The effect of glyphosate on soil microbial activity,microbial community structure,and soil potassium

The herbicide, glyphosate [N-(phosphonomethyl) glycine] is extensively used worldwide. Long-term use of glyphosate can cause micronutrient deficiency but little is known about potassium (K) interactions with glyphosate. The repeated use of glyphosate may create a selection pressure in soil microbial communities that could affect the nutrient dynamics such as K. The objective of this study was to determine the effect of single or repeated glyphosate applications on microbial and K properties of soils. A 54 day incubation study (Exp I) had a 3 × 5 factorial design with 3 soils (silt loam: fine, illitic, mesic Aeric Epiaqualf) of similar physical and chemical characteristics, that varied in long-term glyphosate applications (no, low, and high glyphosate field treatments) and five glyphosate rates (0, 0.5×, 1×, 2×, and 3× recommended field rates applied once at time zero). A second 6 month incubation study (Exp II) had a 3 × 3 factorial design with three soils (as described above) and three rates of glyphosate (0, 1×, and 2× recommended field application rates applied monthly). For each study microbial properties [respiration; community structure measured by ester linked fatty acid methyl ester (EL-FAME) analysis and microbial biomass K] and K fractions (exchangeable and non-exchangeable) were measured periodically. For Exp I, glyphosate significantly increased microbial respiration that was closely related to glyphosate application rate, most notably in soils with a history of receiving glyphosate. For Exp II, there was no significant effect of repeated glyphosate application on soil microbial structure (EL-FAME) or biomass K. We conclude that glyphosate: (1) stimulates microbial respiration particularly on soils with a history of glyphosate application; (2) has no significant effect on functional diversity (EL-FAME) or microbial biomass K; and (3) does not reduce the exchangeable K (putatively available to plants) or affect non-exchangeable K. The respiration response in soils with a long-term glyphosate response would suggest there was a shift in the microbial community that could readily degrade glyphosate but this shift was not detected by EL-FAME.     

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.     

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.     

Arbuscular mycorrhizal fungi are directly and indirectly affected by glyphosate application

Glyphosate is a systemic non-selective herbicide, the most widely used in the world. Alongside with its use in agricultural and forestry systems, this herbicide is used in grasslands in late summer with the aim of promoting winter species with the consequent increase in stocking rate. However, its effects on non-target organisms, such as arbuscular mycorrhizal fungi (AMF), are unclear. Arbuscular mycorrhizal fungi (AMF) colonize the root of more than 80% of terrestrial plants, improving their growth and survival, and therefore playing a key role in ecosystem structure and function. The aim of this work was to investigate the possible pathways through which glyphosate application affects AMF spores viability and root colonization in grassland communities. Our hypothesis is that glyphosate application can damage AMF directly (through contact with spores and external hyphae) or indirectly through the changes it generates on host plants. The experiment had a factorial array with three factors: (1) plant species, at two levels (Paspalum dilatatum and Lotus tenuis), (2) doses of glyphosate, at three levels (0 l ha⁻¹, 0.8 l ha⁻¹ and 3 l ha ⁻¹), and (3) application site, at two levels: soil (direct pathway) and plant foliage (indirect pathway). Spore viability was reduced even under the lowest glyphosate rate, but only when it was applied on the soil. Total root colonization for both species was similarly decreased when glyphosate was applied to plant foliage or on soil, with no difference between 0.8 and 3 l ha⁻¹. The number of arbuscules was 20% lower when glyphosate was applied on plant foliage, than when it was applied on the soil. Our findings illustrate that glyphosate application negatively affects AMF functionality in grasslands, due to different causes depending on the herbicide application site. While, under field conditions, the occurrence of direct and/or indirect pathways will depend on the plant cover at the time of glyphosate application, the consequences of this practice on the plant community structure will vary with the mycorrhizal dependence of the species composition regardless of the pathway involved.     

