The phospholipid fatty acid biomarkers 18:1ω9, 18:2ω6,9 and 18:3ω3,6,9 are commonly used as fungal biomarkers in soils. They have, however, also been found to occur in plant tissues, such as roots. Thus, the use of these PLFAs as fungal biomarkers in sieved soil, which may still contain small remains of roots, has been questioned. We used data from a recent beech tree girdling experiment to calculate the contribution of roots to these biomarkers and were able to demonstrate that not more than 0.61% of 18:1ω9 and 18:2ω6,9 in sieved soil samples originated from roots (but 4% of 18:3ω3,6,9). Additionally, the abundance of the biomarker 18:2ω6,9 in the soil was found to be highly correlated to ectomycorrhizal root colonization, which further corroborates its fungal origin. PLFA biomarkers were substantially reduced in vital roots from girdled trees compared to roots of control trees (by up to 76%), indicating that the major part of PLFAs measured in roots may actually originate from ectomycorrhizal fungi growing inside the roots. We calculated, that even a near to 50% reduction in fine root biomass - as observed in the girdling treatment - accounted for only 0.8% of the measured decrease of 18:2ω6,9. Our results demonstrate that both 18:1ω9 and 18:2ω6,9 are suitable biomarkers for detecting fungal dynamics in soils and that especially 18:2ω6,9 is a reliable biomarker to study mycorrhizal dynamics in beech forests.
Density, diversity and assemblage structure of Mesostigmata (cohorts Gamasina and Uropodina) were investigated in nine grassy arable fallows according to a factorial design with age class (2-3, 6-8, 12-15 years) and plant species (legume: Medicago sativa, herb: Taraxacum officinale, grass: Bromus sterilis) as factors. The response of Mesostigmata to habitat age and plant species was explored because this group belongs to the dominant acarine predators playing a crucial role in soil food webs and being important as biological control agents. To our knowledge, this combination of factors has never been studied before for Mesostigmata. A further rarely applied aspect of the present study is the micro-scale approach investigating the Mesostigmata assemblage of the soil associated with single plants. Four plots were randomly chosen at each fallow in May 2008. At each plot plant roots and the adjacent soil of five randomly selected plant individuals per plant species were dug out with steel cylinders for heat extraction of soil fauna and measurement of environmental parameters. In total, 83 mite taxa were identified, with 50 taxa being new to Austria. GLM analysis revealed a significant effect of plant species on mite density, with significantly more mites in B. sterilis than in T. officinale samples, and M. sativa samples being intermediate. This was in contrast to the assumption that the mite density is highest in M. sativa samples due to the propagation of plant quality effects to higher trophic levels. These results were probably caused by a higher amount of fine roots in grass samples leading to high densities of Collembola, which are preferred prey of predatory mites. Mite density did not significantly differ between the three age classes. A canonical analysis of principal coordinates (CAP) showed that the mite assemblage exhibited a weak yet significant separation between plant species, and a highly significant separation between age classes. Accordingly, different mite assemblages were found for the three age classes, while only few mite species were clearly associated with a single plant species. Finally, canonical correspondence analysis (CCA) revealed that the mite assemblage was best explained by soil organic carbon, total density of Collembola and water content.
The storage of soil samples for PLFA analysis can lead to shifts in the microbial community composition. We show here that conserving samples in RNAlater, which is already widely used to store samples for DNA and RNA analysis, proved to be as sufficient as freezing at -20 °C and preferable over storage at 4 °C for temperate mountain grassland soil. The total amount of extracted PLFAs was not changed by any storage treatment. Storage at 4 °C led to an alteration of seven out of thirty individual biomarkers, while freezing and storage in RNAlater caused changes in the amount of fungal biomarkers but had no effect on any other microbial group. We therefore suggest that RNAlater could be used to preserve soil samples for PLFA analysis when immediate extraction or freezing of samples is not possible, for example during sampling campaigns in remote areas or during transport and shipping.
Humic acids (HAs) play an important role in the global nitrogen cycle by influencing the distribution, bioavailability, and ultimate fate of organic nitrogen. Ammonium oxidation by autotrophic ammonia-oxidizing bacteria (AOB) is a key process in ecosystems and is limited, in part, by the availability of [Formula: see text]. We evaluated the impact of HAs on soil AOB in microcosms by applying urea (1.0%, equal to 10 mg urea/g soil) with 0.1% bHA (biodegraded lignite humic acids, equal to 1 mg/g soil), 0.1% cHA (crude lignite humic acids) or no amendment. AOB population size, ammonium and nitrate concentrations were monitored for 12 weeks after urea and HA application. AOB densities (quantified by real-time PCR targeting the amoA) in the Urea treatments increased about ten-fold (the final abundance: 5.02 × 10(7) copies (g of dry soil)(-1)) after one week of incubation and decreased to the initial density after 12 weeks incubation; the population size of total bacteria (quantified by real-time PCR with a universal bacterial probe) decreased from 1.12 × 10(10) to 2.59 × 10(9) copies (g of dry soil)(-1) at week one and fluctuated back to the initial copy number at week 12. In the Urea + bHA and Urea + cHA treatments, the AOB densities were 4 and 6 times higher, respectively, than the initial density of approximately 5.07 × 10(6) copies (g of dry soil)(-1) at week 1 and did not change much up to week 4; the total bacteria density changed little over time. The AOB and total bacteria density of the controls changed little during the 12 weeks of incubation. The microbial community composition of the Urea treatment, based on T-RFLP using CCA (canonical correspondence analysis) and pCCA (partial CCA) analysis, was clearly different from those of other treatments, and suggested that lignite HAs buffered the change in diversity and quantity of total bacteria caused by the application of urea to the soil. We hypothesize that HAs can inhibit the change in microbial community composition and numbers, as well as AOB population size by reducing the hydrolysis rate from urea to ammonium in soils amended with urea.
Tracking the movement of soil-living herbivores is difficult, albeit important for understanding their spatial ecology as well as for pest management. In this study the movement of Agriotes obscurus larvae between plots harbouring isotopically different plants was examined. Neither between maize and wheat nor between maize and grassland movement could be detected. These data suggest that Agriotes larvae rarely disperse between crops as long as local food supply is sufficient. Moreover, the current approach provides a new means to study the dispersal of soil invertebrates in situ.
We tested whether experimental summer drought affects the transfer of recently photosynthesized carbon from plants to soil mesofauna in a subalpine meadow. From day one after (13)CO(2) pulse-labelling of the plant canopy, roots, collembolans and mites were enriched in δ(13)C in control, but not in drought plots. However, as the difference in δ(13)C between roots and soil animals was not affected by the drought treatment, we conclude that drought affects the tight linkage between photosynthesis and soil mesofauna primarily via functional responses of plants rather than via changes in the mesofauna.
Metagenomic analyses can provide extensive information on the structure, composition, and predicted gene functions of diverse environmental microbial assemblages. Each environment presents its own unique challenges to metagenomic investigation and requires a specifically designed approach to accommodate physicochemical and biotic factors unique to each environment that can pose technical hurdles and/or bias the metagenomic analyses. In particular, soils harbor an exceptional diversity of prokaryotes that are largely undescribed beyond the level of ribotype and are a potentially vast resource for natural product discovery. The successful application of a soil metagenomic approach depends on selecting the appropriate DNA extraction, purification, and if necessary, cloning methods for the intended downstream analyses. The most important technical considerations in a metagenomic study include obtaining a sufficient yield of high-purity DNA representing the targeted microorganisms within an environmental sample or enrichment and (if required) constructing a metagenomic library in a suitable vector and host. Size does matter in the context of the average insert size within a clone library or the sequence read length for a high-throughput sequencing approach. It is also imperative to select the appropriate metagenomic screening strategy to address the specific question(s) of interest, which should drive the selection of methods used in the earlier stages of a metagenomic project (e.g., DNA size, to clone or not to clone). Here, we present both the promising and problematic nature of soil metagenomics and discuss the factors that should be considered when selecting soil sampling, DNA extraction, purification, and cloning methods to implement based on the ultimate study objectives.
