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.     

Enzyme activities and diuron persistence in soil amended with vermicompost derived from spent grape marc and treated with urea

Mineral fertilizers, organic amendments, and pesticides are inputs commonly used in conventional farming practices. The aim of this study was to evaluate the effects of single or combined applications of spent grape marc-vermicompost, urea, and/or diuron on soil-enzyme activities and the persistence of this herbicide in soils with low organic carbon content. The application of vermicompost enhanced dehydrogenase (DHase) enzyme activity over time but altered soil urease activity to a very limited extent. The reduction in diuron concentrations and the increase in DHase activity indicated that the soil microorganisms were capable of degrading the ureic herbicide. Treatment with vermicompost and diuron had a stimulatory effect on soil microbial activity. On the whole, the application of diuron and urea to the vermicompost-amended soil raised DHase and urease activity to maximum levels (>3 μg INTF g^?1 h^?1 and >47 μg NH₄⁺ g^?1 h^?1, respectively). The application of urea to the unamended and vermicompost-amended soil decreased diuron persistence from 18.8 and 33 d to 12.5 and 15 d, respectively. Our findings show that although vermicompost additions reduce diuron availability, this boosts diuron degradation when combined with urea. These additions, under different soil management conditions, minimize the bioavailability and persistence of diuron and consequently the risk of leaching and seepage into aquifers. Compared with untreated soils, these types of treated soils could also improve agricultural sustainability and the quality of the environment.     

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.     

Microbial utilization and mineralization of [14C]glucose added in six orders of concentration to soil

The substrate availability for microbial biomass (MB) in soil is crucial for microbial biomass activity. Due to the fast microbial decomposition and the permanent production of easily available substrates in the rooted top soil mainly by plants during photosynthesis, easily available substrates make a very important contribution to many soil processes including soil organic matter turnover, microbial growth and maintenance, aggregate stabilization, CO₂ efflux, etc. Naturally occurring concentrations of easily available substances are low, ranging from 0.1 μM in soils free of roots and plant residues to 80 mM in root cells. We investigated the effect of adding ¹⁴C-labelled glucose at concentrations spanning the 6 orders of magnitude naturally occurring concentrations on glucose uptake and mineralization by microbial biomass. A positive correlation between the amount of added glucose and its portion mineralized to CO₂ was observed: After 22 days, from 26% to 44% of the added 0.0009 to 257 μg glucose C g^?1 soil was mineralized. The dependence of glucose mineralization on its amount can be described with two functions. Up to 2.6 μg glucose C g^?1 soil (corresponds to 0.78% of initial microbial biomass C), glucose mineralization increased with the slope of 1.8% more mineralized glucose C per 1 μg C added, accompanied by an increasing incorporation of glucose C into MB. An increased spatial contact between micro-organisms and glucose molecules with increasing concentration may be responsible for this fast increase in mineralization rates (at glucose additions <2.6 μg C g^?1). At glucose additions higher than 2.6 μg C g^?1 soil, however, the increase of the glucose mineralization per 1 μg added glucose was much smaller as at additions below 2.6 μg C g^?1 soil and was accompanied by decreasing portions of glucose ¹⁴C incorporated into microbial biomass. This supports the hypothesis of decreasing efficiency of glucose utilization by MB in response to increased substrate availability in the range 2.6–257 μg C g^?1 (=0.78–78% of microbial biomass C). At low glucose amounts, it was mainly stored in a chloroform-labile microbial pool, but not readily mineralized to CO₂. The addition of 257 μg glucose C g^?1 soil (0.78 μg C glucose μg^?1 C micro-organisms) caused a lag phase in mineralization of 19 h, indicating that glucose mineralization was not limited by the substrate availability but by the amount of MB which is typical for 2nd order kinetics.     

