Promoting microbial immobilization of soil nitrogen during restoration of abandoned agricultural fields by organic additions

Application of organic materials to soils to enhance N immobilization into microbial biomass, thereby reducing inorganic N concentrations, was studied as a management option to accelerate the reestablishment of the native vegetation on abandoned arable fields on sandy soils the Kiskunsag National Park, Hungary. Sucrose and sawdust were used at three different topographic sites over 4 years. N availability and extractable inorganic N concentrations were significantly reduced in all sites. Soil microbial biomass C and microbial biomass N increased significantly following C additions, but the microbial C to microbial N ratio remained unaffected. It is concluded that the combined application of the rapidly utilized C source (sucrose) promoted N immobilization, whereas the addition of the slowly utilized C source (sawdust) maintained the elevated microbial biomass C and microbial biomass N in the field.

Shifts in rhizosphere microbial communities and enzyme activity of Poa alpina across an alpine chronosequence

This study quantifies the influence of Poa alpina on the soil microbial community in primary succession of alpine ecosystems, and whether these effects are controlled by the successional stage. Four successional sites representative of four stages of grassland development (initial, 4 years (non-vegetated); pioneer, 20 years; transition, 75 years; mature, 9500 years old) on the Rotmoos glacier foreland, Austria, were sampled. The size, composition and activity of the microbial community in the rhizosphere and bulk soil were characterized using the chloroform-fumigation extraction procedure, phospholipid fatty acid (PLFA) analysis and measurements of the enzymes beta-glucosidase, beta-xylosidase, N-acetyl-beta-glucosaminidase, leucine aminopeptidase, acid phosphatase and sulfatase. The interplay between the host plant and the successional stage was quantified using principal component (PCA) and multidimensional scaling analyses. Correlation analyses were applied to evaluate the relationship between soil factors (C-org, N-t, C/N ratio, pH, ammonium, phosphorus, potassium) and microbial properties in the bulk soil. In the pioneer stage microbial colonization of the rhizosphere of P. alpina was dependent on the reservoir of microbial species in the bulk soil. As a consequence, the rhizosphere and bulk soil were similar in microbial biomass (ninhydrin-reactive nitrogen (NHR-N)), community composition (PLFA), and enzyme activity. In the transition and mature grassland stage, more benign soil conditions stimulated microbial growth (NHR-N, total amount of PLFA, bacterial PLFA, Gram-positive bacteria, Gram-negative bacteria), and microbial diversity (Shannon index H) in the rhizosphere either directly or indirectly through enhanced carbon allocation. In the same period, the rhizosphere microflora shifted from a G(-) to a more G(+), and from a fungal to a more bacteria-dominated community. Rhizosphere beta-xylosidase, N-acetyl-beta-glucosaminidase, and sulfatase activity peaked in the mature grassland soil, whereas rhizosphere leucine aminopeptidase, beta-glucosidase, and phosphatase activity were highest in the transition stage, probably because of enhanced carbon and nutrient allocation into the rhizosphere due to better growth conditions. Soil organic matter appeared to be the most important driver of microbial colonization in the bulk soil. The decrease in soil pH and soil C/N ratio mediated the shifts in the soil microbial community composition (bacPLFA, bacPLFA/fungPLFA, G(-), G(+)/G(-)). The activities of beta-glucosidase, beta-xylosidase and phosphatase were related to soil ammonium and phosphorus, indicating that higher decomposition rates enhanced the nutrient availability in the bulk soil. We conclude that the major determinants of the microllora vary along the successional gradient: in the pioneer stage the rhizosphere microflora was primarily determined by the harsh soil environment; under more favourable environmental conditions, however, the host plant selected for a specific microbial community that was related to the dynamic interplay between soil properties and carbon supply. (C) 2004 Elsevier Ltd. All rights reserved.