Soil extracts usually contain large quantities of dissolved humified organic material, typically reflected by high polyphenolic content. Since polyphenols seriously confound quantification of extracted protein, minimising this interference is important to ensure measurements are representative. Although the Bradford colorimetric assay is used routinely in soil science for rapid quantification protein in soil-extracts, it has several limitations. We therefore investigated an alternative colorimetric technique based on the Lowry assay (frequently used to measure protein and humic substances as distinct pools in microbial biofilms). The accuracies of both the Bradford assay and a modified Lowry microplate method were compared in factorial combination. Protein was quantified in soil-extracts (extracted with citrate), including standard additions of model protein (BSA) and polyphenol (Sigma H1675-2). Using the Lowry microplate assay described, no interfering effects of citrate were detected even with concentrations up to 5 times greater than are typically used to extract soil protein. Moreover, the Bradford assay was found to be highly susceptible to two simultaneous and confounding artefacts: 1) the colour development due to added protein was greatly inhibited by polyphenol concentration, and 2) substantial colour development was caused directly by the polyphenol addition. In contrast, the Lowry method enabled distinction between colour development from protein and non-protein origin, providing a more accurate quantitative analysis. These results suggest that the modified-Lowry method is a more suitable measure of extract protein (defined by standard equivalents) because it is less confounded by the high polyphenolic content which is so typical of soil extracts.
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Recent studies have indicated that plant growth-promoting bacteria (PGPB) can improve revegetation of arid mine tailings as measured by increased biomass production. The goals of the present study were first to evaluate how mode of application of known PGPB affects plant growth, and second to evaluate the effect of this inoculation on rhizosphere microbial community structure. PGPB application strategies investigated include preliminary surface sterilization of seeds (a common practice in phytoremediation trials) followed by a comparison of two application methods; immersion and alginate encapsulation. Results with two native desert plant species, Atriplex lentiformis and Buchloe dactyloides, suggest that seed surface sterilization prior to inoculation is not necessary to achieve beneficial effects of introduced PGPB. Both PGPB application techniques generally enhanced plant growth although results were both plant and PGPB specific. These results demonstrate that alginate encapsulation, which allows for long-term storage and easier application to seeds, is an effective way to inoculate PGPB. In addition, the influence of PGPB application on B. dactyloides rhizosphere community structure was evaluated using PCR-DGGE (denaturing gradient gel electrophoresis) analysis of bacterial DNA extracted from rhizosphere samples collected 75 d following planting. A comparative analysis of DGGE profiles was performed using canonical correspondence analysis (CCA). DGGE-CCA showed that rhizosphere community profiles from PGPB-inoculated treatments are significantly different from both uninoculated tailings rhizosphere profiles and profiles from the compost used to amend the tailings. Further, community profiles from B. dactyloides inoculated with the best performing PGPB (Arthro mix) were significantly different from two other PGPB tested. These results suggest that introduced PGPB have the potential to influence the development of the rhizosphere community structure found in plants grown in mine tailings.
Phytoextraction makes use of trace element-accumulating plants that concentrate the pollutants in their tissues. Pollutants can be then removed by harvesting plants. The success of phytoextraction depends on trace element availability to the roots and the ability of the plant to intercept, take up, and accumulate trace elements in shoots. Current phytoextraction practises either employ hyperaccumulators or fast-growing high biomass plants; the phytoextraction process may be enhanced by soil amendments that increase trace element availability in the soil. This review will focus on the role of plant-associated bacteria to enhance trace element availability in the rhizosphere. We report on the kind of bacteria typically found in association with trace element - tolerating or - accumulating plants and discuss how they can contribute to improve trace element uptake by plants and thus the efficiency and rate of phytoextraction. This enhanced trace element uptake can be attributed to a microbial modification of the absorptive properties of the roots such as increasing the root length and surface area and numbers of root hairs, or by increasing the plant availability of trace elements in the rhizosphere and the subsequent translocation to shoots via beneficial effects on plant growth, trace element complexation and alleviation of phytotoxicity. An analysis of data from literature shows that effects of bacterial inoculation on phytoextraction efficiency are currently inconsistent. Some key processes in plant-bacteria interactions and colonization by inoculated strains still need to be unravelled more in detail to allow full-scale application of bacteria assisted phytoremediation of trace element contaminated soils.
Glucans like cellulose and starch are a major source of carbon for decomposer food webs, especially during early- and intermediate-stages of decomposition. Litter quality has previously been suggested to notably influence decomposition processes as it determines the decomposability of organic material and the nutrient availability to the decomposer community. To study the impact of chemical and elemental composition of resources on glucan decomposition, a laboratory experiment was carried out using beech (Fagus sylvatica, L.) litter from four different locations in Austria, differing in composition (concentration of starch, cellulose and acid unhydrolyzable residue or AUR fraction) and elemental stoichiometry (C:N:P ratio). Leaf litter was incubated in mesocosms for six months in the laboratory under controlled conditions. To investigate the process of glucan decomposition and its controls, we developed an isotope pool dilution (IPD) assay using (13)C-glucose to label the pool of free glucose in the litter, and subsequently measured the dilution of label over time. This enabled us to calculate gross rates of glucose production through glucan depolymerization, and glucose consumption by the microbial community. In addition, potential activities of extracellular cellulases and ligninases (peroxidases and phenoloxidases) were measured to identify effects of resource chemistry and stoichiometry on microbial enzyme production. Gross rates of glucan depolymerization and glucose consumption were highly correlated, indicating that both processes are co-regulated and intrinsically linked by the microbial demand for C and energy and thereby to resource allocation to enzymes that depolymerize glucans. At early stages of decomposition, glucan depolymerization rates were correlated with starch content, indicating that starch was the primary source for glucose. With progressing litter decomposition, the correlation with starch diminished and glucan depolymerization rates were highly correlated to cellulase activities, suggesting that cellulose was the primary substrate for glucan depolymerization at this stage of decomposition. Litter stoichiometry did not affect glucan depolymerization or glucose consumption rates early in decomposition. At later stages, however, we found significant negative relationships between glucan depolymerization and litter C:N and AUR:N ratio and a positive relationship between glucan depolymerization and litter N concentration. Litter C:N and C:P ratios were negatively related to cellulase, peroxidase and phenoloxidase activities three and six months after incubation, further corroborating the importance of resource stoichiometry for glucan depolymerization after the initial pulse of starch degradation.
Plant roots strongly influence C and N availability in the rhizosphere via rhizodeposition and uptake of nutrients. This study aimed at investigating the effect of resource availability on microbial processes and community structure in the rhizosphere. We analyzed C and N availability, as well as microbial processes and microbial community composition in rhizosphere soil of European beech and compared it to the bulk soil. Additionally, we performed a girdling experiment in order to disrupt root exudation into the soil. By this novel approach we were able to demonstrate that enhanced resource availability positively affected N mineralization and hydrolytic enzyme activities in the rhizosphere, but negatively affected nitrification rates and oxidative enzyme activities, which are involved in the degradation of soil organic matter. Both rhizosphere effects on N mineralization and oxidative enzyme activities disappeared in the girdling treatment. Microbial community structure in the rhizosphere, assessed by phospholipid fatty acid analysis, differed only slightly from bulk soil but was markedly altered by the girdling treatment, indicating additional effects of the girdling treatment beyond the reduction of root exudation. Differences in oxidative enzyme activities and nitrification rates between rhizosphere soil and bulk soil, however, suggest considerable differences in the (functional) microbial community composition.
