Showing papers in "Soil Biology & Biochemistry in 2006"

Sources of CO2 efflux from soil and review of partitioning methods

Abstract: Five main biogenic sources of CO2 efflux from soils have been distinguished and described according to their turnover rates and the mean residence time of carbon. They are root respiration, rhizomicrobial respiration, decomposition of plant residues, the priming effect induced by root exudation or by addition of plant residues, and basal respiration by microbial decomposition of soil organic matter (SOM). These sources can be grouped in several combinations to summarize CO2 efflux from the soil including: root-derived CO2, plant-derived CO2, SOM-derived CO2, rhizosphere respiration, heterotrophic microbial respiration (respiration by heterotrophs), and respiration by autotrophs. These distinctions are important because without separation of SOM-derived CO2 from plant-derived CO2, measurements of total soil respiration have very limited value for evaluation of the soil as a source or sink of atmospheric CO2 and for interpreting the sources of CO2 and the fate of carbon within soils and ecosystems. Additionally, the processes linked to the five sources of CO2 efflux from soil have various responses to environmental variables and consequently to global warming. This review describes the basic principles and assumptions of the following methods which allow SOMderived and root-derived CO2 efflux to be separated under laboratory and field conditions: root exclusion techniques, shading and clipping, tree girdling, regression, component integration, excised roots and in situ root respiration; continuous and pulse labeling, 13 C natural abundance and FACE, and radiocarbon dating and bomb- 14 C. A short sections cover the separation of the respiration of autotrophs and that of heterotrophs, i.e. the separation of actual root respiration from microbial respiration, as well as methods allowing the amount of CO2 evolved by decomposition of plant residues and by priming effects to be estimated. All these methods have been evaluated according to their inherent disturbance of the ecosystem and C fluxes, and their versatility under various conditions. The shortfalls of existing approaches and the need for further development and standardization of methods are highlighted. q 2005 Elsevier Ltd. All rights reserved.

Experimental evaluation of methods to quantify dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) in soil

Abstract: A significant proportion of the total nutrient in soil solution can be bound to organic molecules and these often constitute a major loss from soil to freshwater. Our purpose was to determine whether chemical extractants used for measuring inorganic N could also be used to quantify dissolved organic nitrogen (DON) and carbon (DOC) in soil. In a range of soils, DOC and DON were extracted with either distilled water or 2 M KCl and the amount recovered compared with that present in soil solution recovered by centrifugal-drainage. The recovery of DON and DOC from soil was highly dependent upon the method of extraction. Factors such as soil sampling strategy (number of samples over space and time), sample preparation (sieving and drying), soil storage, extraction temperature, shaking time, and soil-to-extractant volume ratio all significantly affected the amount of DOC and DON extracted from soil. To allow direct comparison between independent studies we therefore propose the introduction of a standardized extraction procedure: Replicate samples of unsieved, field-moist soil extracted as soon as possible after collection with distilled water, 0.5 M K2SO4 or 2 M KCl at a 1:5 w/v ratio for 1 h at 20 °C.

PH regulation of carbon and nitrogen dynamics in two agricultural soils

Abstract: Soil pH is often hypothesized to be a major factor regulating organic matter turnover and inorganic nitrogen production in agricultural soils. The aim of this study was to critically test the relationship between soil pH and rates of C and N cycling, and dissolved organic nitrogen (DON), in two long-term field experiments in which pH had been manipulated (Rothamsted silty clay loam, pH 3.5–6.8; Woburn sandy loam, pH 3.4–6.3). While alteration of pH for 37 years significantly affected crop production, it had no significant effect on total soil C and N or indigenous mineral N levels. This implies that at steady state, increased organic matter inputs to the soil are balanced by increased outputs of CO2. This is supported by the positive correlation between both plant productivity and intrinsic microbial respiration with soil pH. In addition, soil microbial biomass C and N, and nitrification were also significantly positively correlated with soil pH. Measurements of respiration following addition of urea and amino acids showed a significant decline in CO2 evolution with increasing soil acidity, whilst glucose mineralization showed no response to pH. In conclusion, it appears that changes in soil pH significantly affect soil microbial activity and the rate of soil C and N cycling. The evidence suggests that this response is partially indirect, being primarily linked to pH induced changes in net primary production and the availability of substrates. In addition, enhanced soil acidity may also act directly on the functioning of the microbial community itself.

Use of organic amendment as a strategy for saline soil remediation: Influence on the physical, chemical and biological properties of soil

Abstract: The effectiveness of adding two organic wastes (cotton gin crushed compost, CGCC, and poultry manure, PM) to a saline soil (Salorthidic Fluvaquent) in dryland conditions near Seville (Guadalquivir Valley, Andalusia, Spain) was studied during a period of 5 years. Organic wastes were applied at rates of 5 and 10 t organic matter ha −1 . One year after the assay began, spontaneous vegetation had appeared in the treated plots, particularly in that receiving a high PM dose. After 5 years the plant cover in this treated plot was around 80% (compared with the 8% of the control soil). The effect on the soils physical and chemical properties, soil microbial biomass, and six soil enzymatic activities (dehydrogenase, urease, protease, β-glucosidase, arylsulfatase, and phosphatase activities) were ascertained. Both added organic wastes had a positive effect on the physical, chemical and biological properties of the soil, although at the end of the experimental period, the soil physical properties, such as bulk density, increased more significantly in the CGCC-amended soils (23%) and the exchangeable sodium percentage (ESP) decreased more significantly in the CGCC-amended soils (50%) compared to the unamended soil. Water soluble carbohydrates and soil biochemical properties were higher in the PM-amended soils compared to the CGCC-amended soils (by 70% for water soluble carbohydrates, and by 34, 18, 37, 39, 40 and 30% for urease, protease, β-glucosidase, phosphatase, arylsulfatase and dehydrogenase activities, respectively). After 5 years, the percentage of plant cover was >50% in all treated plots and 8% in the control soil.

