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).     

Effect of paclobutrazol on microbial biomass,respiration and cellulose decomposition in soil

Paclobutrazol is a plant growth regulator largely utilized in mango cultivation and usually applied directly to soil. The aim of this study was to examine the effect of paclobutrazol on soil microbial biomass, soil respiration and cellulose decomposition in Brazilian soils under laboratory conditions. Soil samples were collected from fields with and without a reported history of paclobutrazol application. A solution of paclobutrazol (8 mg of active ingredient kg^?1 of soil) was added to soils, which were then incubated at 28 °C for 30 days. Paclobutrazol decreased soil microbial biomass, soil respiration and cellulose decomposition in soil with and without a report of paclobutrazol application, while significant increase was observed in the respiratory quotient (qCO₂). Our results show that the soil microbiological attributes were negatively affected by paclobutrazol in short-term experiment.     

Effects of mercury on soil microbial communities in tropical soils of French Guyana

In gold mining regions, the risk of soil pollution by mercury is a major environmental hazard, especially in tropical areas where soil microflora plays a major part in soil functioning, major bio-geochemical cycles and carbon turn-over. The impact of mercury pollution on soil microflora should thus be carefully assessed in such environments while taking into consideration the specificities of tropical soils. The aim of this study was to compare the effects of mercury (0, 1 and 20 μg of inorganic mercury per gram of soil) on the functional diversity and genetic structure of microbial communities in a tropical soil. We investigated the effects of mercury on tropical soil microflora using soil microcosms spiked with mercury and incubated at 28 °C for 1 month. Microcosm flora, its biomass and its activity, as well as its functional and genetic structure, were followed by cultural methods, measures of respiration, ECOLOG plates, and DGGE (denaturing gel gradient electrophoresis), respectively. Fate of total and bioavailable mercury was estimated by CVAFS (cold vapor atomic fluorescence spectrometry). Results obtained for the microcosms enriched with only 1 μg g^?1 mercury were indistinguishable from controls. Conversely, in the presence of high mercury contents (20 μg g⁽¹), an immediate effect was measured on soil respiration, functional diversity (ECOLOG plates) and genetic structure (DGGE), although no significant effect was observed on plate counts or microbial biomass. In addition, whereas microbial activities (respiration and functional diversity) rapidly regained control values, a lasting effect of the high mercury concentration was observed on the genetic structure of the soil microbial community. These modifications took place during the first week of incubation when total mercury concentration was declining and bioavailable mercury was at its highest.This multiple approach study is one of the first attempts at investigating the effects of mercury on soil microbial communities in tropical soils. Our results demonstrate that in the tropical soil under study, mercury affects the soil microbial communities in a different manner than was previously reported in temperate soils. Furthermore, mercury toxicity on soil microbes may be modulated by typical tropical soil characteristics.     

Spatial variability of enzyme activities and microbial biomass in the upper layers of Quercus petraea forest soil

Extracellular lignocellulose-degrading enzymes are responsible for the transformation of organic matter in hardwood forest soils. The spatial variability on a 12 × 12 m plot and vertical distribution (0–8 cm) of the ligninolytic enzymes laccase and Mn-peroxidase, the polysaccharide-specific hydrolytic enzymes endoglucanase, endoxylanase, cellobiohydrolase, 1,4-β-glucosidase, 1,4-β-xylosidase and 1,4-β-N-acetylglucosaminidase and the phosphorus-mineralizing acid phosphatase were studied in a Quercus petraea forest soil profile. Activities of all tested enzymes exhibited high spatial variability in the L and H horizons. Acid phosphatase and 1,4-β-N-acetylglucosaminidase exhibited low variability in both horizons, while the variability of Mn-peroxidase activity in the L horizon, and endoxylanase and cellobiohydrolase activities in the H horizon were very high. The L horizon contained 4× more microbial biomass (based on PLFA) and 7× fungal biomass (based on ergosterol content) than the H horizon. The L horizon also contained relatively more fungi-specific and less actinomycete-specific PLFA. There were no significant correlations between enzyme activities and total microbial biomass. In the L horizon cellulose and hemicellulose-degrading enzymes correlated with each other and also with 1,4-β-N-acetylglucosaminidase and acid phosphatase activities. Laccase, Mn-peroxidase and acid phosphatase activities correlated in the H horizon. The soil profile showed a gradient of pH, organic carbon and humic compound content, microbial biomass and enzyme activities, all decreasing with soil depth. Ligninolytic enzymes showed preferential localization in the upper part of the H horizon. Differences in enzyme activities were accompanied by differences in the microbial community composition where the relative amount of fungal biomass decreased and actinomycete biomass increased with soil depth. The results also showed that the vertical gradients occur at a small scale: the upper and lower parts of the H horizon only 1 cm apart were significantly different with respect to seven out of nine activities, microbial biomass content and community composition.     

