Soil properties associated with organic matter-mediated suppression of bean root rot in field soil amended with fresh and composted paper mill residuals

The ability of an organic amendment to suppress soil-borne disease is mediated by the complex interactions between biotic and abiotic soil factors. Various microbiological and physicochemical soil properties were measured in field soils with histories of receiving 4 or 5 years of spring additions of paper mill residuals (PMR), PMR composted alone (PMRC), PMR composted with bark (PMRB), or no amendment under a conventionally managed vegetable crop rotation. The objectives of this study were to (i) determine the residual and re-amendment effects of the organic materials on root rot disease severity; (ii) determine the influence of amendment type on the structure of bacterial communities associated with snap bean roots grown in these soils; and (iii) quantify the relative contributions of microbiological and physicochemical properties to root rot suppression in the field and greenhouse. While all amendment types significantly suppressed root rot disease compared to non-amended soils in both environments, only soils amended with PMR or PMRB sustained suppressive conditions 1 year after the most recent amendment event. Disease severity was inversely related to microbial activity (fluorescein diacetate assay) in recently amended soils only. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16s rRNA gene was performed to obtain bacterial profiles. Principal component analysis (PCA) of terminal restriction fragments (TRFs) revealed general differences in bacterial community composition (PC1) among amendment types, and specific TRFs contributed to these differences. Correlation and multiple regression analyses of the measured soil variables revealed that the composition of root-associated bacterial communities and the amount of particulate organic matter—carbon in bulk soils imparted independent and relatively equal contributions to the variation in disease severity documented in the field and greenhouse. Together, our findings provide evidence that disease suppression induced by annual PMR inputs was mediated by their differential effects on bacterial communities and the amount and quality of organic matter in these soils.     

Evaluating effects of sewage sludge and household compost on soil physical,chemical and microbiological properties

Recycling of organic wastes within agriculture may help maintain soil fertility via effects on physical, chemical and biological properties. Efficient use, however, requires an individual assessment of waste products, and effects should be compared with natural variations due to climate and soil type. An 11-month incubation experiment was conducted between April 1998 and March 1999, in which a sandy loam without or with anerobically digested sewage sludge (4.2 t dry matter (DM) ha⁻¹) or household compost (17 t DM ha⁻¹) was incubated under constant laboratory conditions at 10 °C, as well as in the field. The following properties were monitored: wet-stability of soil aggregates, clay dispersibility, hot-water extractable carbohydrates, resin-extractable P_i, inorganic N, biomass C and N, PLFA profiles, FDA hydrolysis activity, β-glucosidase activity and CO₂ evolution. In general, effects of waste amendment were positive, but moderate compared to the dynamics observed in unamended soil, and mainly occurred in the first several weeks after amendment. The temporal dynamics of inorganic N, FDA hydrolysis activity, biomass C and PLFA composition appeared to be faster under the fluctuating climatic conditions in the field. To evaluate accumulated effects of repeated waste applications, soil was also sampled from a field trial, in which the sewage sludge and household compost had been applied at the same rates as in the incubation study for three consecutive years. Sampling took place after the final harvest, i.e. 5 months after the final waste application. Compost amendment had increased potentially mineralizable N by a factor of 1.8, and sludge amendment had increased the amount of resin-extractable P_i by a factor of 1.6. However, there were no accumulated effects of waste amendment on the fraction of soil in wet-stable aggregates, or on the microbiological properties tested, which supported the observation from the incubation study that effects of organic wastes were transient.     

Improving soil structure by promoting fungal abundance with organic soil amendments

Building soil structure in agroecosystems is important because it governs soil functions such as air and water movement, soil C stabilization, nutrient availability, and root system development. This study examined, under laboratory conditions, effects of organic amendments comprised of differing proportions of labile and semi-labile C on microbial community structure and macroaggregate formation in three variously textured soils where native structure was destroyed. Three amendment treatments were imposed (in order of increasing C lability): vegetable compost, dairy manure, hairy vetch (Vicia villosa Roth). Formation of water stable macroaggregates and changes in microbial community structure were evaluated over 82 days. Regardless of soil type, formation of large macroaggregates (LMA, >2000 μm diameter) was highest in soils amended with vetch, followed by manure, non-amended control, and compost. Vetch and manure had greater microbially available C and caused an increase in fungal biomarkers in all soils. Regression analysis indicated that LMA formation was most strongly related to the relative abundance of the fungal fatty acid methyl ester (FAME) 18:2ω6c (r = 0.55, p < 0.001), fungal ergosterol (r = 0.58, p < 0.001), and microbial biomass (r = 0.57, p < 0.001). Non-metric multidimensional scaling (NMS) ordination of FAME profiles revealed that vetch and manure drove shifts toward fungal-dominated soil microbial communities and greater LMA formation in these soils. This study demonstrated that, due to their greater amounts of microbially available C, vetch or manure inputs can be used to promote fungal proliferation in order to maintain or improve soil structure.     