The temperature dependence of organic-matter decomposition - still a topic of debate

Abstract: The temperature dependence of organic matter decomposition is of considerable ecosphysiological importance, especially in the context of possible climate-change feedback effects. It effectively controls whether, or how much, carbon will be released with global warming, and to what extent that release of carbon constitutes a dangerous positive feedback effect that leads to further warming. The present paper is an invited contribution in a series of Citation Classics based on a review paper of the temperature dependence of organic matter decomposition that was published in 1995. It discusses the context and main findings of the 1995 study, the progress has been made since then and what issues still remain unresolved. Despite the continuation of much further experimental work and repeated publication of summary articles, there is still no scientific consensus on the temperature dependence of organic matter decomposition. It is likely that this lack of consensus is largely due to different studies referring to different experimental conditions where confounding factors play a greater or lesser role. Substrate availability is particularly important. If it changes during the course of measurements, it can greatly confound the derived apparent temperature dependence. This confounding effect is illustrated through simulations and examples of experimental work drawn from the literature. The paper speculates that much of the current disagreement between studies might disappear if different studies would ensure that they are all studying the same system attributes, and if confounding factors were always considered and, if possible, eliminated.

Emission of N2O, N2 and CO2 from soil fertilized with nitrate: effect of compaction, soil moisture and rewetting

Abstract: Soil compaction and soil moisture are important factors influencing denitrification and N2O emission from fertilized soils. We analyzed the combined effects of these factors on the emission of N2O, N2 and CO2 from undisturbed soil cores fertilized with N 15 O 3 − (150 kg N ha−1) in a laboratory experiment. The soil cores were collected from differently compacted areas in a potato field, i.e. the ridges (ρD=1.03 g cm−3), the interrow area (ρD=1.24 g cm−3), and the tractor compacted interrow area (ρD=1.64 g cm−3), and adjusted to constant soil moisture levels between 40 and 98% water-filled pore space (WFPS). High N2O emissions were a result of denitrification and occurred at a WFPS≥70% in all compaction treatments. N2 production occurred only at the highest soil moisture level (≥90% WFPS) but it was considerably smaller than the N2O–N emission in most cases. There was no soil moisture effect on CO2 emission from the differently compacted soils with the exception of the highest soil moisture level (98% WFPS) of the tractor-compacted soil in which soil respiration was significantly reduced. The maximum N2O emission rates from all treatments occurred after rewetting of dry soil. This rewetting effect increased with the amount of water added. The results show the importance of increased carbon availability and associated respiratory O2 consumption induced by soil drying and rewetting for the emissions of N2O.

Assay for fluorescein diacetate hydrolytic activity: Optimization for soil samples

Abstract: With the increased interest in integrated soil bioecosystem studies, there is a need to have a method of measuring overall microbial activity potential. Hydrolysis of fluorescein diacetate [3',6'-diacetylfluorescein (FDA)] has been suggested as a possible method because the ubiquitous lipase, protease, and esterase enzymes are involved in the hydrolysis of FDA. Following hydrolysis of FDA, fluorescein is released and can be measured spectrophotometrically. Our objective was to optimize the assay for FDA hydrolytic activity in soil samples and determine the kinetic parameters involved in this reaction. The optimized method involves extraction and quantitative measurement of the fluorescein released when 1.0 g of soil is incubated with 50 ml of 60 mM Na-phosphate solution (buffered at pH 7.6) at 37 °C for 3 h. Results showed that FDA hydrolysis was optimum at buffer pH 7.6 and the soil enzymes were denatured at temperatures above 60 °C. Three soils were used to optimize this method: Heiden clay, Raub silt loam, and Cecil sandy loam. This procedure is simple, precise, and can be used in commercial soil testing laboratories to determine general microbial activity and as a soil quality indicator.

Fungal/bacterial ratios in grasslands with contrasting nitrogen management

Abstract: It is frequently hypothesised that high soil fungal/bacterial ratios are indicative for more sustainable agricultural systems. Increased F/B ratios have been reported in extensively managed grasslands. To determine the shifts in fungal/bacterial biomass ratio as influenced by grassland management and to find relations with nitrogen leaching potential, we sampled a two-year-old field experiment at an organic experimental farm in the eastern part of The Netherlands. The effect of crop (grass and grass-clover), N application rate (0, 40, 80, ) and manure type (no manure, farm yard manure and slurry) on the F/B ratio within three growing seasons was tested, as well as relations with soil and crop characteristics, nitrate leaching and partial N balance. Biomass of fungi and bacteria was calculated after direct counts using epifluorescence microscopy. Fungal and bacterial biomass and the F/B ratio were higher in grass than in grass-clover. The F/B ratio decreased with increasing N application rate and multiple regression analysis revealed a negative relationship with pH. Bacterial activity (measured as incorporation of [3H]thymidine and [14C]leucine into bacterial DNA and proteins) showed the exact opposite: an increase with N application rate and pH. Leaching increased with N application rate and was higher in grass-clover than in grass. Partial N balance was more positive at a higher N application rate and showed an inverse relationship with fungal biomass and F/B ratio. We conclude that the fungal/bacterial biomass ratio quickly responded to changes in management. Grasslands with higher N input showed lower F/B ratios. Grass-clover had a smaller fungal biomass and higher N leaching than grass. In general, a higher fungal biomass indicated a lower nitrogen leaching and a more negative partial N balance (or smaller N surplus), but more observations are needed to confirm the relationship between F/B ratio and sustainability.

Decomposition in peatlands: Reconciling seemingly contrasting results on the impacts of lowered water levels

Abstract: Northern peatlands represent about 30% of the global soil C pools. The C pool in peat is a result of a relatively small imbalance between production and decay. High water levels and the consequent anoxia are considered the major causes for the imbalance. As such, the C sink of a peatland is labile, and sensitive to disturbances in environmental conditions. Changes in peatland ecosystem functions may be mediated through land-use change, and/or climatic warming. In both cases, lowering of the water level may be the key factor. Logically, lowered water levels with the consequent increase in oxygen availability in the surface soil may be assumed to result in accelerated rates of organic matter decomposition. Yet, earlier research has given highly contrasting results concerning the effects of lowered water levels on the rates of decomposition and the C sink/source behaviour of peatlands. The mechanisms controlling this variation remain unresolved. This paper summarizes the changes observed in the biotic and abiotic controls of decomposition following natural or artificial lowering of peatland water levels and show that they are complex and their interactions have not been previously explored. Long-term changes in the C cycle may differ from short-term changes. Short-term changes represent a disturbance in the ecosystem adapted to the pre-water-level-lowering conditions, while long-term changes result from several adaptive mechanisms of the ecosystem to the new hydrological regime. While in a short term, the disturbed system will always lose C, the long-term changes inherently vary among peatland types, climates, and extents of change in the water level. The paper closes by identifying the gaps in our knowledge that need to be addressed when proceeding towards a causal and unifying explanation for the C sink/source behaviour of peatlands following persistent lowering of the water level.