Phosphate additions have no effect on microbial biomass and activity in a northern hardwood forest

High rates of atmospheric nitrogen (N) deposition have raised questions about shifting patterns of nutrient limitation in northern hardwood forests. Of particular interest is the idea that increased supply of N may induce phosphorus (P) limitation of plant and microbial processes, especially in acid soils where P sorption by Al is high. In this study, we established field plots and plant-free laboratory mesocosms with P and Ca additions to test the hypotheses that 1) microbial biomass and activity are limited by P in the northern hardwood forest soils at the Hubbard Brook Experimental Forest in NH USA; 2) elevated Ca increases inherent P availability and therefore reduces any effects of added P and 3) P effects are more marked in the more carbon (C) rich Oie compared to the Oa horizon. Treatments included P addition (50 kg P ha⁻¹), Ca addition (850 kg Ca ha⁻¹) and Ca + P addition (850 kg Ca ha⁻¹ and 50 kg P ha⁻¹). The P treatments increased resin-available P levels and reduced phosphatase activity, but had no effect on microbial biomass C, microbial respiration, C metabolizing enzymes, potential net N mineralization and nitrification in the Oie or Oa horizon of either field plots or plant free mesocosms, in either the presence or absence of Ca. Total, prokaryote, and eukaryote PLFA were reduced by P addition, possibly due to reductions in mycorrhizal fungal biomass. These results suggest that increased N deposition and acidification have not created P limitation of microbial biomass and activity in these soils.     

Changing microbial substrate use in Arctic tundra soils through a freeze-thaw cycle

Recent research has established that microbial processes in the arctic continue even when soils are frozen, and that cold-season processes can be important in the overall annual carbon and nitrogen cycles. Despite the importance of wintertime soil microbial processes, our understanding of their controls remains extremely poor. We particularly have a poor understanding of how microbial substrate use patterns change as soils freeze: do microbes use the same substrates as during the growing season, only slower, or do they switch to using different substrates? We used a ¹⁴C isotope equilibration technique to partition respiration between the actively turning over microbial biomass and products pool and the plant detritus pool in a range of Arctic tundra soils. Microbes showed a step-function shift in their metabolism as soils cool from +2 to +0.5 °C, roughly doubling the contribution of recycling of microbial C to total soil respiration. There was no additional shift in substrate use as soils underwent bulk soil freezing. The above-0 °C substrate shift is important because tundra soils spend a long time at or just below 0 °C as they are freezing in the early winter. The change in substrate use represents a shift from processing N-poor detritus to N-rich microbial products, causing N available for either plant uptake or leaching to be greatest when soils are near 0 °C. This may explain the observed patterns of growing season N immobilization vs. cold-season mineralization that appear common in Arctic tundra ecosystems.     

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.     

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.     

Microbial mineralization of biochar and wheat straw mixture in soil: A short-term study

A short-term incubation study was carried out to investigate the effect of biochar addition to soil on CO₂ emissions, microbial biomass, soil soluble carbon (C) nitrogen (N) and nitrate–nitrogen (NO₃–N). Four soil treatments were investigated: soil only (control); soil + 5% biochar; soil + 0.5% wheat straw; soil + 5% biochar + 0.5% wheat straw. The biochar used was obtained from hardwood by pyrolysis at 500 °C. Periodic measurements of soil respiration, microbial biomass, soluble organic C, N and NO₃–N were performed throughout the experiment (84 days). Only 2.8% of the added biochar C was respired, whereas 56% of the added wheat straw C was decomposed. Total net CO₂ emitted by soil respiration suggested that wheat straw had no priming effect on biochar C decomposition. Moreover, wheat straw significantly increased microbial C and N and at the same time decreased soluble organic N. On the other hand, biochar did not influence microbial biomass nor soluble organic N. Thus it is possible to conclude that biochar was a very stable C source and could be an efficient, long-term strategy to sequester C in soils. Moreover, the addition of crop residues together with biochar could actively reduce the soil N leaching potential by means of N immobilization.     

