Showing papers in "Biology and Fertility of Soils in 2011"

Bacillus subtilis SQR 9 can control Fusarium wilt in cucumber by colonizing plant roots

Abstract: Fusarium wilt is one of the major constraints on cucumber production worldwide. Several strategies have been used to control the causative pathogen, Fusarium oxysporum f. sp. cucumerinum J. H. Owen, including soil solarization, fungicide seed treatment and biological control. In this study, F. oxysporum f. sp. cucumerinum was successfully controlled by a newly isolated strain, Bacillus subtilis SQR 9, in vitro and in vivo. Greenhouse experiments were carried out to evaluate the effect of inoculation and solid fermentation of organic fertilizer with B. subtilis SQR 9, hereby defined as bio-organic fertilizer (BIO), on the control of Fusarium wilt. In comparison with the control, the wilt incidence was significantly reduced (49–61% reduction) by application of BIO. The rhizosphere population of F. oxysporum f. sp. cucumerinum, as detected both by selective plating and realtime PCR, was significantly lower in BIO-treated plants than the control. The localization of bacterial cells, pattern of colonization and survival of B. subtilis SQR 9 in the rhizsosphere of cucumber, was examined by fluorescent microscopy and explored following recovery of the green fluorescent protein (gfp)-labeled SQR 9 with the new gfp-marked shuttle vector pHAPII through selective plating. The preferential sites of the labeled strain were the differentiation and elongation zone, root hair and the lateral root junctions. The population of the strain was 106 cfu/g root in rhizoplane. These results indicate that the strain was able to survive well in the rhizosphere of cucumber, suppressed growth of F. oxysporum in the rhizosphere of cucumber and protected the host from the pathogen.

Fixation and defixation of ammonium in soils: a review

Abstract: Fixed NH 4 + (NH 4 + f) and fixation and defixation of NH 4 + in soils have been the subject of a number of investigations with conflicting results. The results vary because of differences in methodology, soil type, mineralogical composition, and agro-climatic conditions. Most investigators have determined NH 4 + f using strong oxidizing agents (KOBr or KOH) to remove organic N and the remaining NH 4 + f does not necessarily reflect the fraction that is truly available to plants. The content of native NH 4 + f in different soils is related to parent material, texture, clay content, clay mineral composition, potassium status of the soil and K saturation of the interlayers of 2:1 clay minerals, and moisture conditions. Evaluation of the literature shows that the NH 4 + f-N content amounts to 10–90 mg kg−1 in coarse-textured soils (e.g., diluvial sand, red sandstone, granite), 60–270 mg kg−1 in medium-textured soils (loess, marsh, alluvial sediment, basalt) and 90–460 mg kg−1 in fine-textured soils (limestone, clay stone). Variable results on plant availability of NH 4 + f are mainly due to the fact that some investigators distinguished between native and recently fixed NH 4 + while others did not. Recently fixed NH 4 + is available to plants to a greater degree than the native NH 4 + f, and soil microflora play an important role in the defixation process. The temporal changes in the content of recently fixed NH 4 + suggest that it is actively involved in N dynamics during a crop growth season. The amounts of NH 4 + defixed during a growing season varied greatly within the groups of silty (20–200 kg NH 4 + -N ha−1 30 cm−1) as well as clayey (40–188 kg NH 4 + -N ha−1 30 cm−1) soils. The pool of recently fixed NH 4 + may therefore be considered in fertilizer management programs for increasing N use efficiency and reducing N losses from soils.

Soil organic carbon active fractions as early indicators for total carbon change under straw incorporation

Abstract: Changes in total organic C (CT), water-soluble organic C (CWS), microbial biomass C (CMB), C mineralization, particulate organic C (CP), labile organic C (CL), C management index (CMI), and C storage in surface Hapli-Ustic Cambisol (0–20 cm) under straw incorporation after both 2- and 10-year durations were investigated in a maize (Zea mays L.) field experiment in northeast China, in order to examine the effectiveness of these active C fractions and CMI as early indicators for total C change. The treatments included straw removal (0%S), 50% of straw incorporation (50%S), and 100% of straw incorporation (100%S). Under the straw incorporation, CT concentration and C storage did not significantly change under 2-year duration, while were significantly increased under 10-year duration. However, CMB, total C mineralization (CTM), CP, and CL, and CMI were significantly increased under the straw incorporation even after only 2-year duration, and the responses were more significant after 10-year duration. There were positive correlations between all these C indicators with each other. Our findings demonstrate that the measured active C fractions (except for CWS) and CMI can provide an early indication of change in total soil organic C induced by straw incorporation.

Salt-tolerant rhizobacteria-mediated induced tolerance in wheat ( Triticum aestivum ) and chemical diversity in rhizosphere enhance plant growth

Abstract: Salt-tolerant isolates Bacillus pumilus, Pseudomonas mendocina, Arthrobacter sp., Halomonas sp., and Nitrinicola lacisaponensis isolated from high saline habitats exhibited plant growth-promoting traits like P solubilization and indole acetic acid (IAA), siderophore, and ammonia production. These isolates were inoculated in wheat to assess microbe-mediated responses and plant growth promotion in salt affected soil. Maximum shoot and root length (33.8 and 13.6 cm) and shoot and root biomass (2.73 and 4.48 g dry weight) was recorded in plants inoculated with B. pumilus after 30 days. Total chlorophyll content was maximum in the leaves of the plants treated with Halomonas sp. (24.22 mg g−1 dry weight) followed by B. pumilus (23.41 mg g−1 dry weight) as compared to control (18.21 mg g−1 dry weight) after 30 days. Total protein content was maximum in Arthrobacter sp. inoculated plant leaves (3.19 mg g−1 dry weight) followed by B. pumilus (2.47 mg g−1 dry weight) as compared to control (2.15 mg g−1 dry weight) after 30 days. Total carotenoid content was maximum in plants inoculated with Halomonas sp. (1,075.45 and 1,113.29 μg g−1 dry weight) in comparison to control (837.32 and 885.85 μg g−1 dry weight) after 15 and 30 days. Inoculation of bacterial isolates increased presence of individual phenolics (gallic, caffeic, syringic, vanillic, ferulic, and cinnamic acids) and flavonoid quercetin in the rhizosphere soil. The concentration of IAA in rhizosphere soil and root exudates was also higher in all treatments than in control. Accumulation of phenolics and quercetin in the plants played a cumulative synergistic role that supported enhanced plant growth promotion of wheat in the stressed soil.