Growth promotion of plants by plant growth-promoting rhizobacteria under greenhouse and two different field soil conditions

Abstract: This study was conducted with sugar beet in greenhouse and field at two soil type with different organic matter (containing 2.4 and 15.9% OM, referred as the low- and high-OM soil) conditions in order to investigate seed inoculation of sugar beet, with five N2-fixing and two phosphate solubilizing bacteria in comparison to control and mineral fertilizers (N and P) application. Three bacterial strains dissolved P; all bacterial strains fixed N2 and significantly increased growth of sugar beet. In the greenhouse, inoculations with PGPR increased sugar beet root weight by 2.8–46.7% depending on the species. Leaf, root and sugar yield were increased by the bacterial inoculation by 15.5–20.8, 12.3–16.1, and 9.8–14.7%, respectively, in the experiment of low- and high-OM soil. Plant growth responses were variable and dependent on the inoculants strain, soil organic matter content, growing stage, harvest date and growth parameter evaluated. The effect of PGPR was greater at early growth stages than at the later. Effective Bacillus species, such as OSU-142, RC07 and M-13, Paenibacillus polymyxa RC05, Pseudomonas putida RC06 and Rhodobacter capsulatus RC04 may be used in organic and sustainable agriculture.

Response of soil microbial communities to compost amendments

Abstract: Soil organic matter is considered as a major component of soil quality because it contributes directly or indirectly to many physical, chemical and biological properties. Thus, soil amendment with composts is an agricultural practice commonly used to improve soil quality and also to manage organic wastes. We evaluated in laboratory scale experiments the response of the soilborne microflora to the newly created soil environments resulting from the addition of three different composts in two different agricultural soils under controlled conditions. At a global level, total microbial densities were determined by classical plate count methods and global microbial activities were assessed by measuring basal respiration and substrate induced respiration (SIR). Soil suppressiveness to Rhizoctonia solani diseases was measured through bioassays performed in greenhouses. At a community level, the modifications of the metabolic and molecular structures of bacterial and fungal communities were assessed. Bacterial community level physiological profiles (CLPP) were determined using Biolog™ GN microtiter plates. Bacterial and fungal community structures were investigated using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Data sets were analyzed using analysis of variance and ordination methods of multivariate data. The impact of organic amendments on soil characteristics differed with the nature of the composts and the soil types. French and English spent mushroom composts altered all the biological parameters evaluated in the clayey soil and/or in the sandy silty clay soil, while green waste compost did not modify either bacterial and fungal densities, SIR values nor soil suppressiveness in any of the soils. The changes in bacterial T-RFLP fingerprints caused by compost amendments were not related to the changes in CLPP, suggesting the functional redundancy of soil microorganisms. Assessing the density, the activity and the structure of the soil microflora allowed us not only to detect the impact of compost amendment on soil microorganisms, but also to evaluate its effect at a functional level through the variation of soil disease suppressiveness. Differences in disease suppressiveness were related to differences in chemical composition, in availability of nutrients at short term and in microbial composition due to both incorporation and stimulation of microorganisms by the compost amendments.

The soil carbon dilemma: Shall we hoard it or use it?

Abstract: Rapidly rising concentrations of atmospheric CO2 have prompted a flurry of studies on soils as potential carbon (C) ‘sinks’. Sequestering C in soils is often seen as a ‘win–win’ proposition; it not only removes excess CO2 from the air, but also improves soils by augmenting organic matter, an energy and nutrient source for biota. But organic matter is most useful, biologically, when it decays. So we face a dilemma: can we both conserve organic matter and profit from its decay? Or must we choose one or the other? In this essay, I contemplate the merits, first of building soil C and then of decaying (losing) it, partly from a historical perspective. I then consider the apparent trade-off between accrual and decay, and reflect on how the dilemma might be resolved or assuaged. These fledgling thoughts, offered mostly to stir more fruitful debate, include: finding ways to increase C inputs to soil; seeking to optimize the timing of decay; and understanding better, from an ecosystem perspective, the flows of C, rather than only the stocks. Carbon sequestration is a sound and worthy goal. But soil organic matter is far more than a potential tank for impounding excess CO2; it is a relentless flow of C atoms, through a myriad of streams—some fast, some slow—wending their way through the ecosystem, driving biotic processes along the way. Now, when we aim to regain some of the C lost, we may need new ways of thinking about soil C dynamics, and tuning them for the services expected of our ecosystems. This objective, perhaps demanding more biology along with other disciplines, is especially urgent when we contemplate the stresses soon to be imposed by coming global changes.

Organic C and N stabilization in a forest soil: Evidence from sequential density fractionation