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.     

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.     

Effect of warming on the temperature dependence of soil respiration rate in arctic,temperate and tropical soils

We examined the response of the temperature coefficient (Q₁₀) for soil respiration rate to changes in environmental temperature through a laboratory incubation experiment. Soil samples were collected from three climatic areas: arctic (Svalbard, Norway), temperate (Tsukuba, Japan) and tropical (Pasoh, Malaysia). The arctic and temperate soils were incubated at 8 °C (control), 12 °C (4 °C warming) and 16 °C (8 °C warming) for 17 days. The tropical soil was incubated at 16 °C (8 °C cooling), 24 °C (control) and 32 °C (8 °C warming). Before and after the incubation experiment, the temperature dependence of soil microbial respiration was measured using an open-airflow method with IRGA by changing the temperature in a water bath. The initial Q₁₀ before the incubation experiment was larger in the soils from higher latitudes: 3.4 in the arctic soil, 2.9 in the temperate soil, and 2.1 in the tropical soil. The response of the microbial respiration rate to change in temperature differed among the three soil types. The temperature dependence of respiration rate in the arctic soil did not change in response to warming by 4 and 8 °C with a Q₁₀ of about 3. On the other hand, the Q₁₀ in the temperate soil decreased with increasing incubation temperature: from 2.8 in soils incubated at 8 °C to 2.5 at 12 °C and 2.0 at 16 °C. In the tropical soil, the Q₁₀ was not changed even by the 8 °C warming with a value of 2.1, whereas the Q₁₀ was increased from 2.1 to 2.7 by the 8 °C cooling. These results suggest that the response of microbial respiration to climatic warming may differ between soils from different latitudes.     

Earthworm communities and soil properties in shaded coffee plantations with and without application of glyphosate

In central Veracruz, Mexico, many coffee plantations are managed using agrochemicals for weed control, with glyphosate-based herbicides (GBH) the most commonly used. To date, however, no studies in this region have characterized the soil biological and physicochemical properties in coffee plantations under such glyphosate application. In this study, earthworms were used as bioindicator organisms by measuring differences in the earthworm community in plots within shaded coffee plantations, with and without repeated applications of glyphosate. Differences in earthworm-induced soil processes, such as water infiltration rates, potential net carbon mineralization rates and soil physicochemical properties were also evaluated. Eight plots were selected in shaded coffee plantations; four had received regular applications of GBH over the preceding 22 years, while the other four had received no herbicides over the preceding 7 years. The earthworm species found in plots with no GBH treatment were Pontoscolex corethrurus (99%) and Amynthas corticis (1%), while A. corticis was absent in plots that had been treated with GBH. Significant differences (P < 0.01) in earthworm density (168 ± 16 and 353 ± 37 ind m⁻²) and biomass (22.7 ± 1.1 and 45.4 ± 6.9 g m⁻²) were observed in soils with and without GBH, respectively. No significant difference (P = 0.08) was observed in the water infiltration rate (2 × 10⁻⁴ ± 4 × 10⁻⁵ and 4 × 10⁻⁴ ± 1 × 10⁻⁴ cm s⁻¹ with and without GBH, respectively). Soil carbon flow was greater in plots with GBH (76 ± 7 μg dry soil⁻¹ d⁻¹) than in those without GBH (62 ± 1 μg dry soil⁻¹ d⁻¹, P < 0.005). Significant differences (P < 0.05) were found in pH and in the clay, silt and Ca content of the soil. Our findings indicated reduced species number, density and biomass of earthworms, and increased net carbon mineralization rate in plots with GBH. The plots managed with glyphosate presented a negative effect on the earthworm parameters measured, and we conclude that the earthworms therefore acted as indicators of perturbation. It is also possible that this effect could be due to factors unrelated to the glyphosate that were not considered in this study, such as chemical fertilization or legume litter spatial variability, among others.     

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.     