Applying an oxygen-based respiratory assay to assess soil microbial responses to substrate and N availability

Documented approaches for measuring soil microbial activities and their controlling factors under field conditions are needed to advance understanding of soil microbial processes for numerous applications. We manipulated field plots with carbon (C) and nitrogen (N) additions to test the capability of a respiratory assay to: (1) measure respiration of endogenous soil C in comparison to field-measured CO₂ fluxes; (2) determine substrate-induced respiratory (SIR) activities that are consistent with substrate availability in the field; and, (3) report N availability in the field based on assay responses with and without added N. The respiratory assay utilizes a microplate containing an oxygen-sensitive fluorescent ruthenium dye. Respiratory activities measured with this approach have previously been shown to occur within short (6–8 h) incubation periods using low substrate concentrations that minimize enrichment during the assay. Field treatments were conducted in a randomized full-factorial design with C substrate (casamino acids, glucose, or none) and inorganic N (±) as the treatment factors. With one exception, we found that respiration of endogenous soil C in the assay responded to the field treatments in a similar manner to CO₂ fluxes measured in the field. Patterns of SIR with low concentrations of added amino acid or carbohydrate substrate (200 μg C g⁻¹ soil) were consistent with field treatments. The ratio (N_ratio) of carbohydrate respiration with added N (25 μg N g⁻¹ soil) to the same without N in the assay was significantly (P < 0.05) decreased by field N amendment. The carbohydrate N_ratio exhibited a logarithmic relationship (r = 0.64, P < 0.05) with extractable inorganic soil nitrate and ammonium concentrations. These data significantly extend and support the capability of this oxygen-based respiratory assay to evaluate in situ soil activities and examine factors that limit these activities.     

Influence of carbon amendments on soil denitrifier abundance in soil microcosms

It is known that carbon (C) amendments increase microbial activity in anoxic soil microcosm studies, however the effects on abundance of total and denitrifier bacterial communities is uncertain. Quantitative PCR was used to target the 16S rRNA gene for the total bacterial community, the nosZ functional gene to reflect a broad denitrifier community, and functional genes from narrow denitrifier communities represented by Pseudomonas mandelii and related species (cnorB_P) and Bosea/Bradyrhizobium/Ensifer spp. (cnorB_B). Repacked soil cores were amended with varying amounts of glucose and red clover plant tissue (0–1000 mg C kg^? 1 of soil) and incubated for 96 h. Carbon amendment significantly increased respiration as measured by cumulative CO₂ emissions. Inputs of red clover or glucose at 1000 mg C kg^? 1 of soil caused increased abundance in the total bacteria under the conditions used. There was about an approximate 2-fold increase in the abundance of bacteria bearing the nosZ gene, but only in treatments receiving 500 or 1000 mg C kg^? 1 of soil of glucose or red clover, respectively. Additions of ≥ 500 mg C kg^? 1 soil of red clover and ≥ 250 mg C kg^? 1 of glucose increased cnorB_P-gene bearing denitrifiers. Changes in abundance of the targeted communities were related to C availability in soil, as indicated by soil respiration, regardless of C source. Applications of C amendments at rates that would occur in agricultural soils not only increase microbial activity, but can also induce changes in abundance of total bacterial and denitrifier communities in studies of anoxic soil microcosms.     

Impact of allelochemical exuded from allelopathic rice on soil microbial community