Abstract: In mineral soil, organic matter (OM) accumulates mainly on and around surfaces of silt- and clay-size particles. When fractionated according to particle density, C and N concentration (per g fraction) and C/N of these soil organo-mineral particles decrease with increasing particle density across soils of widely divergent texture, mineralogy, location, and management. The variation in particle density is explained potentially by two factors: (1) a decrease in the mass ratio of organic to mineral phase of these particles, and (2) variations in density of the mineral phase. The first explanation implies that the thickness of the organic accumulations decreases with increasing particle density. The decrease in C/N can be explained at least partially by especially stable sorption of nitrogenous N-containing compounds (amine, amide, and pyrrole) directly to mineral surfaces, a phenomenon well documented both empirically and theoretically. These peptidic compounds, along with ligand-exchanged carboxylic compounds, could then form a stable inner organic layer onto which other organics could sorb more readily than onto the unconditioned mineral surfaces (“onion” layering model). To explore mechanisms underlying this trend in C concentration and C/N with particle density, we sequentially density fractionated an Oregon andic soil at 1.65, 1.85, 2.00, 2.28, and 2.55 g cm −3 and analyzed the six fractions for measures of organic matter and mineral phase properties. All measures of OM composition showed either: (1) a monotonic change with density, or (2) a monotonic change across the lightest fractions, then little change over the heaviest fractions. Total C, N, and lignin phenol concentration all decreased monotonically with increasing density, and 14 C mean residence time (MRT) increased with particle density from ca. 150 years to >980 years in the four organo-mineral fractions. In contrast, C/N, 13 C and 15 N concentration all showed the second pattern. All these data are consistent with a general pattern of an increase in extent of microbial processing with increasing organo-mineral particle density, and also with an “onion” layering model. X-ray diffraction before and after separation of magnetic materials showed that the sequential density fractionation (SDF) isolated pools of differing mineralogy, with layer-silicate clays dominating in two of the intermediate fractions and primary minerals in the heaviest two fractions. There was no indication that these differences in mineralogy controlled the differences in density of the organo-mineral particles in this soil. Thus, our data are consistent with the hypothesis that variation in particle density reflects variation in thickness of the organic accumulations and with an “onion” layering model for organic matter accumulation on mineral surfaces. However, the mineralogy differences among fractions made it difficult to test either the layer-thickness or “onion” layering models with this soil. Although SDF isolated pools of distinct mineralogy and organic-matter composition, more work will be needed to understand mechanisms relating the two factors.

Soil microbial biomass and activity in organic tomato farming systems: Effects of organic inputs and straw mulching.

Abstract: Organic farming is rapidly expanding worldwide. Plant growth in organic systems greatly depends on the functions performed by soil microbes, particularly in nutrient supply. However, the linkages between soil microbes and nutrient availability in organically managed soils are not well understood. We conducted a long-term field experiment to examine microbial biomass and activity, and nutrient availability under four management regimes with different organic inputs. The experiment was initiated in 1997 by employing different practices of organic farming in a coastal sandy soil in Clinton, NC, USA. Organic practices were designed by applying organic substrates with different C and N availability, either in the presence or absence of wheat–straw mulch. The organic substrates used included composted cotton gin trash (CGT), animal manure (AM) and rye/vetch green manure (RV). A commercial synthetic fertilizer (SF) was used as a conventional control. Results obtained in both 2001 and 2002 showed that microbial biomass and microbial activity were generally higher in organically than conventionally managed soils with CGT being most effective. The CGT additions increased soil microbial biomass C and activity by 103–151% and 88–170% over a period of two years, respectively, leading to a 182–285% increase in potentially mineralizable N, compared to the SF control. Straw mulching further enhanced microbial biomass, activity, and potential N availability by 42, 64, and 30%, respectively, relative to non-mulched soils, likely via improving C and water availability for soil microbes. The findings that microbial properties and N availability for plants differed under different organic input regimes suggest the need for effective residue managements in organic tomato farming systems.

Suppressiveness of 18 composts against 7 pathosystems: Variability in pathogen response

Abstract: Compost is often reported as a substrate that is able to suppress soilborne plant pathogens, but suppression varies according to the type of compost and pathosystem. Reports often deal with a single pathogen while in reality crops are attacked by multiple plant pathogens. The goal of the present study was to evaluate the disease suppression ability of a wide range of composts for a range of plant pathogens. This study was conducted by a consortium of researchers from several European countries. Composts originated from different countries and source materials including green and yard waste, straw, bark, biowaste and municipal sewage. Suppressiveness of compost-amended (20% vol./vol.) peat-based potting soil was determined against Verticillium dahliae on eggplant, Rhizoctonia solani on cauliflower, Phytophthora nicotianae on tomato, Phytophthora cinnamomi on lupin and Cylindrocladium spathiphylli on Spathiphyllum sp., and of compost-amended loamy soil (20% vol./vol.) against R. solani on Pinus sylvestris and Fusarium oxysporum f. sp. lini on flax. From the 120 bioassays involving 18 composts and 7 pathosystems, significant disease suppression was found in 54% of the cases while only 3% of the cases showed significant disease enhancement. Pathogens were affected differently by the composts. In general, prediction of disease suppression was better when parameters derived from the compost mixes were used rather than those derived from the pure composts. Regression analyses of disease suppression of the individual pathogens with parameters of compost-amended peat-based mixes revealed the following groupings: (1) competition-sensitive: F. oxysporum and R. solani/cauliflower; (2) rhizosphere-affected: V. dahliae; (3) pH-related: P. nicotianae; and (4) specific/unknown: R. solani/pine, P. cinnamomi and C. spathiphylli. It was concluded that application of compost has in general a positive or no effect on disease suppression, and only rarely a disease stimulating effect.

Activities of extracellular enzymes in physically isolated fractions of restored grassland soils

Abstract: Extracellular enzymes degrade complex organic compounds and contribute to carbon turnover in soils. We used physical fractionation procedures to investigate whether soil carbon is spatially isolated from degradative enzymes across a prairie restoration chronosequence in Illinois, USA. We found that carbon-degrading enzymes were abundant in all soil fractions, including macroaggregates, microaggregates, and the clay-sized fraction. The activities of two cellulose-degrading enzymes and a chitin-degrading enzyme were 2–10 times greater in particulate organic matter (POM) fractions than in bulk soil, consistent with the rapid turnover of POM fractions. Polyphenol oxidase activity in the clay-sized fraction was 3 times that in the bulk soil, despite a higher mean residence time for carbon in the clay-sized fraction. For most enzymes, differences in activity among fractions and across the restoration chronosequence diminished when adjusted for differences in carbon concentrations. However, glycine aminopeptidase activity per unit carbon increased four-fold across the chronosequence in the clay fraction, while polyphenol oxidase activity declined by 40%. These results suggest that enzyme production and carbon turnover occur rapidly in POM fractions, but slowly in mineral-dominated fractions where enzymes and their carbon substrates are immobilized on mineral surfaces. Soil carbon accumulation in mineral fractions and across the prairie restoration chronosequence probably reflects increasing physical isolation of enzymes and substrates on the molecular to micron scale, rather than exclusion of enzymes from entire soil fractions. Based on these mechanisms, land managers could increase soil C stocks by reducing the physical disruption of soil structure associated with cultivation. Published by Elsevier Ltd.