Substrate quality and the availability of nutrients are major factors controlling microbial decomposition processes in soils. Seasonal alteration in resource availability, which is driven by plants via belowground C allocation, nutrient uptake and litter fall, also exerts effects on soil microbial community composition. Here we investigate if seasonal and experimentally induced changes in microbial community composition lead to alterations in functional properties of microbial communities and thus microbial processes. Beech forest soils characterized by three distinct microbial communities (winter and summer community, and summer community from a tree girdling plot, in which belowground carbon allocation was interrupted) were incubated with different (13)C-labeled substrates with or without inorganic N supply and analyzed for substrate use and various microbial processes. Our results clearly demonstrate that the three investigated microbial communities differed in their functional response to addition of various substrates. The winter communities revealed a higher capacity for degradation of complex C substrates (cellulose, plant cell walls) than the summer communities, indicated by enhanced cellulase activities and reduced mineralization of soil organic matter. In contrast, utilization of labile C sources (glucose) was lower in winter than in summer, demonstrating that summer and winter community were adapted to the availability of different substrates. The saprotrophic community established in girdled plots exhibited a significantly higher utilization of complex C substrates than the more plant root associated community in control plots if additional nitrogen was provided. In this study we were able to demonstrate experimentally that variation in resource availability as well as seasonality in temperate forest soils cause a seasonal variation in functional properties of soil microorganisms, which is due to shifts in community structure and physiological adaptations of microbial communities to altered resource supply.
This study coupled stable isotope probing with phospholipid fatty acid analysis ((13)C-PLFA) to describe the role of microbial community composition in the short-term processing (i.e., C incorporation into microbial biomass and/or deposition or respiration of C) of root- versus residue-C and, ultimately, in long-term C sequestration in conventional (annual synthetic fertilizer applications), low-input (synthetic fertilizer and cover crop applied in alternating years), and organic (annual composted manure and cover crop additions) maize-tomato (Zea mays - Lycopersicum esculentum) cropping systems. During the maize growing season, we traced (13)C-labeled hairy vetch (Vicia dasycarpa) roots and residues into PLFAs extracted from soil microaggregates (53-250 μm) and silt-and-clay (<53 μm) particles. Total PLFA biomass was greatest in the organic (41.4 nmol g(-1) soil) and similar between the conventional and low-input systems (31.0 and 30.1 nmol g(-1) soil, respectively), with Gram-positive bacterial PLFA dominating the microbial communities in all systems. Although total PLFA-C derived from roots was over four times greater than from residues, relative distributions (mol%) of root- and residue-derived C into the microbial communities were not different among the three cropping systems. Additionally, neither the PLFA profiles nor the amount of root- and residue-C incorporation into the PLFAs of the microaggregates were consistently different when compared with the silt-and-clay particles. More fungal PLFA-C was measured, however, in microaggregates compared with silt-and-clay. The lack of differences between the mol% within the microbial communities of the cropping systems and between the PLFA-C in the microaggregates and the silt-and-clay may have been due to (i) insufficient differences in quality between roots and residues and/or (ii) the high N availability in these N-fertilized cropping systems that augmented the abilities of the microbial communities to process a wide range of substrate qualities. The main implications of this study are that (i) the greater short-term microbial processing of root- than residue-C can be a mechanistic explanation for the higher relative retention of root- over residue-C, but microbial community composition did not influence long-term C sequestration trends in the three cropping systems and (ii) in spite of the similarity between the microbial community profiles of the microaggregates and the silt-and-clay, more C was processed in the microaggregates by fungi, suggesting that the microaggregate is a relatively unique microenvironment for fungal activity.
The relative effectiveness of average-well-color-development-normalized single-point absorbance readings (AWCD) vs the kinetic parameters mu(m), lambda, A, and integral (AREA) of the modified Gompertz equation fit to the color development curve resulting from reduction of a redox sensitive dye from microbial respiration of 95 separate sole carbon sources in microplate wells was compared for a dilution series of rhizosphere samples from hydroponically grown wheat and potato ranging in inoculum densities of 1 x 10(4)-4 x 10(6) cells ml-1. Patterns generated with each parameter were analyzed using principal component analysis (PCA) and discriminant function analysis (DFA) to test relative resolving power. Samples of equivalent cell density (undiluted samples) were correctly classified by rhizosphere type for all parameters based on DFA analysis of the first five PC scores. Analysis of undiluted and 1:4 diluted samples resulted in misclassification of at least two of the wheat samples for all parameters except the AWCD normalized (0.50 abs. units) data, and analysis of undiluted, 1:4, and 1:16 diluted samples resulted in misclassification for all parameter types. Ordination of samples along the first principal component (PC) was correlated to inoculum density in analyses performed on all of the kinetic parameters, but no such influence was seen for AWCD-derived results. The carbon sources responsible for classification differed among the variable types with the exception of AREA and A, which were strongly correlated. These results indicate that the use of kinetic parameters for pattern analysis in CLPP may provide some additional information, but only if the influence of inoculum density is carefully considered.
Real-time quantitative PCR assays, targeting part of the ammonia-monooxygenase (amoA), nitrous oxide reductase (nosZ), and 16S rRNA genes were coupled with (15)N 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 (~5.15×10(8) copies g(-1) soil). However, amoA gene densities were ~2 times higher in the organic (1.75×10(8) 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 (7.65×10(7) 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 N(2)O losses.
Soil microbial communities mediate the decomposition of soil organic matter (SOM). The amount of carbon (C) that is respired leaves the soil as CO(2) (soil respiration) and causes one of the greatest fluxes in the global carbon cycle. How soil microbial communities will respond to global warming, however, is not well understood. To elucidate the effect of warming on the microbial community we analyzed soil from the soil warming experiment Achenkirch, Austria. Soil of a mature spruce forest was warmed by 4 °C during snow-free seasons since 2004. Repeated soil sampling from control and warmed plots took place from 2008 until 2010. We monitored microbial biomass C and nitrogen (N). Microbial community composition was assessed by phospholipid fatty acid analysis (PLFA) and by quantitative real time polymerase chain reaction (qPCR) of ribosomal RNA genes. Microbial metabolic activity was estimated by soil respiration to biomass ratios and RNA to DNA ratios. Soil warming did not affect microbial biomass, nor did warming affect the abundances of most microbial groups. Warming significantly enhanced microbial metabolic activity in terms of soil respiration per amount of microbial biomass C. Microbial stress biomarkers were elevated in warmed plots. In summary, the 4 °C increase in soil temperature during the snow-free season had no influence on microbial community composition and biomass but strongly increased microbial metabolic activity and hence reduced carbon use efficiency.
Turbic Cryosols (permafrost soils characterized by cryoturbation, i.e., by mixing of soil layers due to freezing and thawing) are widespread across the Arctic, and contain large amounts of poorly decomposed organic material buried in the subsoil. This cryoturbated organic matter exhibits retarded decomposition compared to organic material in the topsoil. Since soil organic matter (SOM) decomposition is known to be tightly linked to N availability, we investigated N transformation rates in different soil horizons of three tundra sites in north-eastern Siberia and Greenland. We measured gross rates of protein depolymerization, N mineralization (ammonification) and nitrification, as well as microbial uptake of amino acids and NH4 (+) using an array of (15)N pool dilution approaches. We found that all sites and horizons were characterized by low N availability, as indicated by low N mineralization compared to protein depolymerization rates (with gross N mineralization accounting on average for 14% of gross protein depolymerization). The proportion of organic N mineralized was significantly higher at the Greenland than at the Siberian sites, suggesting differences in N limitation. The proportion of organic N mineralized, however, did not differ significantly between soil horizons, pointing to a similar N demand of the microbial community of each horizon. In contrast, absolute N transformation rates were significantly lower in cryoturbated than in organic horizons, with cryoturbated horizons reaching not more than 32% of the transformation rates in organic horizons. Our results thus indicate a deceleration of the entire N cycle in cryoturbated soil horizons, especially strongly reduced rates of protein depolymerization (16% of organic horizons) which is considered the rate-limiting step in soil N cycling.
