbial growth were observed and gross N mineralization was stimulated only at the beginning of the incubation period. Bacterial plate count was significantly correlated with direct bacterial count and fungal count was correlated with N_mic. Therefore, it is suggested that both bacterial and fungal plate counts may be used as indicators of the overall bacterial and fungal populations inhabiting soil, respectively. The knowledge of the impact of these materials on soil N dynamics is crucial for their correct use in agriculture because it has been shown that NO₃ ⁻ availability can be strongly influenced by the addition of different amounts and quality of organic amendment.     

Respiration pattern and microbial use of field-grown transgenic Bt-maize residues

A 49-day incubation experiment was carried out with the addition of field-grown maize stem and leaf residues to soil at three different temperatures (5, 15, and 25 °C). The aim was to study the effects of two transgenic Bt-maize varieties in comparison to their two parental non-Bt varieties on the mineralization of the residues, on their incorporation into the microbial biomass and on changes in the microbial community structure. The stem and leaf residues of Novelis-Bt contained 3.9 μg g⁻¹ dry weight of the Bt toxin Cry1Ab and those of Valmont-Bt only 0.8 μg g⁻¹. The residues of the two parental non-Bt varieties Nobilis and Prelude contained higher concentrations of ergosterol (+220%) and glucosamine (+190%) and had a larger fungal C-to-bacterial C ratio (+240%) than the two Bt varieties. After adding the Bt residues, an initial peak in respiration of an extra 700 μg CO₂-C g⁻¹ soil or 4% of the added amount was observed in comparison to the two non-Bt varieties at all three temperatures. On average of the four varieties, 19-38% of the maize C added was mineralized during the 49-day incubation at the three different temperatures. The overall mean increase in total maize-derived CO₂ evolution corresponded to a Q₁₀ value of 1.4 for both temperature steps, i.e. from 5 to 15 °C and from 15 to 25 °C. The addition of maize residues led to a strong increase in all microbial properties analyzed. The highest contents were always measured at 5 °C and the lowest at 25 °C. The variety-specific contents of microbial biomass C, biomass N, ATP and adenylates increased in the order Novelis-Bt ? Prelude<Valmont-Bt ? Nobilis. The mineralization of Novelis-Bt residues with the highest Bt concentration and lowest N concentration and their incorporation into the microbial biomass was significantly reduced compared to the parental non-Bt variety Nobilis. These negative effects increased considerably from 5 to 25 °C. The transgenic Bt variety Valmont did not show further significant effects except for the initial peak in respiration at any temperature.     

Coarse particulate organic matter is the primary source of mineral N in the topsoil of three beech forests

Forest soils contain a variable amount of organic N roughly repartitioned among particles of different size, microbial biomass and associated with mineral compounds. All pools are alimented by annual litter fall as main input of organic N to the forest floor. Litter N is further subject to mineralization/stabilization recognized as the crucial process for the turnover of litter N. Although it is well documented that different soil types have different soil N stocks, it is presently unknown how different soil types affect the turnover of recent litter N. Here, we compared the potential mineralization of the total soil organic N with that of recent litter-released N in three beech forests varying in their soil properties. Highly ¹⁵N-labelled beech litter was applied to stands located at Aubure, Ebrach, Collelongo, which differ in humus type, soil type and soil chemistry. After 4-5 years of litter decomposition, the upper 3 cm of the organo-mineral A horizon was sampled and the net N mineralization was measured over 112 days under controlled conditions. The origin of mineralized N (litter N versus soil organic N) was calculated using ¹⁵N labeling. In addition, soils were fractionated according to their particle size (>2000 μm, 200-2000 μm, 50-200 μm, <50 μm) and particulate organic matter (POM) was separated from the mineral fraction in size classes, except the <50 μm fraction. Between 41 and 69% of soil organic N was recovered as POM. Litter-released ¹⁵N was mainly to be found in the coarse POM fractions >200 μm. On a soil mass basis, N mineralization was two-fold higher at Aubure and Collelongo than at Ebrach, but, on a soil N basis, N mineralization was the lowest at Collelongo and the highest at Ebrach. On a soil N (or ¹⁵N) basis, mineralization of litter ¹⁵N was two to four-fold higher than mineralization of the average soil N. Furthermore, the δ¹⁵N of the mineral N produced was closer to that of POM than to that of the mineral-bound fraction (<50 μm). Highest rates of ¹⁵N mineralization happened in the soil with the lowest N content, and we found a negative relationship between accumulations of N in the upper A horizon and the mineralization of ¹⁵N from the litter. Our results show that mineral N is preferentially mineralized from POM in the upper organo-mineral soil irrespective of the soil chemistry and that the turnover rate of litter N is faster in soils with a low N content.     