Microbial community utilization of added carbon substrates in response to long-term carbon input manipulation

Abstract: The chemical composition and quantity of plant inputs to soil are primary factors controlling the size and structure of the soil microbial community. Little is known about how changes in the composition of the soil microbial community affect decomposition rates and other ecosystem functions. This study examined the degradation of universally 13 C-labeled glucose, glutamate, oxalate, and phenol in soil from an old-growth Douglas-fir (Pseudotsuga menziesii)—western hemlock (Tsuga heterophylla) forest in the Oregon Cascades that has experienced 7 y of chronic C input manipulation. The soils used in this experiment were part of a larger Detritus Input and Removal Treatment experiment and have received normal C inputs (control), doubled wood inputs, or root and litter input exclusion (no inputs). Soil from the doubled wood treatment had a higher fungal:bacterial ratio, and soil from the no inputs treatment had a lower fungal:bacterial ratio, than the control soil. Differences in the utilization of the compounds added to the field-manipulated soils were assessed by following the 13 C tracer into microbial biomass and respiration. In addition, 13 C-phospholipid fatty acids (PLFA) analysis was used to examine differential microbial utilization of the added substrates. Glucose and glutamate were metabolized similarly in soils of all three litter treatments. In contrast, the microbial community in the double wood soil respired more added phenol and oxalate, whereas microbes in the no inputs soil respired less added phenol and oxalate, than the control soil. Phenol was incorporated primarily into fungal PLFA, especially in soil of the double wood treatment. The addition of all four substrates led to enhanced degradation of soil organic matter (priming) in soils of all three litter treatments, and was greater following the addition of phenol and oxalate as compared to glucose and glutamate. Priming was greater in the no inputs soil as compared to the control or doubled wood soils. These results demonstrate that altering plant inputs to soil can lead to changes in microbial utilization of C compounds. It appears that many of these changes are the result of alteration in the size and composition of the microbial community. r 2006 Elsevier Ltd. All rights reserved.

Microbiological degradation index of soils in a semiarid climate

Abstract: Soil degradation and desertification affect many areas of the planet. One such area is the Mediterranean region of SE Spain, where the climatological and lithological conditions, together with the relief of the landscape and anthropological activity, including agricultural abandonment, are responsible for increasing desertification. It is therefore considered to be of extreme importance to be able to measure soil degradation quantitatively. The aim of this study was to make a microbiological and biochemical characterisation of different soil catenas in SE Spain, including in a wide range of plant cover densities in an attempt to assess the suitability of the parameters measured to reflect the state of soil degradation and the possibility of using the parameters to elaborate a microbiological degradation index (MDI) valid for use in semiarid climates. For this, several indices related with the organic matter content (total organic carbon, TOC, water-soluble carbon, WSC, and water-soluble carbohydrates, WSCh), with the size of microbial populations (microbial biomass carbon, MBC) and related activity (respiration and enzymatic activities) were determined in the soils of three different catenas in different seasons of the year. The values of these parameters were seen to be closely related with the degree of vegetal cover, forest soils with a high cover value showing the highest indices. There was a highly significant positive correlation (p<0.01) between the TOC and WSC content, and other parameters such as MBC, ATP, dehydrogenase activity and the activity of different hydrolases (urease, protease, phosphatase and β-glucosidase). The results show that the parameters analysed are a good reflection of a soil's microbiological quality since the soils with the worst characteristics (saline and with low organic matter and nutrient content) showed the lowest values. The study provides a soil degradation index based on its microbiological properties: MDI. This index is a function of the following five parameters, which showed the greatest weight in the factorial analysis made with all the parameters analysed: dehydrogenase activity, WSCh, urease activity, WSC and respiration.

Diversity and distribution of Victoria Land biota

Abstract: Understanding the relationship between soil biodiversity and ecosystem functioning is critical to predicting and monitoring the effects of ecosystem changes on important soil processes. However, most of Earth's soils are too biologically diverse to identify each species present and determine their functional role in food webs. The soil ecosystems of Victoria Land (VL) Antarctica are functionally and biotically simple, and serve as in situ models for determining the relationship between biodiversity and ecosystem processes. For a few VL taxa (microarthropods, nematodes, algae, mosses and lichens), species diversity has been intensively assessed in highly localized habitats, but little is known of how community assemblages vary across broader spatial scales, or across latitudinal and environmental gradients. The composition of tardigrade, rotifer, protist, fungal and prokaryote communities is emerging. The latter groups are the least studied, but potentially the most diverse. Endemism is highest for microarthropods and nematodes, less so for tardigrades and rotifers, and apparently low for mosses, lichens, protists, fungi and prokaryotes. Much of what is known about VL diversity and distribution occurs in an evolutionary and ecological vacuum; links between taxa and functional role in ecosystems are poorly known and future studies must utilize phylogenetic information to infer patterns of community assembly, speciation, extinction, population processes and biogeography. However, a comprehensive compilation of all the species that participate in soil ecosystem processes, and their distribution across regional and landscape scales is immediately achievable in VL with the resources, tools, and expertise currently available. We suggest that the soil ecosystems of VL should play a major role in exploring the relationship between biodiversity and ecosystem functioning, and in monitoring the effects of environmental change on soil processes in real time and space.