Structural and functional diversity of bacterial community in soil treated with the herbicide napropamide estimated by the DGGE,CLPP and r/K-strategy approaches

Napropamide is one of the most commonly used herbicide in agricultural practice and can exhibit toxic effect to soil microorganisms. Therefore, the main objective of this study was to examine the genetic and functional diversity of microbial communities in soil treated with napropamide at field rate (FR, 2.25 mg kg⁻¹ of soil) and 10 times the FR (10 × FR, 22.5 mg kg⁻¹ of soil) by the denaturing gradient gel electrophoresis (DGGE) and the community level physiological profile (CLPP) methods. In addition, the r/K-strategy approach was used to evaluate the effect of this herbicide on the community structure of the culturable soil bacteria. DGGE patterns revealed that napropamide affected the structure of microbial community; however, the richness (S) and genetic diversity (H) values indicated that the FR dosage of napropamide experienced non-significant changes. In turn, the 10 × FR dosage of herbicide caused significant changes in the S and H values of dominant soil bacteria. DGGE profiles suggest an evolution of bacteria capable of degrading napropamide among indigenous microflora. Analysis of the CLPPs indicated that the catabolic activity of microbial community expressed as AWCD (average well-color development) was temporary positively affected after napropamide application and resulted in an increase of the substrate richness (S_R) as well as functional biodiversity (H) values. Analysis of the bacterial growth strategy revealed that napropamide affected the r- or K-type bacterial classes (ecotypes). In treated-soil samples K-strategists dominated the population, as indicated by the decreased ecophysiological (EP) index. Napropamide significantly affected the physiological state of culturable bacteria and caused a reduction in the rate of colony formation as well as a prolonged time of growth rate. Obtained results indicate that application of napropamide may poses a potential risk for soil functioning.     

Effects of trifluralin on soil carbon mineralization at different temperature conditions

Trifluralin is a herbicide intensively used in Turkish cotton agriculture. The recommended field dose [(RFD), 480 g active ingredient l^?1], 2 × RFD, 4 × RFD and 6 × RFD of this herbicide were added to virgin (previously no trifluralin applied) and cotton field soils (previously trifluralin applied) from a district (Yumurtal?k, Adana) under Mediterranean climate conditions in order to determine their effects on soil microbial activity as measured by carbon mineralization at the different temperature conditions (20 °C, 25 °C and 30 °C). C mineralization of all samples was determined by the CO₂ respiration method over 30 days (20 °C, 25 °C and 30 °C at constant moist). The ratio (%) of carbon mineralization at all doses of cotton field soil at 30 °C was significantly higher than all other field dose–temperature combinations (P < 0.001). Based on these results, trifluralin is used as a carbon source by soil microorganisms. The herbicide trifluralin was degraded completely in the cotton field but a small fraction remained in the virgin field. This result can be explained by the cotton field soil having both more active microbial populations and more microorganisms adapted to the trifluralin applications than the virgin field.     

Changes in soil microbial biomass and functional diversity with a nitrogen gradient in soil columns

Fertilization generates nutrient patches that may impact soil microbial activity. In this study, nitrogen patches were generated by adding ammonium sulfate or urea to soil columns (length 25 cm; internal diameter 7.2 cm). Changes in nitrogen transformation, soil microbial biomass, and microbial functional diversity with the nitrogen gradients were investigated to evaluate the response of microbial activity to chemical fertilizer nutrient patches. After applying of ammonium sulfate or urea, the added nitrogen migrated about 7 cm. Microbial biomass carbon (MBC) was lower in fertilized soil than in the control (CK) treatment at the same soil layers. MBC increased with soil depth while microbial biomass nitrogen (MBN) decreased. BIOLOG analysis indicated that the average well color development (AWCD) and functional diversity indices of the microbial communities were lower in the 1 cm and 2 cm soil layers after application of ammonium sulfate; the highest values were in the 3 cm soil layer. AWCD and Shannon indices from the 1 to 5 cm soil layers were higher than those from other soil layers under urea application. Both principal component analysis and carbon substrate utilization analysis showed significant separation of soil microbial communities among different soil layers under application of ammonium sulfate or urea. Microbial activity was substantially decreased when NH₄⁺-N concentration was higher than 528.5 mg kg⁻¹ (1–3 cm soil layer under ammonium sulfate application) or 536.8 mg kg⁻¹ (1 cm soil layer under urea application). These findings indicated that changes in soil microbial biomass and microbial functional diversity can occur with a nitrogen gradient. The extent of changes depends on the nitrogen concentration and the form of inorganic fertilizer.     