Nitrapyrin effectiveness in reducing nitrous oxide emissions decreases at low doses of urea in an Andosol

In the tropics,frequent nitrogen(N)fertilization of grazing areas can potentially increase nitrous oxide(N₂O)emissions.The application of nitrification inhibitors has been reported as an effective management practice for potentially reducing N loss from the soil-plant system and improving N use efficiency(NUE).The aim of this study was to determine the effect of the co-application of nitrapyrin(a nitrification inhibitor,NI)and urea in a tropical Andosol on the behavior of N and the emissions of N₂O from autotrophic and heterotrophic nitrification.A greenhouse experiment was performed using a soil(pH 5.9,organic matter content 78 g kg^-1,and N 5.6 g kg^-1)sown with Cynodon nlemfuensis at 60%water-filled pore space to quantify total N₂O emissions,N₂O derived from fertilizer,soil ammonium(NH₄⁺)and nitrate(NO₃^-),and NUE.The study included treatments that received deionized water only(control,NI).No significant differences were observed in soil NH₄⁺content between the UR and UR+NI treatments,probably because of soil mineralization and NO₃^-produced by heterotrophic nitrification,which is not effectively inhibited by nitrapyrin.After 56 d,N₂O emissions in UR(0.51±0.12 mg N₂O-N concluded that the soil organic N mineralization and heterotrophic nitrification are the main processes of NH₄⁺and NO₃^-production.Additionally,it was found that N₂O emissions were partially a consequence of the direct oxidation of the soil's organic N via heterotrophic nitrification coupled to denitrification.Finally,the results suggest that nitrapyrin would likely exert significant mitigation on N₂O emissions only if a substantial N surplus exists in soils with high organic matter content.     

Interactions between residue placement and earthworm ecological strategy affect aggregate turnover and N2O dynamics in agricultural soil

Previous laboratory studies using epigeic and anecic earthworms have shown that earthworm activity can considerably increase nitrous oxide (N₂O) emissions from crop residues in soils. However, the universality of this effect across earthworm functional groups and its underlying mechanisms remain unclear. The aims of this study were (i) to determine whether earthworms with an endogeic strategy also affect N₂O emissions; (ii) to quantify possible interactions with epigeic earthworms; and (iii) to link these effects to earthworm-induced differences in selected soil properties. We initiated a 90-day ¹⁵N-tracer mesocosm study with the endogeic earthworm species Aporrectodea caliginosa (Savigny) and the epigeic species Lumbricus rubellus (Hoffmeister). ¹⁵N-labeled radish (Raphanus sativus cv. Adagio L.) residue was placed on top or incorporated into the loamy (Fluvaquent) soil. When residue was incorporated, only A. caliginosa significantly (p < 0.01) increased cumulative N₂O emissions from 1350 to 2223 μg N₂O-N kg⁻¹ soil, with a corresponding increase in the turnover rate of macroaggregates. When residue was applied on top, L. rubellus significantly (p < 0.001) increased emissions from 524 to 929 μg N₂O-N kg⁻¹, and a significant (p < 0.05) interaction between the two earthworm species increased emissions to 1397 μg N₂O-N kg⁻¹. These effects coincided with an 84% increase in incorporation of residue ¹⁵N into the microaggregate fraction by A. caliginosa (p = 0.003) and an 85% increase in incorporation into the macroaggregate fraction by L. rubellus (p = 0.018). Cumulative CO₂ fluxes were only significantly increased by earthworm activity (from 473.9 to 593.6 mg CO₂-C kg⁻¹ soil; p = 0.037) in the presence of L. rubellus when residue was applied on top. We conclude that earthworm-induced N₂O emissions reflect earthworm feeding strategies: epigeic earthworms can increase N₂O emissions when residue is applied on top; endogeic earthworms when residue is incorporated into the soil by humans (tillage) or by other earthworm species. The effects of residue placement and earthworm addition are accompanied by changes in aggregate and SOM turnover, possibly controlling carbon, nitrogen and oxygen availability and therefore denitrification. Our results contribute to understanding the important but intricate relations between (functional) soil biodiversity and the soil greenhouse gas balance. Further research should focus on elucidating the links between the observed changes in soil aggregation and controls on denitrification, including the microbial community.     