Allelopathic rice releases allelochemicals from its roots to paddy soils at early growth stages to inhibit neighboring weeds. However, little is currently known about the effects of allelochemicals on soil microbes. In this study, we show that allelopathic rice can have great impact on the population and community structure of soil microbes. Allelopathic rice PI312777 seedlings reduced the culturable microbial population and total PLFA when compared to non-allelopathic rice Liaojing-9. Similar results were observed when, instead of growing seedlings, soils were incubated with plant root exudates. This result demonstrates that the composition of root exudates from the rice varieties tested contributes to the soil microbial community. Further experiments showed that the microbial community was affected by the allelochemical 5,4′-dihydroxy-3′,5′-dimethoxy-7-O-β-glucopyranosylflavone exuded from allelopathic rice roots, through immediately hydrolyzing glucose with stimulation on soil bacteria and aglycone (5,7,4′-trihydroxy-3′,5′-dimethoxyflavone) with inhibition on soil fungi. This result indicates that the flavone O-glycoside can provide carbon and interact with soil microbes. PC analysis of the fatty acid data clearly separated the allelopathic PI312777 and the non-allelopathic Liaojing-9 variety (PC1 = 46.4%, PC2 = 20.3%). Similarly, the first principal component (PC1 = 37.4%) together with the second principal component (PC2 = 17.3%) explained 54.7% of the variation between the allelopathic and non-allelopathic root exudates. Furthermore, the canonical correlation between allelopathic root exudates and the flavone O-glycoside was statistically significant (Canonical R = 0.889, χ² (25) = 69.72, p = 0.0041). Although the data generated in this study were not completely consistent between culturable microbes and PLFA profile, it is a fact that variation in soil microbial populations and community structures could be distinguished by the allelopathic and non-allelopathic rice varieties tested. Our results suggest that individual components of rice root exudates, such as allelochemicals from allelopathic rice, can modify the soil microbial community.     

The effects of fresh and stabilized pruning wastes on the biomass,structure and activity of the soil microbial community in a semiarid climate

The incorporation of organic amendments from pruning waste into soil may help to mitigate soil degradation and to improve soil fertility in semiarid ecosystems. However, the effects of pruning wastes on the biomass, structure and activity of the soil microbial community are not fully known. In this study, we evaluate the response of the microbial community of a semiarid soil to fresh and composted vegetal wastes that were added as organic amendments at different doses (150 and 300 t ha⁻¹) five years ago. The effects on the soil microbial community were evaluated through a suite of different chemical, microbiological and biochemical indicators, including enzyme activities, community-level physiological profiles (CLPPs) and phospholipid fatty acid analysis (PLFA). Our results evidenced a long-term legacy of the added materials in terms of soil microbial biomass and enzyme activity. For instance, cellulase activity reached 633 μg and 283 μg glucose g⁻¹ h⁻¹ in the soils amended with fresh and composted waste, respectively. Similarly, bacterial biomass reached 116 nmol g⁻¹ in the soil treated with a high dose of fresh waste, while it reached just 66 nmol g⁻¹ in the soil amended with a high dose of composted waste. Organic amendments produced a long-term increase in microbiological activity and a change in the structure of the microbial community, which was largely dependent on the stabilization level of the pruning waste but not on the applied dose. Ultimately, the addition of fresh pruning waste was more effective than the application of composted waste for improving the microbiological soil quality in semiarid soils.     

Sewage sludge processing determines its impact on soil microbial community structure and function

Composting and thermal drying are amongst the most commonly used post-digestion processes for allowing sanitation and biological stabilization of sewage sludge from municipal treatment plants, and making it suitable as soil conditioner for use in agriculture. To assess the impact of sludge-derived materials on soil microbial properties, fresh (LAF), composted (LAC) and thermally dried (LAT) sludge fractions, each resulting from a different post-treatment process of a same aerobically digested sewage sludge, were added at 1% (w/w) application rate on two contrasting (a loam and a loamy sand) soils and incubated under laboratory conditions for 28 days. Soil respiration, microbial ATP content, hydrolytic activities and arginine ammonification rate were monitored throughout the incubation period. Results showed that soil biochemical variables, including the metabolic quotient (qCO₂), were markedly stimulated after sludge application, and the magnitude of this stimulatory effect was dependent on sludge type (precisely LAT > LAF > LAC), but not on soil type. This effect was related to the content of stable organic matter, which was lower in LAT. Genetic fingerprinting by PCR–DGGE revealed that compositional shifts of soil bacterial and, at greater extent, actinobacterial communities were responsive to the amendment with a differing sludge fraction. The observed time-dependent changes in the DGGE profiles of amended soils reflected the microbial turnover dependent on the sludge nutrient input, whereas no indications of adverse effects of sludge-borne contaminants were noted. Our findings indicate that composting rather thermal drying can represent a more appropriate post-digestion process to make sewage sludge suitable for use as soil conditioner in agriculture.     