Differences in soil enzyme activities,microbial community structure and short-term nitrogen mineralisation resulting from farm management history and organic matter amendments

Changes in soil microbial biomass, enzyme activities, microbial community structure and nitrogen (N) dynamics resulting from organic matter amendments were determined in soils with different management histories to gain better understanding of the effects of long- and short-term management practices on soil microbial properties and key soil processes. Two soils that had been under either long-term organic or conventional management and that varied in microbial biomass and enzyme activity levels but had similar fertility levels were amended with organic material (dried lupin residue, Lupinus angustifolius L.) at amounts equivalent to 0, 4 and 8 t dry matter lupin ha^?1. Microbial biomass C and N, arginine deaminase activity, fluorescein diacetate hydrolysis, dehydrogenase enzyme activity and gross N mineralisation were measured in intervals over an 81-day period. The community structure of eubacteria and actinomycetes was examined using PCR–DGGE of 16S rDNA fragments. Results suggested that no direct relationships existed between microbial community structure, enzyme activities and N mineralisation. Microbial biomass and activity changed as a result of lupin amendment whereas the microbial community structure was more strongly influenced by farm management history. The addition of 4 t ha^?1 of lupin was sufficient to stimulate the microbial community in both soils, resulting in microbial biomass growth and increased enzyme activities and N mineralisation regardless of past management. Amendment with 8 t lupin ha^?1 did not result in an increase proportional to the extra amount added; levels of soil microbial properties were only 1.1–1.7 times higher than in the 4 t ha^?1 treatment. Microbial community structure differed significantly between the two soils, while no changes were detected in response to lupin amendment at either level during the short-term incubation. Correlation analyses for each treatment separately, however, revealed differences that were inconsistent with results obtained for soil biological properties suggesting that differences might exist in the structure or physiological properties of a microbial component that was not assessed in this study.     

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.     

Perchlorate biodegradation in contaminated soils and the deep unsaturated zone

In the United States, perchlorate has been officially recognized as an environmental contaminant. In Israel, widespread perchlorate contamination has been found in the 40-m deep vadose zone near an ammonium perchlorate manufacturing plant north of Tel Aviv, above the central part of Israel's coastal aquifer, with peak concentrations of 1200 mg kg_sediment^?1. In this study, we examined the perchlorate-reduction potential by native microbial communities along this deep contaminated vadose zone profile. We analyzed the effect of various concentrations of nitrate on perchlorate reduction and determined whether perchlorate concentrations in the profile are toxic to the native microbial population. All experiments were performed in soil slurries with sediments taken from the contaminated site. Perchlorate was reduced to chloride in three (1, 15 and 35 m) of the four examined sediment samples taken from different depths (1, 15, 20, and 35 m below surface). No activity was observed in the sediment sample from 20 m below land surface, suggesting low viable microbial communities and water content, and high perchlorate concentrations. In the presence of nitrate, the lag time for perchlorate degradation was inversely correlated to nitrate concentration. We found no perchlorate degradation as long as nitrate was present in the system, and perchlorate degradation initiated only after all the nitrate had been reduced. Nitrate-reduction rates were correlated to the initial concentrations of nitrate and no lag period was observed for nitrate reduction. Viable microbial populations were observed at both high concentrations (10,000 mg l^?1 and 20,000 mg l^?1) and with no addition of perchlorate, at levels of 2.35 × 10⁵, 4.01 × 10⁵, and 3.41 × 10³ CFU ml^?1, respectively; these results were well correlated to those found by PCR amplification analysis of chlorite dismutase. We suggest that the microbial community has adapted to the conditions of high perchlorate concentrations in the unsaturated zone over 30 years of exposure. When no external carbon source was added to the slurry of soil from land surface, all perchlorate was removed after 134 days of incubation. The average perchlorate-reduction rate using natural organic matter as a carbon source was 0.45 mg day^?1, while the average rate using acetate as an external carbon source was 7.2 mg day^?1.     