Adaptation of the Integrated Nitrogen Model for Catchments (INCA) to seasonally snow-covered catchments

Testing of the Integrated Nitrogen model for Catchments (INCA) in a wide range of ecosystem types across Europe has shown that the model underestimates N transformation processes to a large extent in northern catchments of Finland and Norway in winter and spring. It is found, and generally assumed, that microbial activity in soils proceeds at low rates at northern latitudes during winter, even at sub-zero temperatures. The INCA model was modified to improve the simulation of N transformation rates in northern catchments, characterised by cold climates and extensive snow accumulation and insulation in winter, by introducing an empirical function to simulate soil temperatures below the seasonal snow pack, and a degree-day model to calculate the depth of the snow pack. The proposed snow-correction factor improved the simulation of soil temperatures at Finnish and Norwegian field sites in winter, although soil temperature was still underestimated during periods with a thin snow cover. Finally, a comparison between the modified INCA version (v. 1.7) and the former version (v. 1.6) was made at the Simojoki river basin in northern Finland and at Dalelva Brook in northern Norway. The new modules did not imply any significant changes in simulated NO3- concentration levels in the streams but improved the timing of simulated higher concentrations. The inclusion of a modified temperature response function and an empirical snow-correction factor improved the flexibility and applicability of the model for climate effect studies.

Shifts in rhizosphere microbial communities and enzyme activity of Poa alpina across an alpine chronosequence

This study quantifies the influence of Poa alpina on the soil microbial community in primary succession of alpine ecosystems, and whether these effects are controlled by the successional stage. Four successional sites representative of four stages of grassland development (initial, 4 years (non-vegetated); pioneer, 20 years; transition, 75 years; mature, 9500 years old) on the Rotmoos glacier foreland, Austria, were sampled. The size, composition and activity of the microbial community in the rhizosphere and bulk soil were characterized using the chloroform-fumigation extraction procedure, phospholipid fatty acid (PLFA) analysis and measurements of the enzymes beta-glucosidase, beta-xylosidase, N-acetyl-beta-glucosaminidase, leucine aminopeptidase, acid phosphatase and sulfatase. The interplay between the host plant and the successional stage was quantified using principal component (PCA) and multidimensional scaling analyses. Correlation analyses were applied to evaluate the relationship between soil factors (C-org, N-t, C/N ratio, pH, ammonium, phosphorus, potassium) and microbial properties in the bulk soil. In the pioneer stage microbial colonization of the rhizosphere of P. alpina was dependent on the reservoir of microbial species in the bulk soil. As a consequence, the rhizosphere and bulk soil were similar in microbial biomass (ninhydrin-reactive nitrogen (NHR-N)), community composition (PLFA), and enzyme activity. In the transition and mature grassland stage, more benign soil conditions stimulated microbial growth (NHR-N, total amount of PLFA, bacterial PLFA, Gram-positive bacteria, Gram-negative bacteria), and microbial diversity (Shannon index H) in the rhizosphere either directly or indirectly through enhanced carbon allocation. In the same period, the rhizosphere microflora shifted from a G(-) to a more G(+), and from a fungal to a more bacteria-dominated community. Rhizosphere beta-xylosidase, N-acetyl-beta-glucosaminidase, and sulfatase activity peaked in the mature grassland soil, whereas rhizosphere leucine aminopeptidase, beta-glucosidase, and phosphatase activity were highest in the transition stage, probably because of enhanced carbon and nutrient allocation into the rhizosphere due to better growth conditions. Soil organic matter appeared to be the most important driver of microbial colonization in the bulk soil. The decrease in soil pH and soil C/N ratio mediated the shifts in the soil microbial community composition (bacPLFA, bacPLFA/fungPLFA, G(-), G(+)/G(-)). The activities of beta-glucosidase, beta-xylosidase and phosphatase were related to soil ammonium and phosphorus, indicating that higher decomposition rates enhanced the nutrient availability in the bulk soil. We conclude that the major determinants of the microllora vary along the successional gradient: in the pioneer stage the rhizosphere microflora was primarily determined by the harsh soil environment; under more favourable environmental conditions, however, the host plant selected for a specific microbial community that was related to the dynamic interplay between soil properties and carbon supply. (C) 2004 Elsevier Ltd. All rights reserved.