Mineralization of the herbicide MCPA in urban soils is linked to presence and growth of class III tfdA genes

Mineralization and sorption of ¹⁴C-ring labeled herbicide 2-methyl-4-chlorophenoxyacetic acid (MCPA) were quantified along with the tfdA gene abundance in 7 different soils. The soils tested were five gravel soils from urban locations, one soil from the embankment of a railway track, and finally an agricultural soil as a control. The mineralization experiments were performed with a concentration of MCPA of 5 mg/kg and incubated at 10 °C for a period of 60 days.With K_d values ranging from 0.04 to 0.41 l kg⁻¹ the sorption experiments revealed that binding of MCPA to the six gravel soils was lower compared to the control soil which had a K_d value of 0.91 l kg⁻¹. The potential for MCPA mineralization varied from less than 5 to over 55% mineralized in 60 days. The most rapid MCPA mineralization was observed in the soil from the Danish railway tracks with 55% mineralized after only 18 days. The mineralization data was fitted to degradation kinetic models, which indicated that growth occurred as a response to MCPA degradation in most of the soils.Soil DNA was extracted and tfdA genes responsible for the first step in MCPA degradation were quantified by real-time PCR (qPCR) at appropriate time points throughout the mineralization experiments. Indicating growth of specific MCPA degraders, the abundance of class III tfdA genes showed an increase during MCPA mineralization in those soils able to mineralize MCPA.These findings emphasize the importance of the presence of microorganisms that are able to readily degrade MCPA, to avoid groundwater leaching following use on urban gravel areas that possess low binding ability of the compound.     

Nitrate removal from drained and reflooded fen soils affected by soil N transformation processes and plant uptake

Knowledge about nitrate transformation processes and how they are affected by different plants is essential in order to reduce the loss of valuable N fertiliser as well as to prevent environmental pollution due to nitrate leaching or N₂O emission after fertilisation or the reflooding of degraded fens with nitrate-containing municipal sewage. Therefore four microcosm ¹⁵N tracer experiments were performed to evaluate the effect of common wetland plants (Phalaris arundinacea, Phragmites australis) combined with different soil moisture conditions (from dry to reflooded) on nitrate turnover processes. At the end of experiment, the total formation of gaseous N compounds was calculated using the ¹⁵N balance method. In two experiments (wet and reflooded soil conditions) the N₂O and N₂ emissions were also directly determined.Our results show that in degraded fen soils, which process mainly takes place—denitrification or transformation into organic N compounds—is determined by the soil moisture conditions. Under dry soil moisture conditions (water filled pore space: 31%) up to 80% of the ¹⁵N nitrate added was transformed into organic N compounds. This transformation process is not affected by plant growth. Under reflooded conditions (water filled pore space: 100%), the total gaseous N losses were highest (77-95% of the ¹⁵N-nitrate added) and the transformation into organic N compounds was very low (1.8% of ¹⁵N nitrate added). Under almost all soil conditions plant growth reduced the N losses by 20-25% of the ¹⁵N nitrate added due to plant uptake. The N₂ emissions exceeded the N₂O emissions by a factor of 10-20 in planted soil, and as much as 30 in unplanted soil. In the treatments planted with Phragmites australis, N₂O emission was about two times higher than in the corresponding unplanted treatment. 15% of the N₂O and N₂ formed was transported via the Phragmites shoots from the soil into the atmosphere. By contrast, Phalaris arundinacea did not affect N₂O emissions and no emission via the shoots was observed.     

Sulphur immobilization and availability in soils assessed using isotope dilution

Increasing recognition of S deficiency in soils has raised the need for understanding processes governing S cycling and availability in soils. However, the quantification of the two main processes of S cycling, i.e. mineralization and immobilization, remains difficult as these processes occur simultaneously. A modified isotope ³⁵SO₄ dilution technique was developed and used to measure the effect of sulphate (SO₄) fertilization on S mineralization and immobilization in planted (pot experiment with ryegrass (Lolium multiflorum L.)) and unplanted soils (incubation). The immobilization and mineralization of S was calculated from the dynamics of stable and labelled S in soil KH₂PO₄ extracts containing an anion exchange membrane that concentrates SO₄ and mainly excludes other S species. The mathematical analysis of the isotope dilution data differs from methods proposed earlier. The radiolabile S in unplanted soil (E value) and in ryegrass (L value) were used as a measure of total available S in soils. Sulphate immobilization rate significantly declined during incubation. Sulphate application reduced gross mineralization but surprisingly reduced SO₄ immobilization. The E value significantly increased during the incubation in all soils as a result of gross mineralization, e.g. from 3.8 mg S kg⁻¹ at day 0 to 11.5 mg S kg⁻¹ at day 43 in the sandy soil with no sulphate addition. A full recovery in the E value of S added in (+S) treatments was achieved. Similarly, radiolabile S in the above-ground ryegrass biomass (L value) increased with S addition, with a full recovery of added S. The E and L values nearly fit a 1:1 line suggesting identical S dynamics in a planted and unplanted soil. The method proposed has operational advantages compared to methods used earlier.     