Mineralization dynamics and biochemical properties during initial decomposition of plant and animal residues in soil

The use of organic residues as soil amendments or fertilisers may represent a valuable recycling strategy. In this study, a series of laboratory assays was performed to study the effects of the application of organic residues on C and N mineralization and biochemical properties in a Mediterranean agricultural soil. Two crop residues (straw and cotton) and two animal by-products (meat bone meal and blood meal) were added at three rates (5, 10 and 20 mg g^?1 on dry weight basis) to a moist (40% water holding capacity) sandy soil and incubated at 20 °C for 28 days. Each residue underwent a different mineralization pattern depending on the nature and complexity of its chemical constituents. In all cases, the addition of the waste produced, after a short lag-phase, an exponential increase in the soil respiration rate, reflecting the growth of microbial biomass. The amount of total extra CO₂-C evolved after 28 days, expressed as % in respect to added C, differed significantly (P < 0.005) among application doses: 5 > 10 > 20 mg g^?1 and residue type: meat bone meal > blood meal > cotton cardings > wheat straw. Plant residues led to a rapid immobilisation of N that affected microbial size and activity and further mineralization. Animal by-products produced an immediate and remarkable increase of mineral N in the soil. However, the large amounts of NH₄⁺ released in the soil at high rates of animal residues led, in some cases, to temporary adverse effects on microbial biomass growth and nitrification. All residues produced a significant increase in soil microbial biomass size and activity, being the intensity of the response related to their chemical properties.     

Rapid estimation of microbial biomass in grassland soils by ultra-violet absorbance

A reliable and simple technique for estimating soil microbial biomass (SMB) is essential if the role of microbes in many soil processes is to be quantified. Conventional techniques are notoriously time-consuming and unreproducible. A technique was investigated that uses the UV absorbance at 280 nm of 0.5 M K₂SO₄ extracts of fumigated and unfumigated soils to estimate the concentrations of carbon, nitrogen and phosphorus in the SMB. The procedure is based on the fact that compounds released after chloroform fumigation from lysed microbial cells absorb in the near UV region. Using 29 UK permanent grassland soils, with a wide range of organic matter (2.9–8.0%) and clay contents (22–68%), it was demonstrated that the increase in UV absorbance at 280 nm after soil fumigation was strongly correlated with the SMB C (r=0.92), SMB N (r=0.90) and SMB P (r=0.89), as determined by conventional methods. The soils contained a wide range of SMB C (412–3412 μg g⁻¹ dry soil), N (57–346 μg g⁻¹ dry soil) and P (31–239 μg g⁻¹ dry soil) concentrations. It was thus confirmed that the UV absorbance technique described was a rapid, simple, precise and relatively inexpensive method of estimating soil microbial biomass.     

Microbial activity,community structure and potassium dynamics in rhizosphere soil of soybean plants treated with glyphosate

With the advent of glyphosate [N-(phosphonomethyl)glycine] tolerant crops, soils have now been receiving repeated applications of the herbicide for over 10 years in the Midwestern USA. There is evidence that long-term use of glyphosate can cause micronutrient deficiency but little is known about plant potassium (K) uptake interactions with glyphosate. The repeated use of glyphosate may create a selection pressure in soil microbial communities that could affect soil K dynamics and ultimately K availability for crops. Therefore, the objectives of this study were to characterize the effect of foliar glyphosate applied to GR (glyphosate resistant) soybeans on: (1) rhizosphere microbial community profiles using ester linked fatty acid methyl ester (EL-FAME) biomarkers, (2) exchangeable, non-exchangeable, and microbial K in the rhizosphere soil, and (3) concentrations of soybean leaf K. A greenhouse study was conducted in a 2 × 2 × 3 factorial design with two soil treatments (with or without long-term field applications of glyphosate), two plant treatments (presence and absence of soybean plants), and three rates of glyphosate treatments (0×, 1× at 0.87, and 2× at 1.74 kg ae ha^?1, the recommended field rate). After each glyphosate application, rhizosphere soils were sampled and analyzed for microbial community structure using ester linked fatty acid methyl ester biomarkers (EL-FAME), and exchangeable, plant tissue and microbial biomass K. Glyphosate application caused a significant decrease in the total microbial biomass in soybean rhizosphere soil that had no previous exposure to glyphosate, at 7 days after glyphosate application. However, no significant changes were observed in the overall microbial community structure. In conclusion, the glyphosate application lowered the total microbial biomass in the GR soybean rhizosphere soil that had no previous exposure to glyphosate, at 7 days after glyphosate application; caused no changes in the microbial community structure; and did not reduce the plant available K (soil exchangeable or plant tissue K).     