Invertebrate soil macrofauna under different ground cover plants in the no-till system in the Cerrado

This work was aimed at evaluating the invertebrate macrofauna community in the soil, by means of its abundance and richness of groups under different plant covers in the no-till system. Evaluations were performed at the experimental field of Embrapa Agropecuária Oeste, in the municipal district of Dourados-MS, on a Typic Hapludox under conventional, no-till, and natural systems. Samplings were performed in December 2000, June 2001, January 2002, and June 2002. Five soil monoliths measuring 0.25 × 0.25 m width and 0.30 m depth were sampled along a transect. Turnip residues before a corn crop (turnip/corn) and soybean residues before wheat and turnip crops (soybean/wheat and soybean/turnip) provided positive effects on the density and diversity of the edaphic macrofauna community.     

Survival and persistence of genetically modified Sinorhizobium meliloti in soil

Studies were conducted to evaluate the survival and persistence of Sinorhizobium meliloti 104A14 and two acid phosphatase-negative mutants in Kirkland (fine, mixed, thermic Udertic Paleustolls) silt loam soils with various fertility levels, and to assess the impact of inoculation on nodule occupancy and soil microbial community structure in the inoculated alfalfa (Medicago sativa L.) rhizosphere. Recovery of the inoculated strains was 100% (in the order of 10⁸ cells g⁻¹ soil) immediately following inoculation to soils, but decreased from 10⁸ cells g⁻¹ soil to undetectable levels in a nutrient-poor soil within 32 days. In a nutrient-rich soil, approximately 2–3% (4.7–7.43×10⁶ cells g⁻¹ soil) of the mutants and 23% (5.84×10⁷ cells g⁻¹ soil) of the wild-type inocula persisted for more than 64 days. Survivability and persistence of the wild-type S. meliloti were significantly greater than that of the genetically modified acid phosphatase negative mutants in all the soils tested. The persistence and nodule occupancy of the introduced S. meliloti in sterile and non-sterile soils were also tested for two repeated alfalfa growth periods in the same plant growth units, with a 1 month interval in between and no additional inoculation for the second period. Nodule occupancy of the introduced S. meliloti in non-sterile soils ranged from 30 to 60% for the first period and 85 to 100% for the second period. Our results suggest that survival and persistence of S. meliloti was enhanced by alfalfa cultivation and increased soil fertility, but impaired by mutation of acid phosphatase genes regardless of phosphorus nutritional levels. Moreover, inoculation with genetically modified S. meliloti strain 104A14 promoted indigenous bacterial growth in soil (increased bacterial population from 1.4×10⁶ to 4.3×10⁶ cells g⁻¹ soil), but not the growth of fungi and yeast. However, inoculation of the wild-type S. meliloti or genetically modified mutants did not result in significant changes in microbial community structure as indicated by EP indices and ratios of r/K strategists.     

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.     

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.     

Responses of soil nematode community structure to different long-term fertilizer strategies in the soybean phase of a soybean–wheat–corn rotation

The impact of long-term application of fertilizers in soybean fields on soil nematode community structure was studied. The long-term application model of fertilizers lasted 13 years in a soybean–wheat–corn rotation, and included three treatments: no fertilizer (NF), chemical fertilizer (urea and ammonium phosphate, CF), and pig manure combined with chemical fertilizer (MCF). The soil nematode community structures and ecological indices were determined from soil samples taken at five soybean growth stages from May to October in the soybean phase of the rotation. Fertilizer application had significant effects on abundance of plant parasites, bacterivores and fungivores (P < 0.05), but had no significant effects on total nematodes and omnivores-predators. Abundance of plant parasites was higher in NF than in MCF and CF, and abundance of bacterivores was highest in MCF. Fertilizer application significantly affected Plant-parasitic Nematode Maturity Index (PPI) and Nematode Channel Ratio (NCR) ecological indices (P < 0.05). Shannon–Weaver Index (H′) and Species Richness (SR) indices were higher in MCF than in either NF or CF. The abundances of total nematode and plant parasites showed increasing trend with soybean growth in all three treatments. This is probably due to soil environment being more suitable for soil nematode survival with more food available for plant parasites as the soybean grows. Soybean growth stage significantly affected the H′, Free Living Nematode Maturity Index (MI) and PPI. Bacterivores significantly correlated with soil nutrient status suggesting that they could be used as a potential indicator of soil fertility.     