Towards development of on-line soil moisture content sensor using a fibre-type NIR spectrophotometer

As the soil moisture content (w) is a deterministic factor for site-specific irrigation, seeding, transplanting and compaction detection, an on-line measurement system will bring these applications into practice. A fibre-type visible (VIS) and near-infrared (NIR) spectrophotometer, with a light reflectance measurement range of 306.5–1710.9 nm was used to measure w during field operation. The spectrophotometer optical unit was attached to the subsoiler chisel backside to perform the light reflectance measurement from the soil surface on the bottom of the trench opened by the proceeded chisel. The spectrophotometer–optical unit system was calibrated for w under stationary laboratory conditions on samples collected from an Arenic Cambisol field with different soil textures. A partial least square analysis was carried out in order to establish a statistical model relating soil light spectra with the gravimetric w of the 0.005–0.26 kg kg⁻¹ range. This model was validated with the full cross validation method resulting in a small root mean square error of cross validation (RMSECV) of 0.0175 kg kg⁻¹ and a high validation correlation of 0.978. Further validation of the model developed in the laboratory under stationary state showed also a small root mean square error of prediction (RMSEP) of 0.0165 kg kg⁻¹ and a prediction correlation of 0.982. When the NIR sensor-model system was used to determine w, based on on-line field measurement, a relatively larger RMSEP of 0.025 kg kg⁻¹ and lower prediction correlation of 0.75 were found. However, a reasonably similar spatial distribution of w was found between the on-line NIR measurement and oven drying methods. Therefore, the on-line NIR w sensor developed is recommended to provide valuable information towards the site-specific applications in soils.     

Molecular and physiological bacterial diversity of a semi-arid soil contaminated with different levels of formulated atrazine

A semi-arid soil treated with different concentrations of formulated atrazine in a laboratory experiment was studied over 45 days, by different biological and molecular parameters (bacterial enumeration (cfu), community level physiological profiles (CLPPs) measured by Biolog^® and denaturing gradient gel electrophoresis (DGGE)), to study the bacterial community diversity.Formulated atrazine was almost totally degraded at different concentrations after this incubation time. The number of colony forming units (cfu) for soils with 100 and 1000 mg kg⁻¹ atrazine was significantly (p ≤ 0.05) higher than for the control, 1 and 10 mg kg⁻¹ treatments. DGGE banding patterns showed that regardless of time elapsed, concentrations of 10, 100 and 1000 mg kg⁻¹ atrazine in soil, affected the bacterial community compared to control and 1 mg kg⁻¹.The Shannon diversity index (H′) based on CLPP data showed a significant (p ≤ 0.05) decrease at atrazine concentrations of 100 and 1000 mg kg⁻¹. The Shannon diversity indices for different guilds of source carbon and the parameters K and r (based on the kinetics of colour formation rather than on the degree of colour development) were related to guilds of carbon substrates and atrazine concentration at a sampling time. The parameter K was very sensitive to atrazine effects on microbial communities.These biological and molecular parameters can be used to monitor changes in soils treated with atrazine at different concentrations, even when the pesticide is degraded.     

Soil compaction and poultry litter effects on factors affecting nitrogen availability in a claypan soil

Soil compaction may affect N mineralization and the subsequent fate of N in agroecosystems. Laboratory incubation and field experiments were conducted to determine the effects of surface soil compaction on soil N mineralization in a claypan soil amended with poultry litter (i.e., Turkey excrement mixed with pine shavings as bedding). In a laboratory study, soil from the surface horizon of a Mexico silt loam soil was compacted to four bulk density levels (1.2, 1.4, 1.6 and 1.8 Mg m⁻³) with and without poultry litter and incubated at 25 °C for 42 days. A field trial planted to corn (Zea mays L.) was also conducted in 2002 on a Mexico silt loam claypan soil in North Central Missouri. Soil was amended with litter (0 and 19 Mg ha⁻¹) and left uncompacted or uniformly compacted. Soil compaction decreased soil inorganic N by a maximum of 1.8 times in the laboratory study; this effect was also observed at all depths of the field trial. Compacted soil with a litter amendment accumulated NH₄⁺-N up to 7.2 times higher than the noncompacted, litter-amended soil until Day 28 of the laboratory incubation and in the beginning of the growing season of the field study. Ammonium accumulation may have been due to decreased soil aeration under compacted conditions. Application of litter increased soil N mineralization throughout the growing season. In the laboratory study, soil inorganic N in unamended soil was negatively correlated with soil bulk density and the proportion of soil micropores, but was positively related with soil total porosity and the proportion of soil macropores. These results indicate that soil compaction, litter application and climate are interrelated in their influences on soil N mineralization in agroecosystems.     