Evaluation of an optimal extraction method for measuring d-ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) in agricultural soils and its association with soil microbial CO2 assimilation

Assimilating atmospheric carbon (C) into terrestrial ecosystems is recognized as a primary measure to mitigate global warming. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is the dominant enzyme by which terrestrial autotrophic bacteria and plants fix CO₂. To investigate the possibility of using RubisCO activity as an indicator of microbial CO₂ fixation potential, a valid and efficient method for extracting soil proteins is needed. We examined three methods commonly used for total soil protein extraction. A simple sonication method for extracting soil protein was more efficient than bead beating or freeze–thaw methods. Total soil protein, RubisCO activity, and microbial fixation of CO₂ in different agricultural soils were quantified in an incubation experiment using ¹⁴C-CO₂ as a tracer. The soil samples showed significant differences in protein content and RubisCO activity, defined as nmol CO₂ fixed g⁻¹ soil min⁻¹. RubisCO activities ranged from 10.68 to 68.07 nmol CO₂ kg⁻¹ soil min⁻¹, which were closely related to the abundance of cbbL genes (r = 0.900, P = 0.0140) and the rates of microbial CO₂ assimilation (r = 0.949, P = 0.0038). This suggests that RubisCO activity can be used as an indicator of soil microbial assimilation of atmospheric CO₂.     

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.     

Changes of microbial properties in (near-) rhizosphere soils after phytoextraction by Sedum alfredii H: A rhizobox approach with an artificial Cd-contaminated soil

The ultimate goal of soil remediation is to restore soil health. Soil microbial parameters are considered to be effective indicators of soil health. The aim of this study was to determine the effects of phytoextraction on microbial properties through the measurement of soil microbial biomass carbon, soil basal respiration and enzyme activities. For this purpose, a pre-stratified rhizobox experiment was conducted with the Cd hyperaccumulator Sedum alfredii H. for phytoextraction Cd from an artificial contaminated soil (15.81 mg kg⁻¹) under greenhouse conditions. The plant and soil samples were collected after growing the plant for three and six months with three replications. The results indicated that the ecotype of S. alfredii H. originating from an ancient silver mining site was a Cd-hyperaccumulator as it showed high tolerance to Cd stress, the shoot Cd concentration were as high as 922.6 mg kg⁻¹ and 581.9 mg kg⁻¹ at the two samplings, and it also showed high BF (58.4 and 36.8 after 3 and 6 months growth), and TF (5.8 and 5.1 after 3 and 6 months growth). The amounts of Cd accumulated in the shoots of S. alfredii reached to an average of 1206 μg plant⁻¹ after 6 months growth. Basal respiration, invertase and acid phosphatase activities of the rhizosphere soil separated by the shaking method were significantly higher (P < 0.01) than that of the near-rhizosphere soil and the unplanted soil after 3 months growth, so were microbial biomass carbon, urease, invertase and acid phosphatase activities of the rhizosphere soil after 6 months growth. Acid phosphatase activity of the 0–2 mm sub-layer rhizosphere soil collected by the pre-stratified method after 3 months growth was significantly higher (P < 0.05) than that of other sub-layer rhizosphere soils and bulk soil, and so were microbial biomass carbon, basal respiration, urease, invertase and acid phosphatase activities of the 0–2 mm sub-layer rhizosphere soil after 6 months growth. It was concluded that phytoextraction by S. alfredii could improve soil microbial properties, especially in rhizosphere, and this plant poses a great potential for the remediation of Cd contaminated soil.     