Edge effects and trampling in boreal urban forest fragments – impacts on the soil microbial community

Fragmentation of forest ecosystems increases the proportion of edge habitat and is accompanied by a change in plant species composition. The recreational use of urban forests leads to decreased vegetation cover and the formation of paths, and thus, to fragmentation at small scales. We studied the impacts of forest and path edge effects on the soil microbial community structure (by using the phospholipid fatty acid (PLFA) method) and microbial activity (measured as basal respiration) in 34 mesic boreal urban forest fragments in Finland. We sampled the humus layer 1) from the forest edge into the interior (0–80 m), and 2) at different distances from paths. Microbial community structure was only slightly affected by the forest edge but differences were found between distances of 0–10 m and over 50 m from the edge. These changes correlated with changes in soil pH. Although changes in the microbial community structure were not pronounced, microbial biomass and activity were 30–45% lower at the first 20 m into the forest fragments, due to a low moisture content of the humus near the edge. The decreased microbial activity detected at forest edges implies decreased litter decomposition rates, and thus, a change in ecosystem nutrient cycling. The microbial community structure differed between paths and surrounding areas and correlated with changes in soil pH. Paths also supported approximately 25–30% higher microbial biomass with a transition zone of at least 1 m from the path edge. Path associated disturbances (mainly alterations in vegetation and soil pH) were reflected in the soil microbial community structure up to 1.5 m from the paths.     

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 fate and toxicity of the flavonoids naringenin and formononetin in soil

The flavonoid class of plant secondary metabolites play a multifunctional role in below-ground plant–microbe interactions with their best known function as signals in the nitrogen fixing legume–rhizobia symbiosis. Flavonoids enter rhizosphere soil as a result of root exudation and senescence but little is known about their subsequent fate or impacts on microbial activity. Therefore, the present study examined the sorptive behaviour, biodegradation and impact on dehydrogenase activity (as determined by iodonitrotetrazolium chloride reduction) of the flavonoids naringenin and formononetin in soil. Organic carbon normalised partition coefficients, log K_oc, of 3.12 (formononetin) and 3.19 (naringenin) were estimated from sorption isotherms and, after comparison with literature log K_oc values for compounds whose soil behaviour is better characterised, the test flavonoids were deemed to be moderately sorbed. Naringenin (spiked at 50 μg g^?1) was biodegraded without a detectable lag phase with concentrations reduced to 0.13±0.01 μg g^?1 at the end of the 96 h time course. Biodegradation of formononetin proceeded after a lag phase of ～24 h with concentrations reduced to 4.5±1% of the sterile control after 72 h. Most probable number (MPN) analysis revealed that prior to the addition of flavonoids, the soil contained 5.4×10⁶ MPN g^?1 (naringenin) and 7.9×10⁵ MPN g^?1 (formononetin) catabolic microbes. Formononetin concentration had no significant (p>0.05) effect on soil dehydrogenase activity, whereas naringenin concentration had an overall but non-systematic impact (p=0.045). These results are discussed with reference to likely total and bioavailable concentrations of flavonoids experienced by microbes in the rhizosphere.     

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 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.     

Evaluating the potential of plant growth promoting cyanobacteria as inoculants for wheat

Diazotrophic heterocystous cyanobacteria are known to possess the ability to form associations with vascular/non-vascular plants and produce growth-promoting substances. Most of the work on cyanobacterial inoculants has been focused on rice and other crops have received little attention. Our investigation was directed towards evaluating the potential of three cyanobacterial isolates from the rhizosphere of wheat, with emphasis on their plant growth promoting activity in pot culture experiments. All treatments were taken up in sterile soil, under controlled conditions of National Phytotron Facility, IARI and in the Glasshouse, using unsterile soil. The treatments in which all the three-cyanobacterial isolates were applied along with 1/3 N + P + K gave statistically equivalent results as compared to application of with full dose of chemical fertilizers in terms of grain yields. Significant enhancement in microbial biomass carbon in the treatments was observed at mid-crop and harvest stage, over uninoculated controls. Field level evaluation of these strains and testing under different agro-climatic conditions will help to further evaluate their agronomic efficiency and utility in integrated nutrient management of wheat crop.     