Controlling factors of environmental flooding,soil pH and Diaprepes abbreviatus (L.) root weevil feeding in citrus: Larval survival and larval growth

The underlying influences of soil flooding, pH level and soil-inhabiting Diaprepes abbreviatus (L.) root weevil larval feeding in citrus were examined in two separate greenhouse studies, rootstock × flooding × Diaprepes-larvae (RFD) and liming × rootstock × flooding × Diaprepes-larvae (LRFD). Our objectives were to determine the combined effects of soil flooding and pH level on survival and growth of Diaprepes root weevil larvae to gain insights of insect-environmental relations for the weevil control. We used a Floridana sandy loam (pH 4.8) from a citrus grove infested by Diaprepes root weevil in center Florida. The RFD experiment consisted of two citrus rootstocks (Swingle and Smooth Flat Seville), three flooding durations (0, 20, and 40 days) and two larval infestation rates (0 and 5 larvae) for 40-day feeding. The LRFD experiment consisted of two citrus rootstocks (Swingle and Carrizo), three pH levels (non-limed control, and target pH 6 and 7), two flooding durations (0 and 40 days), and two larval rates (0 and 5 larvae) for 56-day feeding. Dolomite (54% CaCO₃ and 46% MgCO₃) was used for soil liming in the LRFD. Treatments were arranged with 15 replicates in a completely randomized design. In the RFD, flooded soil pH was 0.3 units higher than non-flooded soil and larval survival was the lowest in the longest flooded treatment (P < 0.05). In the LRFD, soil pH increased 0.5–0.9 units for the target pH 6, and 0.7–1.1 units for the target pH 7. The effects of rootstock, liming and flooding treatments and their interactions were significant on soil pH and larval survival (P < 0.05). Larval survival decreased from 80% to 60% with increasing soil pH from 4.8 to 5.7. Total larval weight per seedling decreased significantly from 0.060 g to 0.012 g when the soil pH increased from 5.1 to 5.7. Flooding reduced larval survival and growth, and increasing acidic soil pH by 1 unit would be an option for controlling soil acidity and for promoting integrated management of Diaprepes root weevil in citrus.     

Relationships of soil properties with Mn and Zn distribution in acidic soils and their uptake by a barley crop

The extractability and solid-phase fractionation of manganese (Mn) and zinc (Zn) in acid-to-neutral agricultural soils from Central Spain was evaluated by sampling and analysing twenty-nine representative soils and by greenhouse cropping eleven of them with spring barley (Hordeum vulgare, L.). All soil samples were extracted with three chemical extractants commonly used for soil fertility evaluation (0.43 M HOAc, DTPA and Mehlich-3). The soil samples were also operationally determined in six steps with the following extractants: 1 M Mg(NO₃)₂ extractable (WSEX, water soluble plus exchangeable), 0.7 M NaOCl extractable (OC, organically complexed), 0.1 M NH₂OH·HCl extractable (MnOX, Mn-oxide), 0.2 M (NH₄)₂C₂O₄ + 0.2 M H₂C₂O₄ extractable (AFeOX, amorphous Fe-oxide), 0.2 M (NH₄)₂C₂O₄ + 0.2 M H₂C₂O₄ + 0.1 M ascorbic acid extractable (CFeOX, crystalline Fe-oxide), and HCl, HNO₃, and HF in mixture (RES, residual). Soil-extractable amounts for the three single extractants were highly correlated with each other for both metals. Distributions among metal fractions showed that Mn was mainly found in the MnOX fraction (30.9%, ranging from 13.0 to 51.2%), whereas Zn was predominantly found in the RES fraction (44.3%, ranging from 26.4 to 56.8%). The proportion of Mn fractions extracted from the soils was in the order as follows: CFeOX ≤ WSEX = OC ≤ AFeOX = RES < MnOX, whereas Zn was in the order: WSEX ≤ OC ≤ AFeOX < MnOX < CFeOX < RES. The soil properties that correlated best with the distribution of Mn and Zn forms in these soils were soil organic matter and pH. The “availability factor” values [AF = (WSEX + OC) 100 / total metal], were higher for Mn than for Zn in these soils. Plant metal concentrations (Y) and soil-extractable and sequential extracted fractions showed few significant correlations. However, it was possible to significantly predict the phytoavailability of Mn and Zn for barley using a series of empirical equations involving extractable metals, solid-phase fractions and soil properties as components. The R² values of the best-fit regression models ranging from 0.50 [Y-Zn = 19.3 + 6.32 (WSEX + OC)-Zn] to 0.92 [Y-Zn = 57.3 + 0.23 P − 8.56 pH + 20.6 DTPA-Zn].     