Modelling the inorganic nitrogen behaviour in a small Mediterranean forested catchment, Fuirosos (Catalonia)

The aim of this work was to couple a nitrogen (N) sub-model to already existent hydrological lumped (LU4-N) and semi-distributed (LU4-R-N and SD4-R-N) conceptual models, to improve our understanding of the factors and processes controlling nitrogen cycling and losses in Mediterranean catchments. The N model adopted provides a simplified conceptualization of the soil nitrogen cycle considering mineralization, nitrification, immobilization, denitrification, plant uptake, and ammonium adsorption/desorption. It also includes nitrification and denitrification in the shallow perched aquifer. We included a soil moisture threshold for all the considered soil biological processes. The results suggested that all the nitrogen processes were highly influenced by the rain episodes and that soil microbial processes occurred in pulses stimulated by soil moisture increasing after rain. Our simulation highlighted the riparian zone as a possible source of nitrate, especially after the summer drought period, but it can also act as an important sink of nitrate due to denitrification, in particular during the wettest period of the year. The riparian zone was a key element to simulate the catchment nitrate behaviour. The lumped LU4-N model (which does not include the riparian zone) could not be validated, while both the semi-distributed LU4-R-N and SD4-R-N model (which include the riparian zone) gave satisfactory results for the calibration process and acceptable results for the temporal validation process.

Utilisation by ruminants of nitrogen compounds in silage-based diets

This paper considers the various complex changes that occur to nitrogen (N) containing compounds in forages through the processes of ensiling, rumen degradation and microbial synthesis, post-ruminal digestion and absorption and synthesis into milk protein. Particular emphasis is placed on reviewing recent data on the efficiency of utilisation of N-containing compounds in silages by rumen microbes, since low efficiency here is believed to be a major cause of large N losses to the environment on some silage-based diets. Data are reviewed which show that although rumen degradation of N compounds in silage is rapid and extensive, up to 10% of the soluble N can escape the rumen by being associated with the liquid phase. There is now firm evidence that the composition of the amino acids (AAs) absorbed is heavily dependent on the process of ensiling and that witting or use of certain silage additives conserve the initial amino acid profile of the forage. This provides an opportunity to manipulate the amino acid supply to better match demand thus potentially enhancing utilisation. This review confirms that utilisation of the N fractions in grass and legume silages in particular, is poor and the efficiency of microbial protein synthesis (EMPS) is consistently higher on maize silage-based diets. It is concluded that the way in which grass and legume silages in particular are produced and used in the future needs a radical rethink. New research needs to be aimed at enhancing the utilisation of N in the rumen through a better understanding of N/carbohydrate relationships and the ability of forages to supply degraded carbohydrate. Also more emphasis is needed on understanding of the potentially different role of the different N fractions that exist in silages. (C) 2004 Elsevier B.V. All rights reserved.

Nitrogen recycling through the gut and the nitrogen economy of ruminants: An asynchronous symbiosis

The extensive development of the ruminant forestomach sets apart their N economy from that of nonruminants in a number of respects. Extensive pregastric fermentation alters the profile of protein reaching the small intestine, largely through the transformation of nitrogenous compounds into microbial protein. This process is fueled primarily by carbohydrate fermentation and includes extensive recycling of N between the body and gut lumen pools. Nitrogen recycling occurs via blood and gut lumen exchanges of urea and NH3, as well as endogenous gut and secretory N entry into the gut lumen, and the subsequent digestion and absorption of microbial and endogenous protein. Factors controlling urea transfer to the gut from blood, including the contributions of urea transporters, remain equivocal. Ammonia produced by microbial degradation of urea and dietary and endogenous AA is utilized by microbial fermentation or absorbed and primarily converted to urea. Therefore, microbial growth and carbohydrate fermentation affect the extent of NH3 absorption and urea N recycling and excretion. The extensive recycling of N to the rumen represents an evolutionary advantage of the ruminant in terms of absorbable protein supply during periods of dietary protein deficiency, or asynchronous carbohydrate and protein supply, but incurs a cost of greater N intakes, especially in terms of excess N excretion. Efforts to improve the efficiency of N utilization in ruminants by synchronizing fermentable energy and N availability have generally met with limited success with regards to production responses. In contrast, imposing asynchrony through oscillating dietary protein concentration, or infrequent supplementation, surprisingly has not negatively affected production responses unless the frequency of supplementation is less than once every 3 d. In some cases, oscillation of dietary protein concentration has improved N retention compared with animals fed an equal amount of dietary protein on a daily basis. This may reflect benefits of Orn cycle adaptations and sustained recycling of urea to the gut. The microbial symbiosis of the ruminant is inherently adaptable to asynchronous N and energy supply. Recycling of urea to the gut buffers the effect of irregular dietary N supply such that intuitive benefits of rumen synchrony in terms of the efficiency of N utilization are typically not observed in practice.