Organic acid exudation by mycorrhizal Andropogon virginicus L. (broomsedge) roots in response to aluminum

Elevated aluminum (Al) availability limits plant growth on acidic soils. Although this element is found naturally in soils, acidic conditions create an environment where Al solubility increases and toxic forms of Al impact plant function. Plant resistance to Al is often attributed to organic acid exudation from plant roots and the chelation of cationic Al in the rhizosphere. The association of arbuscular mycorrhizal (AM) fungi with the roots of plants may alleviate Al toxicity by altering soil Al availability or plant exposure through the binding of Al to fungal structures or through the influence of fungi on exudation from roots. Diverse communities of AM fungi are found in soil ecosystems and research suggests that AM fungi exhibit functional diversity that may influence plant performance under varying edaphic environments. In the present study, we evaluated acidic isolates of six AM species in their responses to Al. Andropogon virginicus (broomsedge), a warm-season grass that commonly grows in a range of stressful environments including acidic soils, was used as a plant host for Acaulospora morrowiae, Glomus claroideum, Glomus clarum, Glomus etunicatum, Paraglomus brasilianum, and Scutellospora heterogama. Fungal spores were germinated and exposed to 0 or 100 μM Al on filter paper in sand culture or were grown and exposed to Al in sand culture in association with A. virginicus. Short- and long-term responses to Al were evaluated using direct measurements of fungal spore germination, hyphal elongation, and measurements of A. virginicus colonization and plant growth as a phytometer of AM function in symbio. Spore germination and hyphal elongation varied among AM species in response to Al, but patterns were not consistent with the influences of these AM species on A. virginicus under Al exposure. Exposure to Al did not influence colonization of roots, although large differences existed in colonization among fungal species. Plants colonized by G. clarum and S. heterogama exhibited the least reduction in growth when exposed to Al, produced the highest concentrations of Al-chelating organic acids, and had the lowest concentrations of free Al in their root zones. This pattern provides evidence that variation among AM fungi in Al resistance conferred to their plant hosts is associated with the exudation of Al-binding organic acids from roots and highlights the role that AM fungal diversity may play in plant performance in acidic soil environments.     

Effect of lignite amendment on carbon and nitrogen mineralization from raw and composted manure during incubation with soil

The application of animal manure as a source of plant nutrients requires the determination of the amount and pattern of nutrient mineralization from manure.A laboratory incubation study was conducted to investigate the influence of lignite amendment and lignite type on carbon(C) and nitrogen(N)mineralization in raw(feedstock) and composted cattle manure following application to soil at 30 and 60 t ha^-1.The mineralization of C and N was determined by measuring changes in CO2 evolution ...     

Rhizosphere priming effect of Populus fremontii obscures the temperature sensitivity of soil organic carbon respiration

C efflux from soils is a large component of the global C exchange between the biosphere and the atmosphere. However, our understanding of soil C efflux is complicated by the “rhizosphere priming effect,” in which the presence of live roots may accelerate or suppress the decomposition of soil organic C. Due to technical obstacles, the rhizosphere priming effect is under-studied, and we know little about rhizosphere priming in tree species. We measured the rates of soil-derived C mineralization in root-free soil and in soil planted with cottonwood (Populus fremontii) trees. Live cottonwood roots greatly accelerated (a rhizosphere priming effect) or suppressed (a negative rhizosphere priming effect) the mineralization of soil organic C, depending upon the time of the year. At its maximum, soil organic C was mineralized nine times faster in the presence of cottonwood roots than in the unplanted controls. Over the course of the experiment, approximately twice as much soil organic C was mineralized in pots planted with cottonwoods compared to unplanted control pots. Soil organic C mineralization rates in the unplanted controls were temperature-sensitive. In contrast, soil organic C mineralization in the cottonwood rhizosphere was unresponsive to seasonal temperature changes, due to the strength of the rhizosphere priming effect. The rhizosphere priming effect is of key importance to our understanding of soil C mineralization, because it means that the total soil respiration is not a simple additive function of soil-derived and plant-derived respiration.     