Impact of bovine urine deposition on soil microbial activity,biomass, and community structure

Nitrogen (N) from urine excreted by grazing animals can be transformed into N compounds that have detrimental effects on the environment. These include nitrate, which can cause eutrophication of waterways, and nitrous oxide, which is a greenhouse gas. Soil microbes mediate all of these N transformations, but the impact of urine on microbes and how initial soil conditions and urine chemical composition alter their responses to urine are not well understood. This study aimed to determine how soil inorganic N pools, nitrous oxide fluxes, soil microbial activity, biomass, and the community structure of bacteria containing amoA (nitrifiers), nirK, and nirS (denitrifiers) genes responded to the addition of urine over time. Bovine urine containing either a high (15.0 g K⁺ l^?1) or low salt content (10.4 g K⁺ l^?1) was added to soil cores at either low or high moisture content (hereafter termed dry and wet soil respectively; 35% or 70% water-filled pore space after the addition of urine). Changes in soil conditions, inorganic N pools, nitrous oxide fluxes, and the soil microbial community were then measured 1, 3, 8, 15, 29 and 44 days after urine addition. Urine addition increased soil ammonium concentrations by up to 2 mg g d.w.^?1, soil pH by up to 2.7 units, and electrical conductivity (EC) by 1.0 and 1.6 dS m^?1 in the low and high salt urine treatments respectively. In response, nitrate accumulation and nitrous oxide fluxes were lower in dry compared to wet urine-amended soils and slightly lower in high compared to low salt urine-amended soils. Nitrite concentrations were elevated (>3 μg g d.w.^?1) for at least 15 days after urine addition in wet urine-amended soils, but were only this high in the dry urine-amended soils for 1 day after the addition of urine. Microbial biomass was reduced by up to half in the wet urine-amended soils, but was largely unaffected in the dry urine-amended soils. Urine addition affected the community structure of ammonia-oxidising and nitrite-reducing bacteria; this response was also stronger and more persistent in wet than in dry urine-amended soils. Overall, the changes in soil conditions caused by the addition of urine interacted to influence microbial responses, indicating that the effect of urine on soil microbes is likely to be context-dependent.     

Effects of vegetation on soil microbial C,N, and P dynamics in a tropical forest and savanna of Central Africa

The forest–savanna transition zone is widely distributed on nutrient-poor oxisols in Central Africa. To reveal and compare the nutrient cycle in relation to soil microbes for forest and savanna vegetation in this area, we evaluated seasonal fluctuations in microbial biomass carbon (MBC), nitrogen (MBN), and phosphorus (MBP) for 13 months as well as soil moisture, temperature, soil pH levels, and nutrients for both vegetation types in eastern Cameroon. Soil pH was significantly lower in forest (4.3) than in savanna (5.6), and soil N availability was greater in forest (87.1 mg N kg⁻¹ soil) than in savanna (32.9 mg N kg⁻¹ soil). We found a significant positive correlation between soil moisture and MBP in forest, indicating the importance of organic P mineralization for MBP, whereas in savanna, we found a significant positive correlation between soil N availability and MBP, indicating N limitation for MBP. These results suggest that for soil microbes, forest is an N-saturated and P-limited ecosystem, whereas savanna is an N-limited ecosystem. Additionally, we observed a significantly lower MBN and larger MB C:N ratio in forest (50.7 mg N kg⁻¹ soil and 8.6, respectively) than in savanna (60.0 mg N kg⁻¹ soil and 6.5, respectively) during the experimental period, despite the rich soil N condition in forest. This may be due to the significantly lower soil pH in forest, which influences the different soil microbial communities (fungi-to-bacteria ratio) in forest versus savanna, and therefore, our results indicate that, in terms of microbial N dynamics, soil pH rather than soil substrate conditions controls the soil microbial communities in this area. Further studies should be focused on soil microbial community, such as PLFA, which was not evaluated in the present study.     