Arbuscular mycorrhizal modulation of diazotrophic and denitrifying microbial communities in the (mycor)rhizosphere of Plantago lanceolata

Impacts of divergent arbuscular mycorrhizal (AM) fungi, Glomus intraradices and Gigaspora margarita, on denitrifying and diazotrophic bacterial communities of Plantago lanceolata in nutrient-limited dune soil were assessed. We hypothesized AM species-related modifications that were confirmed in respective bacterial nirK and nifH sequence polymorphism -based community clustering and community variance allocation. The denitrifying community appeared more responsive to AM fungi than the nitrogen-fixing community. Nevertheless, the main explanatory variable, in both cases, was plant age. We conclude that AM fungi can modify N-cycling microbial rhizosphere communities and future work should aim to verify the functional significance and mechanistic basis.

Microbial community dynamics in the forefield of glaciers

Retreating ice fronts (as a result of a warming climate) expose large expanses of deglaciated forefield, which become colonized by microbes and plants. There has been increasing interest in characterizing the biogeochemical development of these ecosystems using a chronosequence approach. Prior to the establishment of plants, microbes use autochthonously produced and allochthonously delivered nutrients for growth. The microbial community composition is largely made up of heterotrophic microbes (both bacteria and fungi), autotrophic microbes and nitrogen-fixing diazotrophs. Microbial activity is thought to be responsible for the initial build-up of labile nutrient pools, facilitating the growth of higher order plant life in developed soils. However, it is unclear to what extent these ecosystems rely on external sources of nutrients such as ancient carbon pools and periodic nitrogen deposition. Furthermore, the seasonal variation of chronosequence dynamics and the effect of winter are largely unexplored. Modelling this ecosystem will provide a quantitative evaluation of the key processes and could guide the focus of future research. Year-round datasets combined with novel metagenomic techniques will help answer some of the pressing questions in this relatively new but rapidly expanding field, which is of growing interest in the context of future large-scale ice retreat.

Microbial decomposition of skeletal muscle tissue (Ovis aries) in a sandy loam soil at different temperatures

A laboratory experiment was conducted to determine the effect of temperature (2, 12, 22 °C) on the rate of aerobic decomposition of skeletal muscle tissue (Ovis aries) in a sandy loam soil incubated for a period of 42 days. Measurements of decomposition processes included skeletal muscle tissue mass loss, carbon dioxide (CO2) evolution, microbial biomass, soil pH, skeletal muscle tissue carbon (C) and nitrogen (N) content and the calculation of metabolic quotient (qCO2). Incubation temperature and skeletal muscle tissue quality had a significant effect on all of the measured process rates with 2 °C usually much lower than 12 and 22 °C. Cumulative CO2 evolution at 2, 12 and 22 °C equaled 252, 619 and 905 mg CO2, respectively. A significant correlation (P<0.001) was detected between cumulative CO2 evolution and tissue mass loss at all temperatures. Q10s for mass loss and CO2 evolution, which ranged from 1.19 to 3.95, were higher for the lower temperature range (Q10(2– 12 °C)>Q10(12–22 °C)) in the Ovis samples and lower for the low temperature range (Q10(2–12 °C)microbial catabolic requirements at lower temperature.