Although a significant proportion of plant tissue is located in roots and other below-ground parts of plants, little is known on the dietary choices of root-feeding insects. This is caused by a lack of adequate methodology which would allow tracking below-ground trophic interactions between insects and plants. Here, we present a DNA-based approach to examine this relationship. Feeding experiments were established where either wheat (Triticum aestivum) or maize (Zea mays) was fed to Agriotes larvae (Coleoptera: Elateridae), allowing them to digest for up to 72 h. Due to the very small amount of plant tissue ingested (max = 6.76 mg), DNA extraction procedures and the sensitivity of polymerase chain reaction (PCR) had to be optimized. Whole-body DNA extracts of larvae were tested for the presence of both rbcL and trnL plastid DNA using universal primers. Moreover, based on cpDNA sequences encoding chloroplast tRNA for leucine (trnL), specific primers for maize and wheat were developed. With both, general and specific primers, plant DNA was detectable in the guts of Agriotes larvae for up to 72 h post-feeding, the maximum time of digestion in these experiments. No significant effect of time since feeding on plant DNA detection success was observed, except for the specific primers in maize-fed larvae. Here, plant DNA detection was negatively correlated with the duration of digestion. Both, meal size and initial mass of the individual larvae did not affect the rate of larvae testing positive for plant DNA. The outcomes of this study represent a first step towards a specific analysis of the dietary choices of soil-living herbivores to further increase our understanding of animal-plant feeding interactions in the soil.
Zoosporic true fungi have frequently been identified in samples from soil and freshwater ecosystems using baiting and molecular techniques. In fact some species can be components of the dominant groups of microorganisms in particular soil habitats. Yet these microorganisms have not yet been directly observed growing in soil ecosystems. Significant physical characteristics and features of the three-dimensional structures of soils which impact microorganisms at the microscale level are discussed. A thorough knowledge of soil structures is important for studying the distribution of assemblages of these fungi and understanding their ecological roles along spatial and temporal gradients. A number of specific adaptations and resource seeking strategies possibly give these fungi advantages over other groups of microorganisms in soil ecosystems. These include chemotactic zoospores, mechanisms for adhesion to substrates, rhizoids which can penetrate substrates in small spaces, structures which are resistant to environmental extremes, rapid growth rates and simple nutritional requirements. These adaptations are discussed in the context of the characteristics of soils ecosystems. Recent advances in instrumentation have led to the development of new and more precise methods for studying microorganisms in three-dimensional space. New molecular techniques have made identification of microbes possible in environmental samples.
The temperature dependence of soil respiration (R(S)) is widely used as a key characteristic of soils or organic matter fractions within soils, and in the context of global climatic change is often applied to infer likely responses of R(S) to warmer future conditions. However, the way in which these temperature dependencies are calculated, interpreted and implemented in ecosystem models requires careful consideration of possible artefacts and assumptions. We argue that more conceptual clarity in the reported relationships is needed to obtain meaningful meta-analyses and better constrained parameters informing ecosystem models. Our critical assessment of common methodologies shows that it is impossible to measure actual temperature response of R(S), and that a range of confounding effects creates the observed apparent temperature relations reported in the literature. Thus, any measureable temperature response function will likely fail to predict effects of climate change on R(s). For improving our understanding of R(S) in changing environments we need a better integration of the relationships between substrate supply and the soil biota, and of their long-term responses to changes in abiotic soil conditions. This is best achieved by experiments combining isotopic techniques and ecosystem manipulations, which allow a disentangling of abiotic and biotic factors underlying the temperature response of soil CO(2) efflux.
The organic C (EC), total N (EN), anthrone-, phenol- and orcinol-reactive C (ARC, PRC and ORC, respectively), ninhydrin-reactive N (NRN), Folin-Ciocalteu's reagent-reactive C and N compounds (FRC and FRN) and deoxyribose containing compounds (diphenylamine-reactive compounds, DRC) extracted by 0.5 m K2SO4 before (non-fumigated extracts) and after (fumigated extracts) CHC13 fumigation were evaluated in 8 very different soils. All quantities were significantly linearly correlated between them and with total organic C (TOC) and total N (TN) as well. The frequency distribution of the significance levels passing from non-fumigated to fumigated extracts and γ-values (fumigated minus non-fumigated values for the same class of compounds) showed a shift towards the highest significances; this may indirectly confirm the action of chloroform in lysing soil microbial cells. The significance levels (P) of TOC correlated vs fumigated extracts were higher than vs non-fumigated extracts and γ -values, thus indicating a release of non-biomass C organic compounds after CHCl3 fumigation. Since TN vs fumigated extracts showed significance levels higher than non-fumigated extracts but equal to γ-values, any release of non-biomass N probably did not occur. These considerations were confirmed by multiple regression analysis when EC and EN (dependent variables) were reconstituted taking into account TOC and TN as additional independent variables, respectively. However, released non-biomass C organic compounds (likely sugars) compared to TOC were very low and could be considered to be negligible.
Amato and Ladd showed that the amount of ninhydrin-reactive nitrogen (ninhydrin-N) extracted from soil by 2 m KCl following chcl3 fumigation is a reliable and sensitive indicator of the amount of soil microbial biomass. However, when we attempted the assay in 0.5 m k2so4 soil extracts, serious analytical problems (e.g. precipitation of CaSO4 and K2SO4) occurred, which invalidated the ninhydrin-N determinations. As measurement of biomass C (and probably biomass N) in soils by fumigation-extraction is more reliable when K2SO4, rather than KCl, is used as the extractant, we modified the ninhydrin-N assay procedure to permit measurements in 0.5 m K2SO4. Our modified procedure is described. A strong relationship (r = 0.99) between ninhydrin-N measured in KCl and K2SO4 soil extracts was obtained (KCl-ninhydrin-N = 0.90 K2SO4-ninhydrin-N). There were also strong linear relationships (r = 0.91−95) between biomass C, biomass N and biomass ninhydrin-N (all extracted with 0.5 M K2SO4). We conclude that reliable ninhydrin-N measurements are obtained in 0.5 m K2SO4 soil extracts by our modified procedure.
By evaluating worldwide data accumulated over the past 20 years on field inoculation experiments with Azospirillum, it can be concluded that these bacteria are capable of promoting the yield of agriculturally-important crops in different soils and climatic regions. Various strains of A. brasilense and A. lipoferum have been used to inoculate cultivars of different species of plants. It is however difficult to accurately estimate the percentage of success due to Azospirillum inoculation. The data indicates 60–70% occurrence of success with statistically significant increases in yield of the order of 5–30%. Successful inoculation experiments appear to be those in which the researchers have paid special attention to the optimal number of cells of Azospirillum in the inoculant, using inoculation methods where the optimal number of cells remained viable and available to colonize the roots. Furthermore, experiments taking into consideration the potentialities and limitations of this technology have been better able to explain successes and failures. The different formulations (analogous to those of rhizobia) of the genus Azospirillum, irrespective of their form of application and their mode of action on the plant, are indeed inoculants. The term biofertilizer is not appropriate as it does not replace fertilizer but improves their utilization. We very strongly suggest the implementation by regulatory authorities of quality control on commercial Azospirillum inoculants.