Land use influences soil fungal community composition across central Victoria,south-eastern Australia

Current theory expects that fungi, on the one hand, are spatially ubiquitous but, on the other, are more susceptible than bacteria to disturbance such as land use change due to dispersal limitations. This study examined the relative importance of location and land use effects in determining soil fungal community composition in south-eastern Australia. We use terminal restriction fragment length polymorphism (T-RFLP; primer pair ITS1-F–ITS4) and multivariate statistical methods (NMDS ordinations, ANOSIM tests) to compare relative similarities of soil fungal communities from nine sites encompassing three locations (ca 50–200 km apart) and four land uses (native eucalypt forest, Pinus radiata plantation, Eucalyptus globulus plantation, and unimproved pasture). Location effects were generally weak (e.g. ANOSIM test statistic R ≤ 0.49) and were, in part, attributed to minor differences in soil texture. By contrast, we found clear and consistent evidence of land use effects on soil fungal community composition (R ≤ 0.95). That is, soils from sites of the same land use grouped together in NMDS ordinations of fungal composition despite geographic separations of up to ca 175 km (native eucalypt forests) and 215 km (P. radiata plantations). In addition, different land uses from the same location were clearly separate in NMDS ordinations, despite, in one case, being just 180 m apart and having similar land use histories (i.e. P. radiata versus E. globulus plantation both established on pasture in the previous decade). Given negligible management of all sites beyond the early establishment phase, we attribute much of the land use effects to changes in dominant plant species based on consistent evidence elsewhere of strong specificity in pine and eucalypt mycorrhizal associations. In addition, weak to moderate correlations between soil fungal community composition and soil chemical variables (e.g. Spearman rank correlation coefficients for individual variables of 0.08–0.32), indicated a minor contributing role of vegetation-mediated changes in litter and soil chemistry. Our data provide evidence of considerable plasticity in soil fungal community composition over time spans as short as 6–11 years. This suggests that – at least within geographic zones characterised by more-or-less contiguous forest cover – soil fungal community composition depends most on availability of suitable habitat because dispersal propagules are readily available for colonisation after land use change.     

Relationships between soil pH and microbial properties in a UK arable soil

Effects of changing pH along a natural continuous gradient of a UK silty-loam soil were investigated. The site was a 200 m soil transect of the Hoosfield acid strip (Rothamsted Research, UK) which has grown continuous barley for more than 100 years. This experiment provides a remarkably uniform soil pH gradient, ranging from about pH 8.3 to 3.7. Soil total and organic C and the ratio: (soil organic C)/(soil total N) decreased due to decreasing plant C inputs as the soil pH declined. As expected, the CaCO₃ concentration was greatest at very high pH values (pH > 7.5). In contrast, extractable Al concentrations increased linearly (R² = 0.94, p < 0.001) from below about pH 5.4, while extractable Mn concentrations were largest at pH 4.4 and decreased at lower pHs. Biomass C and biomass ninhydrin-N were greatest above pH 7. There were statistically significant relationships between soil pH and biomass C (R² = 0.80, p < 0.001), biomass ninhydrin-N (R² = 0.90, p < 0.001), organic C (R² = 0.83, p < 0.001) and total N (R² = 0.83, p < 0.001), confirming the importance of soil organic matter and pH in stimulating microbial biomass growth. Soil CO₂ evolution increased as pH increased (R² = 0.97, p < 0.001). In contrast, the respiratory quotient (qCO₂) had the greatest values at either end of the pH range. This is almost certainly a response to stress caused by the low p. At the highest pH, both abiotic (from CaCO₃) and biotic Co₂ will be involved so the effects of high pH on biomass activity are confounded. Microbial biomass and microbial activity tended to stabilise at pH values between about 5 and 7 because the differences in organic C, total N and Al concentrations within this pH range were small. This work has established clear relationships between microbial biomass and microbial activity over an extremely wide soil pH range and within a single soil type. In contrast, most other studies have used soils of both different pH and soil type to make similar comparisons. In the latter case, the effects of soil pH on microbial properties are confounded with effects of different soil types, vegetation cover and local climatic conditions.     