The influence of plant litter diversity on decomposer abundance and diversity

Abstract: Although there has been much recent interest in the effect of litter mixing on decomposition processes, much remains unknown about how litter mixing and diversity affects the abundance and diversity of decomposer organisms. We conducted a litter mixing experiment using litterbags in a New Zealand rainforest, in which treatments consisted of litter monocultures of each of 8 forest canopy and understory plant species, as well as mixtures of 2, 4 and 8 species. We found litter mixing to have little effect on net decomposition rates after either 279 or 658 days, and for each species decomposition rates in mixture treatments were the same as in monoculture. Litter species identity had important effects on litter microfauna, mesofauna and macrofauna, with different litter types promoting different subsets of the fauna. Litter mixing had few effects on densities of mesofauna and macrofauna, but did have some important effects on components of the microfauna, notably microbe-feeding and predatory nematodes. At day 279, litter mixing also consistently reduced the ratio of bacterial-feeding to microbe-feeding (bacterial-feeding+fungal-feeding) nematodes, pointing to mixing causing a significant switch from the bacterial-based to the fungal-based energy channel. Litter mixing sometimes influenced the community composition and diversity of nematodes and macrofauna, but effects of litter mixing on diversity were not necessarily positive, and were much weaker than effects of litter species identity on diversity. We conclude that litter mixing effects on the abundance and diversity of decomposer biota, when they occur, are likely to be of secondary and generally minor significance when compared to the effects of litter species identity and composition.

Aggregate stability and microbial community dynamics under drying-wetting cycles in a silt loam soil

Abstract: Aggregate stability often exhibits a large inter-annual and seasonal variability which occurs regardless of residue treatments and is often larger than the differences between soils or cropping systems. Variations in soil moisture and seasonal stimulation of microbial activity are frequently cited as the major causes. The goal of this paper was to evaluate the effects of drying-rewetting cycles on aggregate stability and on its main microbially mediated agents from a mechanistic point of view. The 3-5 mm aggregates of a silty soil were incubated at 20 °C for 63 days with the following treatments and their combinations: (i) with or without straw input and (ii) with or without exposure to four dry-wet cycles. Microbial activity was followed by measuring the soil respiration. We estimated the microbial agents of aggregate stability measuring hot-water extractable carbohydrate-C, microbial biomass carbon and ergosterol content. We measured the water drop penetration time to estimate the hydrophobicity and aggregate stability according to Le Bissonnais [1996. Aggregate stability and assessment of soil crustability and erodibility: I. Theory and methodology. European Journal of Soil Science 47, 425-437] to distinguish three breakdown mechanisms: slaking, mechanical breakdown and microcracking. The addition of straw stimulated microbial activity and increased the resistance to the three tests of aggregate stability, enhancing the internal cohesion and hydrophobicity of aggregates. All the estimated microbial agents of aggregate stability responded positively to the addition of organic matter and were highly correlated with aggregate stability. Fungal biomass correlated better with aggregate stability than total microbial biomass did, showing the prominent role of fungi by its triple contribution: physical entanglement, production of extracellular polysaccharides and of hydrophobic substances. Dry-wet cycles had less impact on aggregate stability than the addition of straw, but their effects were more pronounced when microbial activity was stimulated demonstrating a positive interaction.

The role of plant residues in pH change of acid soils differing in initial pH

Abstract: Reports on the effect of plant residues on soil pH have been contradictory. The conflicting accounts have been suggested to result from differences in compositions and types of plant residues and characteristics of soils. This incubation study examined the effect of plant residues differing in concentrations of N (3–49 g kg−1) and of alkalinity (excess cations) (220–1560 mmol kg−1) on pH change of three soils differing in initial pH (3.9–5.1 in 0.01 M CaCl2). The addition of plant residues at a rate of 15 g kg−1 soil weight increased the pH of all soils by up to 3.4 units and the pH reached the maximum at day 42 after incubation for Wodjil (initial pH 3.87) and Bodallin (pH 4.54) soils and day 14 for Lancelin soil (pH 5.1). The amount of pH buffering was decreased by residue addition in Wodjil soil, increased in Bodallin soil and remained unchanged in Lancelin soil, which closely related to changes of soil pH. Residue addition increased NH 4 + concentration and the increase in NH 4 + concentration generally correlated positively with the concentration of residue N. The NH 4 + concentration increased with time, reached the peak at Days 42–105 for Wodjil soil, Days 14–105 for Bodallin soil and Days 14–42 for Lancelin soil, and then decreased only in Lancelin soil. The concentration of NO 3 − was kept minimal in Wodjil and Bodallin soils. In Lancelin soil, NO 3 − concentrations increased with incubation time from days 14–28. Irrespective of plant residue and incubation time, the amounts of alkalinity produced due to residue addition correlated highly with the sum of the alkalinity added as plant residues (excess cations) and those resulting from mineralization of residue N, with the slope of regression lines decreasing with increase of the initial soil pH. Direct shaking of soil with the residues at the same rate of alkalinity (excess cations) under sterile conditions increased the pH of the Wodjil soil but decreased it in the Lancelin soil. It is suggested that the decarboxylation of organic anions (as indicated by excess cations) of added plant residues and ammonification of the residue N causes soil pH increase whereas nitrification of mineralised residue nitrogen causes soil pH decrease, and that the association/dissociation of organic compounds also plays a role in soil pH change, depending initial pH of the soil. The overall effect on soil pH after addition of plant residues would therefore depend on the extent of each of these processes under given conditions.

Temperature and soil moisture interactively affected soil net N mineralization in temperate grassland in Northern China

Abstract: Intact soil cores from three adjacent sites (Site A: grazed, Site B: fenced for 4 years, and Site C: fenced for 24 years) were incubated in the laboratory to examine effects of temperature, soil moisture, and their interactions on net nitrification and N mineralization rates in the Inner Mongolia grassland of Northern China. Incubation temperature significantly influenced net nitrification and N mineralization rates in all the three grassland sites. There were no differences in net nitrification or N mineralization rates at lower temperatures (K10, 0, and 5 8C) whereas significant differences were found at higher temperatures (15, 25, and 35 8C). Soil moisture profoundly impacted net nitrification and N mineralization rates in all the three sites. Interactions of temperature and moisture significantly affected net nitrification and mineralization rates in Site B and C, but not in Site A. Temperature sensitivity of net nitrification and N mineralization varied with soil moisture and grassland site. Our results showed greater net N mineralization rates and lower concentrations of inorganic N in the grazed site than those in the fenced sites, suggesting negative impacts of grazing on soil N pools and net primary productivity. q 2005 Elsevier Ltd. All rights reserved.