Nitrogen dynamics under Lolium perenne after a single application of different sewage sludge types from the same treatment stream

Three sludge types from the same treatment stream (undigested liquid, anaerobically digested liquid and dewatered, anaerobically digested cake) were used in a field based tub study. Amendments (4, 8, and 16 Mg dry solid (ds)ha(-1)) were incorporated into the upper 15 cm of a sandy loam soil prior to sowing with rye-grass (Lolium perenne L.). Nitrogen transformations in the soil were determined for the 80 d period following incorporation. Nitrogen uptake and crop yield were measured in the cut sward 35 and 70 d after sowing. The study showed that application of sewage sludge at rates as low as 4 Mgha(-1) can have a nutritional benefit to rye-grass over the two harvests. Differences in N transformation, and hence crop nutritional benefit, between sludge types were evident throughout the experiment. In particular, the dewatering process changed the mineral N characteristics of the anaerobically digested sludge, which, when not dewatered, outperformed the other sludges in terms of yield and mineralisation rate at both harvests. The dewatered sludge produced the lowest yield of rye-grass. The undigested liquid sludge had the lowest foliar N and soil NO(3)-N concentrations, possibly immobilised as the large oxidisable C component of this sludge was metabolised by the microbial biomass. Correlation data support the concept of preferential uptake of NH(4)-N over NO(3)-N in Lolium perenne. Results are discussed in the context of managing sludge type and application for a plant nutrient source and NO(3)-N release.

Valorisation of side streams from wheat milling and confectionery industries for consolidated production and extraction of microbial lipids

Crude enzymes produced via solid state fermentation (SSF) using wheat milling by-products have been employed for both fermentation media production using flour-rich waste (FRW) streams and lysis of Rhodosporidium toruloides yeast cells. Filter sterilization of crude hydrolysates was more beneficial than heat sterilization regarding yeast growth and microbial oil production. The initial carbon to free amino nitrogen ratio of crude hydrolysates was optimized (80.2 g/g) in fed-batch cultures of R. toruloides leading to a total dry weight of 61.2 g/L with microbial oil content of 61.8 % (w/w). Employing a feeding strategy where the glucose concentration was maintained in the range of 12.2 – 17.6 g/L led to the highest productivity (0.32 g/L∙h). The crude enzymes produced by SSF were utilised for yeast cell treatment leading to simultaneous release of around 80% of total lipids in the broth and production of a hydrolysate suitable as yeast extract replacement.

Formulation of fermentation media from flour-rich waste streams for microbial lipid production by Lipomyces starkeyi

Flour-rich waste (FRW) and by-product streams generated by bakery, confectionery and wheat milling plants could be employed as the sole raw materials for generic fermentation media production, suitable for microbial oil synthesis. Wheat milling by-products were used in solid state fermentations (SSF) of Aspergillus awamori for the production of crude enzymes, mainly glucoamylase and protease. Enzyme-rich SSF solids were subsequently employed for hydrolysis of FRW streams into nutrient-rich fermentation media. Batch hydrolytic experiments using FRW concentrations up to 205 g/L resulted in higher than 90%(w/w) starch to glucose conversion yields and 40% (w/w) total Kjeldahl nitrogen to free amino nitro-gen conversion yields. Starch to glucose conversion yields of 98.2, 86.1 and 73.4% (w/w) were achieved when initial FRW concentrations of 235, 300 and 350 g/L were employed in fed-batch hydrolytic experiments, respectively. Crude hydrolysates were used as fermentation media in shake flask cultures with the oleaginous yeast Lipomyces starkeyi DSM 70296 reaching a total dry weight of 30.5 g/L with a microbial oil content of 40.4% (w/w), higher than that achieved in synthetic media. Fed-batch bioreactor cultures led to a total dry weight of 109.8 g/L with a microbial oil content of 57.8% (w/w) and productivity of 0.4 g/L/h.

SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework designed to simulate microbial dynamics and biogeochemical cycling during initial ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The rationale for model development arises from decades of empirical observations in glacier forefields, and enables a quantitative and process focussed approach. Here, we provide a detailed description of SHIMMER, test its performance in two case study forefields: the Damma Glacier (Switzerland) and the Athabasca Glacier (Canada) and analyse sensitivity to identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Primary production is responsible for the initial build-up of labile substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter, and nitrogen fixation, are important in sustaining this productivity. The development and application of SHIMMER also highlights aspects of these systems that require further empirical research: quantifying nutrient budgets and biogeochemical rates, exploring seasonality and microbial growth and cell death. This will lead to increased understanding of how glacier forefields contribute to global biogeochemical cycling and climate under future ice retreat.

Impact of perturbations of nitrogen oxide emissions from global aviation