Frankia strains from Casuarina (BR, S21, Thr), Allocasuarina (Allo2) and Gymnostoma (G80) genera were found to grow exponentially in stirred, propionate-containing BAP medium supplemented with 1.2 or 2.4 μm synthetic 1,2-dipalmitoyl phosphatidylcholine, 1,2-dipalmitoyl phosphatidic acid or 1,2-dipalmitoyl-sn-glycerol. Phosphatidylcholines containing C15:0 or C17:0 acyl residues instead of C16:0 (palmitoyl) residues were equally beneficial but stearoyl (C18:0) residues favored the formation of small sporangia. Oleoyl residues (C18:1) appeared to be toxic as they produced a progressive post-exponential decrease in biomass. Our results suggest that phospholipids containing palmitoyl residues are part of the beneficial compounds present in the complex egg yolk phosphatidyl choline mixture which promote exponential growth of Frankia strains, inhibit sporangia formation and delay post-exponential biomass degradation. Phosphatidic acids do not appear to mediate the enhancing effect of phosphatidylcholine derivatives. The fact that 1,2-dipalmitoyl-sn-glycerol alone is beneficial, suggests that the phosphate and choline residues of the phosphatidylcholine molecule are not essential for balanced growth of Frankia under our conditions. Taken together our results suggest that a primary target of the beneficial compounds may be the plasma membrane of Frankia cells.
We investigated the effectiveness of different inoculation approaches in enhancing the mineralization of [U-14C] labeled 1,2,4-trichlorobenzene (1,2,4-TCB) in soil. Inoculation was conducted with a soil-borne 1,2,4-TCB mineralizing microbial community (MC) as well as the Bordetella sp. strain F2 originally isolated from this community as the key degrader organism (IS). Both were applied either via liquid medium (LM) or attached on clay particles (CP). Fluorescence in-situ hybridization in combination with 14C-1,2,4-TCB mineralization measurements as well as measurements of 14C-residues in soil were used to investigate the bioaugmentation efficiency of the different approaches. Bordetella sp. cell numbers increased about 2–5 times during the incubation process, indicating that the bacteria could survive and develop in the new soil habitat. While the native soil showed negligible 1,2,4-TCB mineralization rates, soil inoculated with the MC attached on CP showed the highest 1,2,4-TCB mineralization rate per Bordetella cell, whereas the other inoculum approaches showed an increased but lower contaminant mineralization. Additionally, the MC-CP approach showed the highest cumulative 1,2,4-TCB mineralization as well as the highest formation of bound 14C-residues which is most likely equivalent to 14C incorporated into the microbial biomass. Thus, our results allow the conclusion that the application of a specific microbe-clay-particle-complex is the most promising approach for an accelerated in-situ mineralization of chemicals in agricultural soils.
A β-1,3 glucanase-producing bacterium identified as Pseudomonas cepacia was isolated on a synthetic medium with laminarin as sole carbon source. In biocontrol experiments carried out under greenhouse conditions, this bacterium decreased the incidence of diseases caused by Rhizoctonia solani, Sclerotium rolfsii and Pythium ultimwn by 85, 48 and 71%, respectively. A determination of lytic enzymes revealed no chitinolytic activity. However, an active and stable β-1,3 glucanase was detected. The optimal temperature and pH values for its activity were 60°C and 5.0, respectively. The induction of this β-1,3 glucanase by different fungal cell walls as sole carbon source in synthetic medium was correlated with the biocontrol of the respective fungi by Pseudomonas cepacia. The damage caused to R. solani hyphae was observed under light and electron microscopes. The role of the β-1,3 glucanase produced by Pseudomonas cepacia in the biological control of soilborne plant pathogens is discussed.
A new approach, based on the application of soluble, dye-labelled and acid-precipitable polysaccharide derivatives, is introduced for the sensitive assay of polysaccharide endo-hydrolases extracted from soil.An extraction procedure involving sodium acetate-acetic acid buffer (pH 5, 0.5M; 5ml g−1 soil) and an assay system adapted to microtitre plates were developed for routine determinations of endo -acting cellulase, xylanase, chitinase, 1,3-β-glucanase and amylase activities. An Acid Brown Earth under a mature beech forest (Fagus sylvatica L., humusform: typical Moder) was studied with respect to distinct, clearly-developed soil horizons (L, F, H, Ahh, Aeh).Enzymes purified by (NH4)2SO4-precipitation and dialysis were assayed for pH and temperature activity profiles. pH optima were determined in the range of 4.5–5.5, temperature optima were in the range of 40–55°C, revealing stable and fairly similar characteristics of these enzymes in the horizons under study.In routine investigations, highest enzyme activities were determined in the L and F horizons. Significantly decreasing activities with increasing soil depth and decreasing organic matter content were determined in the H, Ahh and Aeh horizons, respectively.Cellulase, xylanase and chitinase activities were highly correlated with total-C content of the soil horizons under study (0.871 ⩽r2⩽ 0.954).
An aerobic, Gram-positive bacterium was isolated from explosives-contaminated soil by enrichment culture, using the nitramine explosive, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), as the sole added N source. The organism, identified by 16S rDNA analysis as a Rhodococcus sp., strain DN22, grew exponentially with a mean generation time of 6.5 h at 25°C in minimal medium containing RDX as the sole N source. The growth medium was depleted of RDX 24 h after inoculation but growth did not cease until 20 h later. It was concluded that strain DN22 was using NO−2, released from RDX, as a growth substrate because, following inoculation of strain DN22 into RDX-containing minimal medium, the concentration of NO−2 increased during the first 10 h of incubation and declined to undetectable amounts 20 h later. The ratio of the growth yields of strain DN22 grown on RDX or NO−3 as N sources indicated that three of the six N atoms of RDX were being incorporated into biomass. Increased concentrations of NH+4 in the growth medium reduced the extent of RDX degradation. Nitrite was produced from RDX by resting cell suspensions grown on RDX, NO−3, NO−2 or glutamine as N sources, but not by cells grown on NH+4–N or in peptone-yeast extract medium. Resting cells grown on RDX showed the highest degradative activity, compared to cells grown on alternative N sources, indicating that the RDX degradation system is inducible. When soil was inoculated with RDX-grown cells of strain DN22rr, a rifampicin-resistant derivative of strain DN22, there was significant biodegradation of RDX. The addition of oat chaff to soil stimulated the growth of strain DN22rr and enhanced biodegradation of RDX, resulting in 90% degradation of the explosive in 21 d.
Fungi and bacteria govern most of the transformations and ensuing long-term storage of organic C in soils. We assessed the relative contributions of these two groups of organisms to the microbial biomass and activity of soils from five different ecosystems with treatments hypothesized to enhance soil C sequestration: (1) desert (an elevation gradient allowed comparison of soil developed in a cooler, moister climate with soil developed in a warmer, drier climate), (2) restored tallgrass prairie (land reverted to native prairie in 1979 and neighboring land farmed to row crops for ∼100 year), (3,4) two forest types (Douglas fir and loblolly pine, unfertilized control and N-fertilized plots), and (5) agricultural land (conventional- and no-till management systems). The selective inhibition technique, using captan (fungicide) and oxytetracycline hydrochloride (bactericide), was used to determine the activities (respiration) of fungi and bacteria in each of these soils and substrate-induced respiration was used to measure total active soil microbial biomass C. Phospholipid fatty acid analysis was used to determine the composition of the soil microbial biomass and determine if the activities and structure of the microbial communities were related. Differences in fungal-to-bacterial (F:B) activities between treatments at a site were greatest at the prairie sites. The restored prairie had the highest F:B (13.5) and high total C (49.9 g C kg−1 soil); neighboring soil farmed to corn had an F:B of 0.85 and total C of 36.0 g C kg−1 soil. Within the pairs of study soils, those that were tilled had lower fungal activities and stored C than those that were managed to native or no-till systems. In all pairs of soils, soils that had higher absolute fungal activities also had more total soil C and when two extreme cases were removed fungal activity was correlated with total soil C (R2=0.85). Thus, in this small set of diverse soils, increased fungal activities, more than F:B ratios, were associated with increased soil C. Practices that involved invasive land management decreased fungal activity and stored soil C compared to similar soils that were less intrusively managed.