Decoupling of microbial glucose uptake and mineralization in soil

The rate of organic matter turnover in soil is a critical component of the terrestrial carbon cycle and is frequently estimated from measurements of respiration. For estimates to be reliable requires that isotopically labelled substrate uptake into the soil microbial biomass and its subsequent mineralization occurs almost simultaneously (i.e. no time delay). Here we investigated this paradigm using glucose added to an agricultural soil. Immediately after collection from the field, various concentrations of ¹⁴C-labeled glucose (1 μM to 10 mM) were added to soil and the depletion from the soil solution measured at 1–60 min after substrate addition. ¹⁴CO₂ production from the mineralization of glucose was simultaneously measured. The microbial uptake of glucose from soil solution was concentration-dependent and kinetic analysis suggests the operation of at least two distinct glucose transport systems of differing affinity. At glucose concentrations reflecting those naturally present in the soil solution (54±10 μM), the half-time (t_1/2) of exogenous glucose was extremely rapid at ca. 30 s. At higher glucose concentrations (100 μM to 10 mM), the t_1/2 values for the high-affinity carrier were altered little, but increasing proportions of glucose were taken up by the low affinity transport system. Glucose mineralization by the soil microbial community showed a significant delay after its uptake into the microbial biomass suggesting a decoupling of glucose uptake and subsequent respiration, possibly by dilution of glucose in labile metabolite pools. By fitting a double first order kinetic equation to the mineralization results we estimated the t_1/2 for the first rapid phase of respiration at natural soil solution glucose concentrations to be 6–8 min, but at least 87% of the added glucose was retained in the microbial biomass prior to mineralization. Our results suggest that in this soil the soil solution glucose pool turns over 100–1000 times each day, an order of magnitude faster than when determined from measurements of mineralization. These results imply that traditional isotopic based measurements of substrate turnover measured using CO₂ may vastly underestimate their rate of cycling in soil.     

Soil organic matter and water-stable aggregates under different tillage and residue conditions in a tropical dryland agroecosystem

Changes in the proportions of water-stable soil aggregates, organic C, total N and soil microbial biomass C and N, due to tillage reduction (conventional, minimum and zero tillage) and crop residue manipulation (retained or removed) conditions were studied in a tropical rice–barley dryland agroecosystem. The values of soil organic C and total N were the highest (11.1 and 1.33 g kg⁻¹ soil, respectively) in the minimum tillage and residue retained (MT+R) treatment and the lowest (7.8 and 0.87 g kg⁻¹, respectively) in conventional tillage and residue removed (CT−R) treatment. Tillage reduction from conventional to minimum and zero conditions along with residue retention (MT+R,ZT+R) increased the proportion of macroaggregates in soil (21–42% over control). The greatest increase was recorded in MT+R treatment and the smallest increase in conventional tillage and residue retained (CT+R) treatment. The lowest values of organic C and total N (7.0–8.9 and 0.82–0.88 g kg⁻¹ soil, respectively) in macro- and microaggregates were recorded in CT−R treatment. However, the highest values of organic C and total N (8.6–12.6 and 1.22–1.36 g kg⁻¹, respectively) were recorded in MT+R treatment. The per cent increase in the amount of organic C in macroaggregates was greater than in microaggregates. In all treatments, macroaggregates showed wider C/N ratio than in microaggregates. Soil microbial biomass C and N ranged from 235 to 427 and 23.9 to 49.7 mg kg⁻¹ in CT−R and MT+R treatments, respectively. Soil organic C, total N, and microbial biomass C and N were strongly correlated with soil macroaggregates. Residue retention in combination with tillage reduction (MT+R) resulted in the greatest increase in microbial biomass C and N (82–104% over control). These variables showed better correlations with macroaggregates than other soil parameters. Thus, it is suggested that the organic matter addition due to residue retention along with tillage reduction accelerates the formation of macroaggregates through an increase in the microbial biomass content in soil.