Sclerotium rolfsii dynamics in soil as affected by crop sequences

Crop rotation has been used for the management of soilborne diseases for centuries, but has not often been planned based on scientific knowledge. Our objective was to generate information on Sclerotium rolfsii dynamics under different crop or intercrop activities, and design and test a research approach where simple experiments and the use of models are combined to explore crop sequences that minimize Southern blight incidence.The effect of seventeen green manure (GM) amendments on sclerotia dynamics was analyzed in greenhouse and field plot experiments during two years. The relative densities of viable sclerotia 90 days after winter GM (WGM) incorporation were generally lower than after summer GM (SGM) incorporation, with average recovery values of 60% and 61% for WGM in the field, 66% and 43% for WGM in the greenhouse, and 162% to 91% for SGM in the greenhouse, in 2009 and 2010, respectively. Sclerotia survival on day d after GM amendment was described by the model S_f = S_i × exp(−b × d), relating initial (S_i) and final (S_f) sclerotia densities. Relative decay rates of the sclerotia (b) in SGM amended soil were largest for alfalfa (0.0077 ± 0.0031 day⁻¹) and sudangrass (0.0072 ± 0.0030 day⁻¹). In WGM amended soil, the largest b values were for oat (0.0096 ± 0.0024 day⁻¹), wheat (0.0090 ± 0.0024 day⁻¹) and alfalfa (0.0087 ± 0.0023 day⁻¹).The effect of three cropping sequences (sweet pepper–fallow, sweet pepper–black oat and sweet pepper–onion) on sclerotia dynamics was analyzed in microplot experiments, and the data were used to calibrate the model P_f = P_i/(α + βP_i), relating initial (P_i) and final (P_f) sclerotia densities. Median values for the relative rate of population increase at low P_i (1/α, dimension less) and the asymptote (1/β, number of viable sclerotia in 100 g of dry soil) were 8.22 and 4.17 for black oat (BO), 1.13 and 8.64 for onion (O), and 6.26 and 17.93 for sweet pepper (SwP).By concatenating the two models, sclerotia population dynamics under several crop sequences were simulated. At steady state, the sequence SwP–O–Fallow–BO resulted in the lowest long-term sclerotia density (7.09 sclerotia/100 g soil), and SwP–Fallow in the highest (17.89 sclerotia/100 g soil). The developed methodology facilitates the selection of a limited number of rotation options to be tested in farmers’ fields.     

Comparing measurements methods of carbon dioxide fluxes in a soil sequence under land use and cover change in North Eastern Spain

Carbon dioxide measurements from soil surface may indicate the potential for soil respiration and carbon consumption according to microbial biomass and root activity. These processes may be influenced by land use and cover change, and abandonment especially in the upper soil organic layer. Seven environments from cultivation to late abandonment, with the same soil type classified as Lithic Xerorthent, were tested to ascertain the respiration capacity according to the current use and cover, and to establish the ability to preserve and eventually increase the organic matter pools after abandonment. Given the importance of carbon dioxide measurements at soil surface, a comparison between the classic soda lime method (SL) and a rapid method based on infrared sensor analyzer (IR) was performed from autumn 2008 to autumn 2009 in the field. The field measurements of CO₂ proved significant correlations between the values from the two techniques under the same natural conditions and along the period of observation. However, the values of CO₂ measured by the soda lime method were always higher than those obtained by the infrared analyzer. This pattern was attributed to the difference in time of measurement, larger in the former method, and type of measurement technique. Despite that the trend of measured CO₂ values was rather similar along the year. On average, the highest values of CO₂ emission in the field were recorded in the warmest periods of the year and with soil surface moisture not lower than 3% independently on the method used. High soil surface temperature with soil moisture below 3% decreased drastically the CO₂ production from the dry soil. The cultivated environments and soil under forests have resulted higher CO₂ producers than abandoned soils depending on the age of abandonment, climatic conditions, and within abandonment perturbations. Those abandoned soils preserved by perturbations like wildfire showed a higher potential for accumulating organic carbon, as indicated by the lowest emission of CO₂ with respect to SOC content, during the period of observation. Results demonstrated the reliability of the methods used to evaluate the soil carbon dioxide production capacity and allowed to classify through environments with increasing potential for carbon sequestration. The classification was rather similar by using both methods indicating a higher susceptibility to carbon loss in the following order: soil under Vines (V) > under Olives (O) > under Pine trees (PI) > under Cork Trees (S) > under Pasture (PR) > under Cistus scrub (MC) > under Erica scrub (MB) by using the SL method and V > O > PI > S > MC > MB > PR by using the IR method. Indications about the need of management of abandoned areas were also considered in order to recover the landscape heterogeneity.     