The interaction of soil microbes with their physical environment affects their abilities to respire, grow and divide. One of these environmental factors is the amount of moisture in the soil. The work we published almost 25 years ago showed that microbial respiration was linearly related to soil-water content and log-linearly related to water potential. The paper arose out of collaboration between two young researchers from different areas of soil science, physics and microbiology. The project was driven by not only our curiosity but also the freedom to operate without the constraints common to the current system of science management. The citation history shows three peaks, 1989, 1999 and from 2002 to the present day. Interestingly, the annual citation rate is as high as it has ever been. The initial peak is due to the application of the work to studies on microbial processes. The second peak is associated with the rise of simulation modelling and the third with the relevance of the findings to climate change research. In this article, our paper is re-evaluated in the light of subsequent studies that allow the principle of separation of variables to be tested. This re-evaluation lends further credence to the linear relationship proposed between soil respiration and water content. A scaled relationship for respiration and water content is presented. Lastly, further research is suggested and more recent work on the physics of gas transport discussed briefly.
This study aimed to: (1) determine whether soil microbial communities along a gradient from intensive (fertilized) to low-input (unfertilized) grassland management, shift in their composition as shown by an increase in the abundance of fungi relative to bacteria and (2) whether these shifts in soil microbial communities vary depending on season. At all sample dates soil microbial biomass-C and -N, and the total abundance of phospholipid fatty acids (PLFA) were highest in unfertilized, undrained treatments and lowest in fertilized and drained grassland. Similarly, microbial activity, measured as CO2-C respiration, was found to be at its lowest in the most intensively managed grassland. Measures of microbial biomass showed a high degree of seasonality, having summer maxima and winter minima. In contrast, PLFA measures had spring maxima and autumn minima. Seasonal and management differences were also observed within the microbial community. PLFA profiles revealed that most individual fatty acids were highest in the unfertilized treatments, and lowest in fertilized grassland. The fungal-to-bacterial biomass ratio was also highest in the unfertilized and lowest in the fertilized soils, suggesting that higher microbial biomass in former were more due to the growth of fungi than bacteria. As with total PLFA, the abundance of individual fatty acids showed a spring maximum and an autumn minimum. Seasonal differences in PLFA patterns were shown to be related to soil mineral-N and soil moisture contents. Factors controlling shifts in microbial community structure between sample dates and sites are discussed in relation to other studies. A critical assessment of the different measures of microbial biomass is also given. Overall, the findings of this study support the thesis that fungi play a more significant role in soil biological processes of low-input, unfertilized grasslands, than in intensively managed systems.
Experiments in liquid culture indicated that nitrification was increased in the presence of bacteriophagous protozoa. There were significant accumulations of NO−3 and NO−2in media containing (NH4)2SO4 only in the presence of amoebae and ciliates. Increasing the concentration of NH+4-N from 1 to 10μml−1 in the absence of protozoa did not increase nitrification, indicating that enhanced nitrification was due to the presence of protozoa rather than the excretion of NH+4by protozoa. The interaction between protozoa and nitrification was also studied during 4 weeks in an amended clay-loam soil held at 15°C. The addition of the biocides, cycloheximide and Triton X-100 reduced both protozoan populations and nitrification. Nitrification was significantly enhanced when protozoan numbers were increased by the addition of supplementary nutrients or extra bacteria.
The degree to which ectomycorrhizal fungi rely on decomposing litter as a carbon source in natural ecosystems is unknown. We used a radiocarbon (14C) tracer to test for uptake of litter carbon by ectomycorrhizal fungi as part of the Enriched Background Isotope Study (EBIS) in Oak Ridge Reservation, Tennessee. In EBIS, leaf litter from a highly 14C-labeled Quercus alba (white oak) forest was reciprocally transplanted with litter from a nearby low-labeled forest that had not been as strongly exposed to 14C. These litter transplants were conducted yearly. We measured Δ14C signatures of ectomycorrhizal fungi collected from each forest four months and 2.25 years after the first litter transplant. The ectomycorrhizas were associated with white oak trees. We found no significant differences in 14C signatures of ectomycorrhizal fungi exposed to low-labeled versus high-labeled litter, indicating that less than 2% of the carbon in ectomycorrhizal biomass originated from transplanted litter. In contrast, ectomycorrhizal Δ14C signatures from the high-labeled forest were 117–140‰ higher than those from the low-labeled forest. This pattern suggests that ectomycorrhizal fungi acquired most (or all) of their carbon from their host plants, probably via direct transfer of photosynthate through the roots.
The effect of inoculum size and the environmental factors of pH, temperature and soil moisture on the biodefluorination of sodium monofluoroacetate (1080) by seven microorganisms (four bacterial species and three fungi) was studied. In the presence of 1080 as the sole carbon source, the effect of pH on 1080 defluorination varied among the organisms. Generally, the optimum pH for 1080 defluorination by soil bacteria (Pseudomonas acidovorans and P. fluorescens 1) was at neutral to alkaline pH and the maximum defluorination by fungi (Fusarium oxysporum and Penicillium restriction) was at pH 5. Most organisms grew on nutrient agar at a pH range of 5–8. The optimal temperature for 1080 defluorination varied with different microorganisms and with different organic carbon sources. On agar, all seven isolates grew best in the temperature range of 28–30°C. The highest rate of 1080 defluorination in soil for all the isolates occurred at fluctuating temperatures (minimum = 11°C, maximum = 24°C) and at soil moisture contents of 8–15%, while the lowest rates occurred at a soil moisture content of 30%. The defluorination rate of 1080 when it was present as the sole carbon source decreased as the inoculum size decreased. In soil the rate of reduction in 1080 defluorination did not appear to be directly proportional to the microbial inoculum size and the rate varied with different microorganisms. Some microorganisms, e.g. P. fluorescens 1, had their highest rate of defluorination activity at a low inoculum density, i.e. (105 cells ml−1 in 1080 solution and 107 cells ml−1 in soil).
The relative contributions to n-hexadecane mineralization by soil bacteria and fungi were assessed using the streptomycin-cycloheximide inhibition technique. In a sandy loam with no history of hydrocarbon pollution 82% n-hexadecane mineralization was attributable to bacteria and only 13% to fungi. In the same soil, glucose mineralization was shared evenly between the bacterial and fungal segments of the soil microbial community.
The repeated addition of organic materials to the soil greatly affects the physical, chemical and biological characteristics. In the present work, we analyzed changes in soil quality properties of the tilled layer caused by different agronomic managements of maize which supply different amounts of carbon (C) and nitrogen (N) through the addition of slurry, farmyard manure or plant residues. The agronomic history of the analyzed soils, which derived from a medium-term (11 yr) field experiment located in NW Italy, represents typical managements of maize for this region. The area is characterized by highly intensive agriculture, with consequent risks to soil degradation that could be limited by the efficient utilization of organic inputs and by recycling within cropping systems, the large amounts of manure that are produced from the many animal breeding farms in this region. We used a combination of both different chemical (soil organic C and total N) and biochemical indicators (potential soil respiration, potentially mineralizable N (PMN) and potential soil microbial biomass (SMB)). We considered the suitability of the selected biochemical indicators to describe the changes in soil characteristics resulting from the past management.