Bacillus amyloliquefaciens BNM122, a potential microbial biocontrol agent applied on soybean seeds,causes a minor impact on rhizosphere and soil microbial communities

The increase in soybean productivity has contributed to a greater use of agrochemicals, which cause major problems, such as soil and water pollution and reduction of biodiversity, and have a negative impact on non-target species. The development of microbial biocontrol agents for soybean diseases can help to reduce pesticide abuse. Bacillus amyloliquefaciens BNM122 is a potential microbial biocontrol agent able to control the damping-off caused by Rhizoctonia solani when inoculated in soybean seeds, both in a plant growth chamber and in a greenhouse. In this study, we report the effect of soybean seed treatments with strain BNM122 or with two fungicides (thiram and carbendazim) on the structure and function of the bacterial community that colonizes the soybean rhizosphere. Also, soybean root nodulation by Bradyrhizobium japonicum, mycorrhization by arbuscular mycorrhizal fungi and plant growth were evaluated. We used the r- and K-strategist concept to evaluate the ecophysiological structure of the culturable bacterial community, community-level physiological profiles (CLPP) in Biolog? EcoPlates to study bacterial functionality, and the patterns of 16S RNA genes amplified by PCR and separated by denaturing gradient gel electrophoresis (PCR–DGGE) to assess the genetic structure of the bacterial community. Neither the ecophysiological structure nor the physiological profiles of the soybean rhizosphere bacterial community showed important changes after seed inoculation with strain BNM122. On the contrary, seed treatment with fungicides increased the proportions of r-strategists and altered the metabolic profiles of the rhizosphere culturable bacterial community. The genetic structure of the rhizosphere bacterial community did not show perceptible changes between treated and non-treated seeds. Regarding the bacterial and fungal symbioses, seed treatments did not affect soybean nodulation, whereas soybean mycorrhization significantly decreased (P < 0.05) in plants obtained from seeds treated with strain BNM122 or with the fungicides. However, a higher negative effect was observed in plants which seeds were treated with the fungicides. Plant growth was not affected by seed treatments.It can be concluded that soybean seed treatment with B. amyloliquefaciens BNM122 had a lesser effect on soil microbial community than that with the fungicides, and that these differences may be attributed to the less environmental persistence and toxic effects of the strain, which deserve further studies in order to develop commercial formulations.     

Soil microbial community responses to sulfadiazine-contaminated manure in different soil microhabitats

Veterinary antibiotics such as sulfadiazine (SDZ) are applied with manure to agricultural soil. Antimicrobial effects of SDZ on soil microbial community structures and functions were reported for homogenized bulk soils. In contrast, field soil is structured. The resulting microhabitats are often hot spots that account for most of the microbial activity and contain strains of different antibiotic sensitivity or resilience. We therefore hypothesize that effects of SDZ are different in diverse soil microhabitats. We combined the results of laboratory and field experiments that evaluated the fate of SDZ and the response of the microbial community in rhizosphere, earthworm burrow, and soil macroaggregate microhabitats. Microbial communities were characterized by phenotypic phospholipid fatty acid (PLFA) and genotypic 16S rRNA gene patterns (DGGE) and other methods. Data was evaluated by principle component analyses followed by two-way ANOVA with post-hoc tests. Extractable SDZ concentrations in rhizosphere soil were not clearly different and varied by a factor 0.7–1.2 from those in bulk soil. In contrast to bulk soil, the extractable SDZ content was two-fold larger in earthworm burrows, which are characterized by a more hydrophobic organic matter along the burrow surface. Also, extractable SDZ was larger by up to factor 2.6 in the macroaggregate surface soil. The rhizosphere effect clearly increased the microbial biomass. Nonetheless, in the 10 mg SDZ kg⁻¹ treatment, the biomass deceased by about 20% to the level of uncontaminated bulk soil. SDZ contamination lowered the total PLFA concentrations by 14% in the rhizosphere and 3% in bulk soil of the field experiment. Structural shifts represented by Pseudomonas DGGE data were larger in SDZ-contaminated earthworm burrows compared to bulk soils. In the laboratory experiment, a functional shift was indicated by a four-fold reduced acid phosphatase activity in SDZ-contaminated burrows compared to bulk soil. Structural and functional shifts after SDZ contamination were larger by a factor of 2.5 in the soil macroaggregate surface versus interior, but this relation reversed over the long-term under field conditions. Overall, the combined effects of soil microhabitat, microbial community composition, and exposure to SDZ influenced the microbial susceptibility towards antibiotics under laboratory and field conditions.     