Glyphosate toxicity and the effects of long-term vegetation control on soil microbial communities

We assessed the direct and indirect effect of the herbicide glyphosate on soil microbial communities from ponderosa pine (Pinus ponderosa) plantations of varying site quality. Direct, toxic effects were tested using culture media and soil bioassays at glyphosate concentrations up to 100-fold greater than expected following a single field application. Indirect effects on microbial biomass, respiration, and metabolic diversity (Biolog and catabolic response profile) were compared seasonally after 9–13 years of vegetation control using repeated glyphosate applications in a replicated field study. Three pine plantations were selected to provide a range of soil characteristics associated with glyphosate binding (clay, Fe and Al oxide content) and site growing potential from the lowest to the highest in northern California. Glyphosate was toxic to bacteria and fungi from each plantation when grown in soil-free media. Culturable populations were reduced, as was the growth rate and metabolic diversity of surviving bacteria, by increasing concentrations of glyphosate. This toxicity was not expressed when glyphosate was added directly to soil, however. Microbial respiration was unchanged at expected field concentrations (5–50 μg g⁻¹), regardless of soil, and was stimulated by concentrations up to 100-fold greater. Increased microbial activity resulted from utilization of glyphosate as an available carbon substrate. Estimated N and P inputs from glyphosate were inconsequential to microbial activity. Long-term, repeated applications of glyphosate had minimal affect on seasonal microbial characteristics despite substantial changes in vegetation composition and growth. Instead, variation in microbial characteristics was a function of time of year and site quality. Community size, activity, and metabolic diversity generally were greatest in the spring and increased as site quality improved, regardless of herbicide treatment. Our findings suggest that artificial media assays are of limited relevance in predicting glyphosate toxicity to soil organisms and that field rate applications of glyphosate should have little or no affect on soil microbial communities in ponderosa pine plantations.     

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.     

The thermodynamic efficiency of soil microbial communities subject to long-term stress is lower than those under conventional input regimes

Isothermal microcalorimetry measures the thermal flows occurring in systems with very high precision and may be used to quantify carbon (C) assimilation and resource-use efficiencies in soils. We determined the thermodynamic efficiency of soil microbial communities located in soils which had received contrasting long-term management regimes (53 y) with respect to organic matter and nitrogen (N) inputs, viz. farmyard manure, sewage sludge, straw and calcium nitrate, calcium nitrate only, or ammonium sulphate. Two thermodynamic efficiency indices were considered: (i) total thermodynamic efficiency of soil microbial communities (η_eff), i.e. general heat production released following substrate addition, per unit heat energy input to the soil system, and (ii) a specific thermodynamic efficiency index of energy retained in the soil system (η_soil). The latter index provides quantitative data on how much C is assimilated and energy retained in the soil system. Further, we derived a ‘substrate-induced heat production’ (SIHP) index, which adjusts for size of the microbial biomass. Optimised concentrations of water or glucose plus water were added to the soil samples and resultant thermal signatures and C mineralisation were determined over a 48-h incubation period at 25 °C. The thermal signatures were further related to the microbial community profiles of the soils. The phenotypic structural and functional diversity profiles of the microbial communities in soils were assessed by phospholipid fatty acid and multi-substrate induced respiration methods at the start of the experiment, confirming significant differences between all five treatments in community composition and functional capabilities. Both the total and specific thermodynamic efficiency indices of the soil microbial communities exposed to long-term stress by heavy metal toxicity (sewage sludge) and low pH ((NH₄)₂SO₄) were significantly smaller in magnitude than those under the three conventional (i.e. Ca(NO₃)₂, Straw + Ca(NO₃)₂, farmyard manure) input regimes (P < 0.05). The SIHP index however, was highest in the treatments receiving long-term inorganic inputs, indicating more heat production per unit biomass, than that found in all three organic input regimes. These differences in efficiencies were reflected in both the phenotypic and functional profiles of the communities. These indices may provide quantification of C assimilation and resource-use efficiency under different land-use and management scenarios, and potentially allow evaluation of the role of soils in governing the terrestrial C balance by studying the fate and regulation of C in soil systems.     