Chemical and microbiological soil quality indicators and their potential to differentiate fertilization regimes in temperate agroecosystems

The study examined the interrelationships between chemical and microbiological quality indicators of soil and their ability to differentiate plots under contrasting fertilization regimes. The study was based on a long-term field experiment established on an Udic Ustocrepts in 1966. The soil was cropped with maize (Zea mays L.) and winter wheat (Triticum aestivum L.) and received no organic fertilization (control), wheat straw and maize stalk (crop residue) or cattle manure (manure) in combination with increasing levels of mineral N (N₀ and N₂₀₀). To asses whether seasonal fluctuations of measured properties might mask the effects of fertilization, soil samples were collected four times within a growing season. Manure amendment increased soil TOC and TN, while crop residue amendment had no significant effects. Mineral N increased TN only in April, while in September it decreased water extractable organic C (WEOC). Data of diffuse reflectance Fourier transform mid-infrared spectroscopy (DRIFTS) gave evidence for a higher relative contribution of the aliphatic peak at 2930 cm⁻¹ and a lower relative contribution of the aromatic peaks at 1620 cm⁻¹ and 1520 cm⁻¹ under manure. Manure amendment stimulated enzymatic activities, increased microbial biomass carbon (C_mic) and total phospholipids (PLFAs), and reduced the metabolic quotient (qCO₂). Patterns of PLFAs indicated that manure amendment increased the ratio of Gram-positive to Gram-negative bacteria. Crop residue amendment had no significant effects, while in September mineral N inhibited protease activity and reduced the Gram-positive to Gram-negative ratio. Microbial-related parameters fluctuated over time but their seasonality did not hamper the identification of fertilization-induced effects. The selected properties proved to be valuable indicators of long-term changes of soil quality and were strongly interrelated: changes in soil organic matter content and composition induced by manure amendment were accompanied by changes in abundance and function of the soil microbial community. Partial least square analysis obtained relating DRIFTS spectra to measured soil properties produced accurate predictive models for TOC and PLFAs, and moderately accurate models for C_mic, showing the potential of DRIFTS to be used as a rapid soil testing technique for soil quality monitoring.     

Quantifying potato pathogen DNA in soil

An improved method for the direct extraction of DNA from soil involving processing of a relatively large sample (60 g) was developed. The accurate and reliable detection and quantification of the soil-borne potato pathogens Colletotrichum coccodes (black dot), Rhizoctonia solani (black scurf) and Spongospora subterranea (powdery scab) following inoculation of soils was demonstrated. With this method, low levels of target DNA (30–40 pg DNA/g soil) could be detected in field soils. DNA recovery was proportionate across a wide range of inoculum (R² > 0.86) and there was no effect of soil type on the recovery of C. coccodes. The method was used to assess levels of naturally occurring pathogen DNA in 122 soil samples obtained from commercial potato fields.     

Effects of nonylphenols on soil microbial activity and water retention

The main aim of this study is to analyze the influence of 4-nonylphenol (NP) on soil water retention and biological activity. Two doses of 4-nonylphenol (25 and 50 mg kg⁻¹) were tested in a loam soil with and without peat amendment. In general, one week after the start of the experiment, the soil water content retained at −0.75 MPa of soil suction was 18% higher in the soil amended and its basal respiration (BR) was 15% higher than soil without peat. In contrast, the microbial activity indices (CM: coefficient of mineralization or BR:total organic carbon (TOC) ratio; Cmic:Corg: microbial biomass carbon (MBC):TOC ratio; qCO₂: metabolic quotient or BR:MBC ratio) were higher in the soil without peat, compared to the soil amended with peat. On the other hand, the addition of NP to soil was able to modify soil biological but not physical (water retention, desorption) properties. When soil was amended with peat, MBC was reduced one week after applying NP. In contrast, no effects of NP on MBC were observed in the soil without peat. BR was reduced by 16% one week after applying 50 mg kg⁻¹ of NP to soil with peat, and was increased by 46% one week after applying 25 mg kg⁻¹ of NP to soil without peat. The effects of NP on MBC and BR could be associated more with the adsorption of NP by soil organic matter, while changes in CM or Cmic:Corg ratio were more closely related to changes in soil water retention. The potential toxic effects of NP (high qCO₂ values) were only observed in the absence of peat amendments. Peat addition reduced NP toxic effects on microorganisms.