Rhizodeposits of Trifolium pratense and Lolium perenne: their comparative effects on 2,4-D mineralization in two contrasting soils

Rhizosphere enhanced biodegradation of organic pollutants has been reported frequently and a stimulatory role for specific components of rhizodeposits postulated. As rhizodeposit composition is a function of plant species and soil type, we compared the effect of Lolium perenne and Trifolium pratense grown in two different soils (a sandy silt loam: pH 4, 2.8% OC, no previous 2,4-D exposure and a silt loam: pH 6.5, 4.3% OC, previous 2,4-D exposure) on the mineralization of the herbicide 2,4-D (2,4-dichlorophenoxyacetic acid). We investigated the relationship of mineralization kinetics to dehydrogenase activity, most probable number of 2,4-D degraders (MPN_2,4-D) and 2,4-D degrader composition (using sequence analysis of the gene encoding α-ketoglutarate/2,4-D dioxygenase (tfdA)). There were significant (P<0.01) plant-soil interaction effects on MPN_2,4-D and 2,4-D mineralization kinetics (e.g. T. pratense rhizodeposits enhanced the maximum mineralization rate by 30% in the acid sandy silt loam soil, but not in the neutral silt loam soil). Differences in mineralization kinetics could not be ascribed to 2,4-D degrader composition as both soils had tfdA sequences which clustered with tfdAs representative of two distinct classes of 2,4-D degrader: canonical R. eutropha JMP134-like and oligotrophic α-proteobacterial-like. Other explanations for the differential rhizodeposit effect between soils and plants (e.g. nutrient competition effects) are discussed. Our findings stress that complexity of soil-plant-microbe interactions in the rhizosphere make the occurrence and extent of rhizosphere-enhanced xenobiotic degradation difficult to predict.     

Methyl parathion degradation and metabolism in soil: Influence of high soil-water contents

Mineralization of [¹⁴C]methyl parathion (MP) in Cecil sandy loam was considerably reduced when soil-water content was near saturation. Despite the fact that amounts of MP residue in soil held at 10?0 kPa after 35 days were about the same, larger amounts of metabolites were accumulated and higher amounts of non-extractable ¹⁴C-activity were formed in soil held at ? 2.5 kPa than held at ? 6 kPa. Three principal metabolites, p-nitrophenol (PNP), p-aminophenol (PAP) and a water-soluble polar product ($\text{R}{}_{\mathrm{?}}\text{= 0}$), were detected in soil held at ? 2.5 kPa but only PNP and PAP were detected in soil held at ? 6 kPa. The major metabolite PNP behaved like parent MP, in that it was rapidly mineralized in soil held at ? 6kPa. Much slower mineralization was observed in soil held at ? 2.5kPa.     

Bacterial populations assimilating carbon from C-labeled plant residue in soil: Analysis by a DNA-SIP approach

In this study, ¹³C-labeled rice callus was prepared as a model material for rice straw and was subjected to a DNA-SIP (stable isotope probing) experiment in which the bacterial population was monitored in a soil sample containing decomposing dried callus. Rice callus (¹³C = 78%) contained the more water-soluble organic carbon and less cellulose and lignin carbon than rice straw. The callus in the soil was 37% decomposed after 56 d of incubation in upland moisture conditions. PCR-DGGE analysis demonstrated that the bacterial community in the soil with the callus changed over time, showing a distinct difference between the first (up to 7 d) and second (14 d and later) stages. After isopycnic centrifugation, DNA in the fractions with a buoyant density between 1.759 and 1.734 g ml⁻¹ was subjected to population analysis (¹³C-assimilating populations). Diverse groups of bacterial sequences were retrieved from the ¹³C-labeled DNA fractions: Actinobacteria, Bacilli, γ-Proteobacteria, Chloroflexi, Sphingobacteria, Flavobacteria, Clostridia, Acidobacteria, Cyanobacteria and Candidate Division. Bacilli were detected mainly in the first stage, and Actinobacteria were detected throughout the incubation period. Several DGGE bands in the light fractions became more prominent in the soil with callus, which suggested that the addition of callus promoted the growth of bacteria that fed on soil organic matter, including α-Proteobacteria, γ-Proteobacteria, Bacilli, Actinobacteria, Nitrospira and Gemmatimonadetes.