Effects of atrazine on microbial activity in semiarid soil

The effect of an atrazine formulation on microbial biomass, microbial respiration, ATP content and dehydrogenase and urease activity in a semiarid soil and the influence of time on the response of soil microbial activity to the herbicide treatment were assessed. The atrazine formulation was added to soil as aqueous solutions of different concentrations of active ingredient to obtain a range of concentrations in the soil from 0.2 to 1000 mg kg⁻¹. Microcosms of soil with the different herbicide concentrations and untreated control soil were incubated for 6 h, 16 and 45 days. In general, an increase in the measured microbiological and biochemical parameters with atrazine concentration in soil was observed. The increase in microbial activity with atrazine pollution was noticeable after lengthy incubation.     

Turnover of low molecular weight dissolved organic C (DOC) and microbial C exhibit different temperature sensitivities in Arctic tundra soils

Polar ecosystems are currently experiencing some of the fastest rates of climate warming. An increase in soil temperature in High Arctic regions may stimulate soil permafrost melting and microbial activity, thereby accelerating losses of greenhouse gases. It is therefore important to understand the factors regulating the rates of C turnover in polar soils. Consequently, our aims were to: (1) assess the concentration of low molecular weight (MW) dissolved organic carbon (DOC) in soil, (2) to investigate the temperature-dependent turnover of specific low MW compounds, and (3) to analyse the influence of substrate concentration on C cycling. Microbial mineralisation of labile low MW DOC in two High Arctic tundra soils was investigated using soil solutions spiked with either ¹⁴C-labelled glucose or amino acids. Spiked solutions were added to the top- and sub-soil from two ecosystem types (lichen and Carex dominated tundra), maintained at three temperatures (4–20 °C), and their microbial mineralisation kinetics monitored. ¹⁴CO₂ evolution from the tundra soils in response to ¹⁴C-glucose and -amino acid addition could best be described by a double first order exponential kinetic equation with rate constants k₁ and k₂. Both forms of DOC had a short half-life (t_1/2) in the pool of microbial respiratory substrate (t_1/2 = 1.07 ± 0.10 h for glucose and 1.63 ± 0.14 h for amino acids; exponential coefficient k₁ = 0.93 ± 0.07 and 0.64 ± 0.06 h^?1 respectively) whilst the second phase of mineralisation, assumed to be C that had entered the microbial biomass, was much slower (average k₂ = 1.30 × 10^?3 ± 0.49 × 10^?4 h^?1). Temperature had little effect on the rate of mineralisation of ¹⁴C used directly as respiratory substrate. In contrast, the turnover rate of the ¹⁴C immobilized in the microbial biomass prior to mineralisation was temperature sensitive (k₂ values of 0.99 × 10^?3 h^?1 and 1.66 × 10^?3 h^?1 at 4 and 20 °C respectively). Concentration-dependent glucose and amino acid mineralisation kinetics of glucose and amino acids (0–10 mM) were best described using Michaelis–Menten kinetics; there was a low affinity for both C substrates by the microbial community (K_m = 4.07 ± 0.41 mM, V_max = 0.027 ± 0.005 mmol kg^?1 h^?1). In conclusion, our results suggest that in these C limiting environments the flux of labile, low MW DOC through the soil solution is extremely rapid and relatively insensitive to temperature. In contrast, the turnover of C incorporated into higher molecular weight microbial C pools appears to show greater temperature sensitivity.     

Differences in soil respiration between different tropical ecosystems

We examined the relationship between soil respiration rate and environmental determinants in three types of tropical forest ecosystem—primary forest, secondary forest, and an oil palm plantation in the Pasoh Forest Reserve on the Malaysian Peninsula. In August 2000, the soil respiration rate and environmental factors (soil temperature, soil water content, soil C and N contents, biomass of fine roots, and microbes) were measured at 12–16 points in research quadrats. Soil respiration rates were 831 ± 480, 1104 ± 995, 838 ± 143, 576 ± 374, and 966 ± 578 (mean ± S.D.) mg CO₂ m⁻² h⁻¹ in the primary forest canopy and gap site, secondary forest canopy and gap site, and oil palm plantation, respectively. Although the mean soil respiration rates in the three forest ecosystems did not differ significantly, differences were evident in the environmental factors affecting the soil respiration. The major causes of spatial variation in soil respiration were fine root biomass, soil water content, and soil C content in the primary and secondary forests and oil palm plantation, respectively.