Non-streptomycete actinomycetes as biocontrol agents of soil-borne fungal plant pathogens and as plant growth promoters

Abstract: Among soil microorganisms, bacteria and fungi and to a lesser extent actinomycetes, have received considerable attention as biocontrol agents of soil-borne fungal plant pathogens and as plant growth promoters. Within actinomycetes, Streptomyces spp. have been investigated predominantly, mainly because of their dominance on, and the ease of isolation from, dilution plates and because of the commercial interest shown on the antibiotics produced by certain Streptomyces spp. Many of non-streptomycete actinomycetes (NSA) taxa are therefore rarely reported in literature dealing with routine isolations of biocontrol agents and/or plant growth promoters from plant and soil. It is clear that special isolation methods need to be employed in routine isolations to selectively isolate NSA. Some interesting information exists, albeit in relatively few reports compared to that on other microorganisms, on the biological activities of NSA, especially in relation to their mechanisms of action in the biological control of soil-borne fungal plant pathogens and plant growth promotion. This review presents an overview of this information and seeks to encourage further investigations into what may be considered a relatively unexplored area of research. Certain soil environmental factors, especially in horticultural systems, could be manipulated to render the soil conducive for the biological activities of NSA. A variety of NSA isolated by selective methods have not only shown to be rhizosphere competent but also adapted for an endophytic life in root cortices. Some of the NSA, including endophytic strains that have shown potential to suppress soil-borne fungal plant pathogens, are able to employ one or more mechanisms of antagonism including antibiosis, hyperparasitism and the production of cell-wall degrading enzymes. Strains of NSA promote plant growth by producing plant growth regulators. Enhancement of plant growth by the antagonists are considered to help the host by producing compensatory roots that mask the impact of root diseases.

Microbial community structure and function in a soil contaminated by heavy metals: effects of plant growth and different amendments

Abstract: We studied the effects of in situ remediation of a heavy metal (HM) contaminated soil on some soil chemical properties, microbial function and microbial structural diversity after 18 months. The experiment was carried out at semifield scale in containers filled with HM contaminated soil from the Aznalcollar mine accident (Southern Spain, 1998). The remediation measures consisted of the application of different amendments and/or establishment of a plant cover (Agrostis stolonifera L.). Seven treatments were established: four organic treatments (municipal waste compost (MWC), biosolid compost (BC), leonardite (LEO) and litter (LIT)), one inorganic treatment (sugar beet lime (SL)) and two controls (control with plant cover (CTRP) and control without plant cover (CTR)). Several soil chemical (pH, soluble HM, total organic C (TOC), water-soluble C (WSC) and available-P) and biochemical properties (microbial biomass C (MBC), MBC/TOC ratio and enzyme activities) were determined. Microbial community structure was studied by means of ARDRA (amplified ribosomal DNA restriction analysis). The SL, MWC and BC treatments were the most efficient to raise soil pH and decrease soluble HM concentrations. Total organic C was increased in the organic treatments by 2 to 4-fold, whereas water-soluble C was statistically similar in the CTRP, SL and the organic treatments, probably due to the presence of a root system in all these treatments. Available-P was also increased in the BC, SL and MWC treatments due to the higher P content of the amendments applied in these treatments. Soil microbial function was generally enhanced in the amended and CTRP treatments. The MWC, BC and SL treatments were particularly efficient to increase microbial biomass C, the MBC/TOC ratio and the dehydrogenase and aryl-sulphatase enzyme activities. These results could be attributed to the amelioration of some of the soil chemical properties: increase in soil pH and water-soluble C and decrease of HM soluble concentrations. ARDRA analyses showed changes in structural diversity in both the bacterial and fungal community under the different treatments. Fingerprinting patterns of the 16S rDNA obtained with Hinf-I and of the 18S rDNA with Hpa-II revealed higher similarity percentages among samples from the same treatment compared with samples from the other treatments. In addition, a higher similarity was found between samples from all treatments under the Agrostis influence. The use of certain amendments and/or a plant cover is important for in situ remediation of HM contaminated soils, since these practices can affect soil chemical properties, as well as the microbial community function and structure.

Variable use of plant- and soil-derived carbon by microorganisms in agricultural soils

Abstract: In this study we used compound specific 13C and 14C isotopic signatures to determine the degree to which recent plant material and older soil organic matter (SOM) served as carbon substrates for microorganisms in soils. We determined the degree to which plant-derived carbon was used as a substrate by comparison of the 13C content of microbial phospholipid fatty acids (PLFA) from soils of two sites that had undergone a vegetation change from C3 to C4 plants in the past 20–30 years. The importance of much older SOM as a substrate was determined by comparison of the radiocarbon content of PLFA from soils of two sites that had different 14C concentrations of SOM. The 13C shift in PLFA from the two sites that had experienced different vegetation history indicated that 40–90% of the PLFA carbon had been fixed since the vegetation change took place. Thus PLFA were more enriched in 13C from the new C4 vegetation than it was observed for bulk SOM indicating recent plant material as preferentially used substrate for soil microorganisms. The largest 13C shift of PLFA was observed in the soil that had high 14C concentrations of bulk SOM. These results reinforce that organic carbon in this soil for the most part cycles rapidly. The degree to which SOM is incorporated into microbial PLFA was determined by the difference in 14C concentration of PLFA derived from two soils one with high 14C concentrations of bulk SOM and one with low. These results showed that 0–40% of SOM carbon is used as substrate for soil microorganisms. Furthermore a different substrate usage was identified for different microorganisms. Gram-negative bacteria were found to prefer recent plant material as microbial carbon source while Gram-positive bacteria use substantial amounts of SOM carbon. This was indicated by 13C as well as 14C signatures of their PLFA. Our results find evidence to support ‘priming’ in that PLFA indicative of Gram-negative bacteria associated with roots contain both plant- and SOM-derived C. Most interestingly, we find PLFA indicative of archeobacteria (methanothrophs) that may indicate the use of other carbon sources than plant material and SOM to a substantial amount suggesting that inert or slow carbon pools are not essential to explain carbon dynamics in soil.