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.     

Soil microbial biomass,crop yields,and bacterial community structure as affected by long-term fertilizer treatments under wheat-rice cropping

Soil microbial biomass carbon (SMBC) and nitrogen (SMBN), soil microbial community structure, and crop yields were studied in a long-term (1982–2004) fertilization experiment carried out in Suining, Sichuan province of PR China. Eight treatments included three chemical fertilizer (CF) treatments (N, NP, NPK), three CF + farmyard manure (M) treatments (NM, NPM, NPKM), M alone and no fertilizer (CK) as control. The results showed that the soil microbial biomass was higher in soil treated with CFM than in soil treated with CF alone, and that NPKM gave the highest rice and wheat yields. The SMBC and SMBN were higher after rice than those after wheat cropping. SMBC correlated closely with soil organic matter. Average yields of wheat and rice for 22 years were higher and more stable in the fertilized plots than in control plots. Bacterial community structure was analyzed by PCR-DGGE targeting eubacterial 16S rRNA genes. A higher diversity of the soil bacterial community was found in soil amended with CFM than in other fertilizer treatments. Some specific band emerged in the soil amended with M. The highest diversity of bacterial communities was found in the NPKM treated soil. The bacterial community structures differed in rice and wheat plots. Sequencing of PCR products separated in DGGE showed that some of the common and dominant bands were closely related to Aquicella lusitana and to Acidobacteria. This study demonstrated that mixed application of N, P, and K with additional M amendment increased soil microbial biomass, diversified the bacterial communities and maintained the crop production in the Calcareous Purplish Paddy soil.     

Arable weeds,cover crops,and tillage drive soil microbial community composition in organic cropping systems

Cover crops have traditionally been used to reduce soil erosion and build soil quality, but more recently cover crops are being used as an effective tool in organic weed management. Many studies have demonstrated microbial community response to individual cover crop species, but the effects of mixed species cover crop communities have received less attention. Moreover, the relationship between arable weeds and soil microbial communities is not well understood. The objective of this study was to determine the relative influence of cover crop diversity, early-season weed communities, and tillage on soil microbial community structure in an organic cropping system through the extraction of fatty acid methyl esters (FAMEs). A field experiment was conducted between 2009 and 2011 near Mead, NE where spring-sown mixtures of zero (control), two, and eight cover crop species were included in a sunflower–soybean–corn crop rotation. A mixture of four weed species was planted in all experimental units (excluding the no-cover control), and also included as an individual treatment. Cover crops and weeds were planted in late-March, then terminated in late-May using a field disk or sweep plow undercutter, and main crops were planted within one week of termination. Three (2009) or four (2010–11) soil cores were taken to a depth of 20 cm in all experimental units at 45, 32, and 25 days following cover crop termination in 2009, 2010, and 2011, respectively. Total FAMEs pooled across 2009 and 2010 were greatest in the two species mixture–undercutter treatment combination (140.8 ± 3.9 nmol g⁻¹) followed by the eight species mixture–undercutter treatment combination (132.4 ± 3.9 nmol g⁻¹). Abundance of five (2009 and 2010) and seventeen (2011) FAME biomarkers was reduced in the weedy treatment relative to both cover-cropped treatments and the no-cover control. In 2009 and 2010, termination with the undercutter reduced abundance of most actinomycete biomarkers while termination with the field disk reduced abundance of C18:1(cis11) and iC16:0. Canonical discriminant analysis of the microbial community successfully segregated most cover crop mixture by termination method treatment combinations in 2009 and 2010. Microbial communities were most strongly influenced by the presence and type of early-spring plant communities, as weeds exerted a strong negative influence on abundance of many key microbial biomarkers, including the AMF markers C16:1(cis11) and C18:1(cis11). Weeds may alter soil microbial community structure as a means of increasing competitive success in arable soils, but this relationship requires further investigation.