Evaluating the biodiversity of microbial communities remains an elusive task because of taxonomic and methodological difficulties. An alternative approach is to examine components of biodiversity for which there exists a reasonable chance of detecting patterns that are biologically meaningful. One such alternative is functional diversity. We propose a procedure based on the Biolog identification system to quickly, effectively, and inexpensively assess aspects of the functional diversity of microbial communities. The numbers and types of substrates utilized by bacterial communities, as well as the levels of activities on various substrates and patterns of temporal development, constitute an information-rich data set from which to assess functional diversity. Data from six plant communities (black grama grassland. Sporobolus grassland, creosotebush bajada, herbaceous bajada, mesquite-playa fringe, and playa grassland) located along an elevational and moisture gradient at the Jornada Long-Term Ecological Research site in the northern Chihuahuan Desert, are analyzed to illustrate the procedure and its relevance to biodiversity. Our analyses demonstrate that the Biolog system can detect considerable variation in the ability of microbial communities to metabolize different carbon compounds. Variation in substrate use was compartmentalized differently along the moisture gradient. Differences in functional diversity were dependent upon the class of carbon sources (guild-specific results). A multifaceted approach to biodiversity that comprises both functional and taxonomic perspectives represents fertile ground for future research endeavors.
This study compared the degradation of [carboxyl-14C] 2,4-dichlorophenoxyacetic acid (2,4-D) (C2,4-D) and [ring-U-14C] 2,4-D (R2,4-D) in 114 agricultural soils (0–15 cm) as affected by 2,4-D sorption and soil properties (organic carbon content, pH, clay content, carbonate content, cation exchange capacity, total microbial activity). The sample area was confined to Alberta, Canada, located 49–60° north longitude and 110–120° west latitude and soils were grouped by soil organic carbon content (SOC) (0–0.99%, 1–1.99%, 2–2.99%, 3–3.99% and >4% SOC). Degradation rates of C2,4-D and R2,4-D followed first-order kinetics in all soils. Although total microbial activity increased with increasing SOC, degradation rates and total degradation of C2,4-D and R2,4-D decreased with increasing SOC because of increased sorption of 2,4-D by soil and reduced bioavailability of 2,4-D and its metabolites. Rates of R2,4-D degradation were more limited by sorption than rates of C2,4-D degradation, possibly because of greater sorption and formation of bound residues of 2,4-D metabolites relative to the 2,4-D parent molecule. Based on the sorption and degradation parameters quantified, there were two distinct groups of soils, those with less than 1% SOC and those with greater than 1% SOC. Specifically, soils with less than 1% SOC had, on average, 2.4 times smaller soil organic carbon sorption coefficients and 1.4 times smaller 2,4-D half-lives than soils with more than 1% SOC. In regional scale model simulations of pesticide leaching to groundwater, covering many soils, input parameters for each pesticide include a single soil organic carbon sorption coefficient and single half-life value. Our results imply, however, that the approach to these regional scale assessments could be improved by adjusting the values of these two input parameters according to SOC. Specifically, this study indicates that for 2,4-D and Alberta soils containing less than 1% SOC, the 2,4-D pesticide parameters obtained from generic databases should be divided by 2.5 (soil organic carbon sorption coefficient) and 1.5 (half-life value).
We characterized field isolates of Bradyrhizobium japonicum from soybeans grown in Missouri soil and measured competitiveness of peat-formulated B. japonicum 123 (serogroup 123) and 138 (serogroup c1) in this soil. Nodule occupancy by serogroup 123, but not serogroup c1, varied with plant age in uninoculated. field-grown soybeans. Serogroups c1 and 38–115 were found in 37% of all nodules of these plants. Serogroups 76, 122, 123. c3 and 94 were also present, and rhizobia of unknown serology occupied 17% of the nodules. Inoculation with either strain 123 or 138 produced similar numbers of nodules. Strain 123 as an inoculant increased nodule occupancy by serogroup 123 13-fold, while a 2-fold increase in serogroup c1 nodule occupancy was obtained with strain 138 inoculation. Increases in nodule occupancy by the inoculant was at the expense of serogroups other than 123 and c1. Inoculation of either strain resulted in increased nodule occupancy in first-formed nodules in unsterile soil. Dual inoculation with both strains in unsterile soil allowed serogroup c1 to occupy twice the number of nodules as did serogroup 123. In sterilized soil, strain 123 outcompetcd strain 138, occupying 74% of all nodules. The effect of inoculant carrier on competitiveness is discussed.
Of the many genomes of prokaryotes that have been sequenced, most are pathogenic organisms and very few of agriculturally beneficial bacteria. Soybean, the most important cash crop in Brazil, can provide its need for nitrogen through a symbiosis with exotic strains of bradyrhizobia. Bradyrhizobium japonicum strain CPAC 15 (equates to SEMIA 5079, the same serogroup as USDA 123), which is a highly competitive commercial strain applied to soybean crops since the early 1990s, is now established on several millions of hectares. As financial resources for sequencing genomes are still very limited in developing countries, a panoramic genomic view of CPAC 15 was generated. A total of 4328 shotgun reads resulted in 2,046,740 bp with a phred score ≥ 20; the assemblage resulted in 1106 phrap contigs scattered by 69 scaffolds and 966 isolated contigs, with an average of 2.5 reads per contig, covering approximately 13% of the genome. Annotation identified 1371 coding DNA sequences (CDSs), 53% with putative known functions, 23% encoding conserved hypothetical and 24% hypothetical genes, representing about 16% of the estimated putative genes. Several comparisons – on COG and KEGG databases, tRNAs, transposases, G + C content of CPAC 15 with the complete genome of B. japonicum strain USDA 110 indicated a successful coverage of the whole genome. However, the two strains were surprisingly different, as at least 35% of the CDS of CPAC 15 shows higher similarity to microorganisms other than strain USDA 110. Several new putative genes and others with low similarity to USDA 110, were identified. These were related to nodulation, interaction with the host plant and adaptation, e.g., nodB, nodW, ndvA, effector nopP, genes of secretion systems, transporters and environmentally related genes.
Carbon and nitrogen isotope ratios in consumer tissues can be used to analyse the diet and trophic level of soil animals. However, life history traits may significantly influence stable isotope patterns. We evaluated in a series of experiments how stable isotope ratios of carbon (13C/12C) and nitrogen (15N/14N) at natural abundance can be used to study the diet and trophic position of long-lived macro-invertebrates, elaterid larvae, which are major below-ground herbivores. Small, but significant differences in δ13C signatures were found between the larvaes’ anterior and posterior body segments, whereas exuvia reflected the body's overall isotopic composition. The species-specific trophic shift (±SE) in δ15N for Agriotes obscurus and Agriotes sputator (1.62±0.24‰ and 1.08±0.27‰, respectively) was significantly lower than “mean enrichment estimates” reported in the literature, showing the limited applicability of such generalised estimates in studies of invertebrate trophic ecology. To avoid false-positive assignments to two trophic levels due to variation in δ15N values, a minimum sample size of three and five individuals for A. obscurus and A. sputator, respectively, was needed to reduce this risk to below α=5%. Keeping elaterid larvae for up to 128 days without food did not affect their isotopic signatures, in contrast to previous studies on starving animals. Switching wireworms to isotopically different diets induced changes in their isotopic signatures within 2 weeks. Changes, however, were significant only when the isotopic difference between diets was large. We conclude that experimental studies evaluating how specific life history traits affect stable isotope signatures in consumers have to precede any interpretation of stable isotope data gathered in the field.