Bacterial inoculants affecting nickel uptake by Alyssum murale from low, moderate and high Ni soils

Abstract: Metal hyperaccumulator plants like Alyssum murale have a remarkable ability to hyperaccumulate Ni from soils containing mostly insoluble Ni. We have shown some rhizobacteria increase the phytoavailability of Ni in soils, thus enhancing Ni accumulation by A. murale. Nine bacterial strains, originally isolated from the rhizosphere of A. murale grown in serpentine Ni-rich soil, were examined for their ability to solubilize Ni in different soils and for their effect on Ni uptake into Alyssum. Microbacterium oxydans AY509223; Rhizobium galegae AY509213; Microbacterium oxydans AY509219; Clavibacter xyli AY509236; Acidovorax avenae AY512827; Microbacterium arabinogalactanolyticum AY509225; M. oxydans AY509222; M. arabinogalactanolyticum AY509226 and M. oxydans AY509221 were added to low, moderate and high Ni-contaminated soils. M. oxydans AY509223 significantly increased Ni extraction by 10 mM Sr(NO3)2 from the high and medium soils and had no effect on Ni extraction from the low Ni soils. The other eight bacterial isolates significantly increased Ni extraction from all soils. There were no significant effects of bacterial inoculation on fresh and dry weight of A . murale shoots grown in the low and high Ni soils compared to an unamended control. M. oxydans AY509223 significantly increased Ni uptake of A. murale grown in the low, medium, and high soils by 36.1%, 39.3%, and 27.7%, respectively, compared with uninoculated seeds. M. oxydans AY509223 increased foliar Ni from the same soils from 82.9, 261.3 and 2829.3 mg kg 1 to 129.7, 430.7, and 3914.3 mg kg 1 , respectively, compared with uninoculated controls. These results show that bacteria are important for Ni

Sources and mechanisms of priming effect induced in two grassland soils amended with slurry and sugar

Abstract: The mechanisms and specific sources of priming effects, ie short term changes of soil organic matter (SOM) decomposition after substance addition, are still not fully understood These uncertainties are partly method related, ie until now only two C sources in released CO2 could be identified We used a novel approach separating three carbon (C) sources in CO2 efflux from soil The approach is based on combination of different substances originated from C3 or C4 plants in different treatments and identical transformation of substances like C3 sugar (from sugar beet) and C4 sugar (from sugar cane) We investigated the influence of the addition of two substances having different microbial utilizability, ie slurry and sugar on the SOM or/and slurry decomposition in two grassland soils with different levels of Corg (23 vs 51% C) Application of slurry to the soil slightly accelerated the SOM decomposition Addition of sugar lead to changes of SOM and slurry decomposition clearly characterized by two phases: immediately after sugar addition, the microorganisms switched from the decomposition of hardly utilizable SOM to the decomposition of easily utilizable sugar This first phase was very short (2‐3 days), hence was frequently missed in other experiments The second phase showed a slightly increased slurry and SOM decomposition (compared to the soil without sugar) The separation of three sources in CO2 efflux from grassland soils allowed us to conclude that the C will be utilized according to its utilizability: sugarOslurryOSOM Additionally, decomposition of more inert C (here SOM) during the period of intensive sugar decomposition was strongly reduced (negative priming effect) We conclude that, priming effects involve a chain of mechanisms: (i) preferential substrate utilization, (ii) activation of microbial biomass by easily utilizable substrate (iii) subsequent increased utilization of following substrates according to their utilizability, and (iv) decline to initial state q 2005 Elsevier Ltd All rights reserved

Microbial activity in soils frozen to below-39 degrees C

Abstract: Recent research on life in extreme environments has shown that some microorganisms metabolize at extremely low temperatures in Arctic and Antarctic ice and permafrost. Here, we present kinetic data on CO2 and (CO2)-C-14 release from intact and C-14-glucose amended tundra soils (Barrow, Alaska) incubated for up to a year at 0 to -39 degrees C. The rate of CO2 production declined exponentially with temperature but it remained positive and measurable, e.g. 2-7 ng CO2-C cm(-3) soil d(-1), at -39 degrees C. The variation of CO2 release rate (v) was adequately explained by the double exponential dependence on temperature (T) and unfrozen water content (W) (r(2)> 0.98): v=A exp(lambda T+kW) and where A, lambda and k are constants. The rate of (CO2)-C-14 release from added glucose declined more steeply with cooling as compared with the release of total CO2, indicating that (a) there could be some abiotic component in the measured flux of CO2 or (b) endogenous respiration is more cold-resistant than substrate-induced respiration. The respiration activity was completely eliminated by soil sterilization (1 h, 121 degrees C), stimulated by the addition of oxidizable substrate (glucose, yeast extract), and reduced by the addition of acetate, which inhibits microbial processes in acidic soils (pH 3-5). The tundra soil from Barrow displayed higher below-zero activity than boreal soils from West Siberia and Sweden. The permafrost soils (20-30 cm) were more active than the samples from seasonally frozen topsoil (0-10 cm, Barrow). Finding measurable respiration to -39 degrees C is significant for determining, understanding, and predicting current and future CO2 emission to the atmosphere and for understanding the low temperature limits of microbial activity on the Earth and on other planets. (c) 2005 Elsevier Ltd. All rights reserved. (Less)

13C and 15N natural abundance of the soil microbial biomass

Abstract: Stable isotope analysis is a powerful tool in the study of soil organic matter formation. It is often observed that more decomposed soil organic matter is 13 C, and especially 15 N-enriched relative to fresh litter and recent organic matter. We investigated whether this shift in isotope composition relates to the isotope composition of the microbial biomass, an important source for soil organic matter. We developed a new approach to determine the natural abundance C and N isotope composition of the microbial biomass across a broad range of soil types, vegetation, and climates. We found consistently that the soil microbial biomass was 15 N-enriched relative to the total (3.2 %) and extractable N pools (3.7 %), and 13 C-enriched relative to the extractable C pool (2.5 %). The microbial biomass was also 13 C-enriched relative to total C for soils that exhibited a C3-plant signature (1.6 %), but 13 C-depleted for soils with a C4 signature (� 1.1 %). The latter was probably associated with an increase of annual C3 forbs in C4 grasslands after an extreme drought. These findings are in agreement with the proposed contribution of microbial products to the stabilized soil organic matter and may help explain the shift in isotope composition during soil organic matter formation. r 2006 Elsevier Ltd. All rights reserved.