An arable soil with organic matter formed from C3-vegetation was amended initially with maize cellulose (C4-cellulose) and sugarcane sucrose (C4-sucrose) in a 67-day laboratory incubation experiment with microcosms at 25 °C. The amount and isotopic composition (13C/12C) of soil organic C, CO2 evolved, microbial biomass C, and microbial residue C were determined to prove whether the formation of microbial residues depends on the quality of the added C source adjusted with NH4NO3 to the same C/N ratio of 15. In a subsequent step, C3-cellulose (3 mg C g−1 soil) was added without N to soil to determine whether the microbial residues formed initially from C4-substrate are preferentially decomposed to maintain the N-demand of the soil microbial community. At the end of the experiment, 23% of the two C4-substrates added was left in the soil, while 3% and 4% of the added C4-cellulose and C4-sucrose, respectively, were found in the microbial biomass. The addition of the two C4-substrates caused a significant 100% increase in C3-derived CO2 evolution during the 5–33 day incubation period. The addition of C3-cellulose caused a significant 50% increase in C4-derived CO2 evolution during the 38–67 day incubation period. The decrease in microbial biomass C4-C accounted for roughly 60% of this increase. Cellulose addition promoted microorganisms strongly able to recycle N immediately from their own tissue by “cryptic growth” instead of incorporating NO3− from the soil solution. The differences in quality of the microbial residues produced by C4-cellulose and C4-sucrose decomposing microorganisms are also reflected by the difference in the rates of CO2 evolution, but not in the rates of net N mineralization.
Lignocellulosic wastes (of maple) were composted and vermicomposted for 10 months under controlled conditions. Chemical and 13C CPMAS NMR spectroscopic analyses were made to characterize the transformations of the organic matter. At first, the total organic matter and carbon mass underwent a relatively rapid decrease. There was a concomitant decomposition of polysaccharides including cellulose. The degradation of aromatic structures and lignin began after one month of composting. The rapidity of this process was at its greatest during the following three months. NMR analysis showed that more ligninolysis occurred in the vermicompost, which was not apparent from the chemical analyses. The C-to-N ratio decreased, reflecting the changes in the C fractions as well as a higher proportion of N in the vermicompost. Polycondensation or neosynthesis was observed during the final stages. The two types of compost evolved differently: a higher proportion of aromatic compounds, polysaccharides and a lower aromaticity ratio occurred in the vermicompost as well as an increase of the ionic protein-to-organic matter ratio, which are interpreted as a more advanced developed state of humification.
Understanding carbon dynamics in soil is the key to managing soil organic matter. Our objective was to quantify the carbon dynamics in microcosm experiments with soils from long-term rye and maize monocultures using natural 13C abundance. Microcosms with undisturbed soil columns from the surface soil (0–25 cm) and subsoil (25–50 cm) of plots cultivated with rye (C3-plant) since 1878 and maize (C4-plant) since 1961 with and without NPK fertilization from the long-term experiment ‘Ewiger Roggen’ in Halle, Germany, were incubated for 230 days at 8 °C and irrigated with 2 mm 10−2 M CaCl2 per day. Younger, C4-derived and older, C3-derived percentages of soil organic carbon (SOC), dissolved organic carbon (DOC), microbial biomass (Cmic) and CO2 from heterothropic respiration were determined by natural 13C abundance. The percentage of maize-derived carbon was highest in CO2 (42–79%), followed by Cmic (23–46%), DOC (5–30%) and SOC (5–14%) in the surface soils and subsoils of the maize plots. The percentage of maize-derived C was higher for the NPK plot than for the unfertilized plot and higher for the surface soils than for the subsoils. Specific production rates of DOC, CO2-C and Cmic from the maize-derived SOC were 0.06–0.08% for DOC, 1.6–2.6% for CO2-C and 1.9–2.7% for Cmic, respectively, and specific production rates from rye-derived SOC of the continuous maize plot were 0.03–0.05% for DOC, 0.1–0.2% for CO2-C and 0.3–0.5% for Cmic. NPK fertilization did not affect the specific production rates. Strong correlations were found between C4-derived Cmic and C4-derived SOC, DOC and CO2-C (r≥0.90), whereas the relationship between C3-derived Cmic and C3-derived SOC, DOC and CO2-C was not as pronounced (r≤0.67). The results stress the different importance of former (older than 40 years) and recent (younger than 40 years) litter C inputs for the formation of different C pools in the soil.
We investigated the behavior of biochars in arable and forest soil in a greenhouse experiment in order to prove that these amendments can increase carbon storage in soils. Two qualities of biochar were produced by hydrothermal pyrolysis from 13C labeled glucose (0% N) and yeast (5% N), respectively. We quantified respiratory losses of soil and biochar carbon and calculated mean residence times of the biochars using the isotopic label. Extraction of phospholipid fatty acids from soil at the beginning and after 4 months of incubation was used to quantify changes in microbial biomass and to identify microbial groups utilizing the biochars. Mean residence times varied between 4 and 29 years, depending on soil type and quality of biochar. Yeast-derived biochar promoted fungi in the soil, while glucose-derived biochar was utilized by Gram-negative bacteria. Our results suggest that residence times of biochar in soils can be manipulated with the aim to “design” the best possible biochar for a given soil type.
Pea plants were grown in γ-irradiated soil in pots with and without addition of the AM fungus Glomus intraradices at sufficient N and limiting P. Depending on the growth phase of the plant presence of AM had negative or positive effect on rhizosphere activity. Before flowering during nutrient acquisition AM decreased rhizosphere respiration and number of protozoa but did not affect bacterial number suggesting top-down regulation of bacterial number by protozoan grazing. In contrast, during flowering and pod formation AM stimulated rhizosphere respiration and the negative effect on protozoa decreased. AM also affected the composition of the rhizosphere bacterial community as revealed from DNA analysis (DGGE). With or without mycorrhiza, rhizosphere respiration was P-limited on very young roots, not nutrient limited at more mature roots and C-limited at withering. This suggests changes in the rhizosphere community during plant growth also supported by changes in the bacteria (DGGE).
In this re-evaluation of our 10-year old paper on priming effects, I have considered the latest studies and tried to identify the most important needs for future research. Recent publications have shown that the increase or decrease in soil organic matter mineralization (measured as changes of CO2 efflux and N mineralization) actually results from interactions between living (microbial biomass) and dead organic matter. The priming effect (PE) is not an artifact of incubation studies, as sometimes supposed, but is a natural process sequence in the rhizosphere and detritusphere that is induced by pulses or continuous inputs of fresh organics. The intensity of turnover processes in such hotspots is at least one order of magnitude higher than in the bulk soil. Various prerequisites for high-quality, informative PE studies are outlined: calculating the budget of labeled and total C; investigating the dynamics of released CO2 and its sources; linking C and N dynamics with microbial biomass changes and enzyme activities; evaluating apparent and real PEs; and assessing PE sources as related to soil organic matter stabilization mechanisms. Different approaches for identifying priming, based on the assessment of more than two C sources in CO2 and microbial biomass, are proposed and methodological and statistical uncertainties in PE estimation and approaches to eliminating them are discussed. Future studies should evaluate directions and magnitude of PEs according to expected climate and land-use changes and the increased rhizodeposition under elevated CO2 as well as clarifying the ecological significance of PEs in natural and agricultural ecosystems. The conclusion is that PEs – the interactions between living and dead organic matter – should be incorporated in models of C and N dynamics, and that microbial biomass should regarded not only as a C pool but also as an active driver of C and N turnover.
Decomposition rates of pine litter and cotton were measured in the litter (AoL) and fermentation (AoF) horizons of two forests in Ireland (Pinus contorta) and the Ukraine (Pinus sylvestris). The extent of decomposition was similar in spite of seasonal climatic differences between the two sites. The amounts of 137Cs and K in litter bags were determined at different stages of decomposition. During the first 2–4 months of decomposition, the K content of litter bags decreased by up to 80%; maximum weight loss in this time was 18%. At both sites decomposition of the litter was accompanied by an increase in 137Cs content of the litter bags. It is suggested that the increase in 137Cs content is due to importation of 137Cs by invading decomposer fungi. Fungus-mediated translocation of 137Cs to fresh litter is proposed to explain the persistence of Chernobyl radiocaesium in the upper horizons of forest soils.