Functional genomics analysis of plant growth-promoting rhizobacterial traits involved in rhizosphere competence

Abstract: In soil, some specific bacterial populations, called plant growth-promoting rhizobacteria are able to promote plant growth and/or reduce the incidence of soil-borne diseases. Rhizosphere competence is an important prerequisite for the efficacy of these biocontrol strains. Therefore, over decades, multiple approaches have been combined to understand the molecular basis of bacterial traits involved in rhizosphere competence. This review addresses the bacterial genes expressed during bacterial–plant interactions in the rhizosphere of different plant species. The distribution of these key genes in natural populations of rhizobacteria is also discussed.

Isolation and characterization of phosphate-solubilizing bacteria from walnut and their effect on growth and phosphorus mobilization

Abstract: The objectives of this work were to isolate and characterize walnut phosphate-solubilizing bacteria (PSB) and to evaluate the effect of inoculation with the selected PSB stains to walnut seedlings fertilized with or without insoluble phosphate. Thirty-four PSB strains were isolated and identified under the genera Pseudomonas, Stenotrophomonas, Bacillus, Cupriavidus, Agrobacterium, Acinetobacter, Arthrobacter, Pantoea, and Rhodococcus through a comparison of the 16S ribosomal DNA sequences. All isolated PSB strains could solubilize tricalcium phosphate (TCP) in solid and liquid media. Phosphate-solubilizing activity of these strains was associated with a drop in the pH of medium. A significantly negative linear correlation was found between culture pH and phosphorus (P) solubilized from inorganic phosphate. Three isolates Pseudomonas chlororaphis (W24), Bacillus cereus (W9), and Pseudomonas fluorescens (W12) were selected for shade house assays because of their higher phosphate-solubilizing abilities. Under shade house conditions, application of W24 or W12 remarkably improved plant height, shoot and root dry weight, and P and nitrogen (N) uptake of walnut seedlings. These increases were higher on combined inoculation of PSB with TCP addition. The most pronounced beneficial effect on growth of walnut plants was observed in the co-inoculation of the three PSB strains with TCP addition. In comparison, the isolate of W9 failed to increase available soil P, nutrient levels in plants, or to promote plant growth, suggesting that more insoluble phosphate compounds than tricalcium phosphate should be used as substrates to assess the phosphate-solubilizing ability of PSB under greenhouse conditions. The present results indicated that strains P. chlororaphis or P. fluorescens could be considered for the formulation of new inoculants of walnut, even of more woody plants.

Effects of biochar addition on N2O and CO2 emissions from two paddy soils

Abstract: Impacts of biochar addition on nitrous oxide (N2O) and carbon dioxide (CO2) emissions from paddy soils are not well documented. Here, we have hypothesized that N2O emissions from paddy soils could be depressed by biochar incorporation during the upland crop season without any effect on CO2 emissions. Therefore, we have carried out the 60-day aerobic incubation experiment to investigate the influences of rice husk biochar incorporation (50 t ha−1) into two typical paddy soils with or without nitrogen (N) fertilizer on N2O and CO2 evolution from soil. Biochar addition significantly decreased N2O emissions during the 60-day period by 73.1% as an average value while the inhibition ranged from 51.4% to 93.5% (P 0.05) in terms of cumulative emissions. Therefore, biochar can be added to paddy fields during the upland crop growing season to mitigate N2O evolution and thus global warming.

Interactions between arbuscular mycorrhizal fungi and phosphate-solubilizing fungus (Mortierella sp.) and their effects on Kostelelzkya virginica growth and enzyme activities of rhizosphere and bulk soils at different salinities

Abstract: This study investigated the interactions between two arbuscular mycorrhizal fungi (AMF) (Glomus aggregatum and Glomus mosseae) and a P-solubilizing fungus (Mortierella sp.), with respect to their effects on growth of Kostelelzkya virginica and urease, invertase, neutral phosphatase, alkaline phosphatase, and catalase activities of rhizosphere and bulk soils at different salinity levels (i.e., 0, 100, 200, and 300 mM NaCl). Percentage of AMF colonization, Mortierella sp. populations, pH, electrical conductivity, and available P concentration in soil were also determined. Combined inoculation of AMF and Mortierella sp. increased the percentage of AMF colonization and Mortierella sp. populations under salt stress (i.e., 100, 200, and 300 mM NaCl). The dual inoculation of Mortierella sp. with AMF (G. aggregatum or G. mosseae) had significant effects on shoot and root dry weights and available P concentrations, pH values, and electrical conductivities of rhizosphere and bulk soils under salt stress. The inoculation of Mortierella sp. significantly enhanced the positive effects of AMF on some enzyme activities (i.e., neutral phosphatase, alkaline phosphatase, and catalase in bulk soil; neutral phosphatase and urease in rhizosphere soil); on the contrary, it produced negative effects on urease activities in bulk soil and invertase activities in bulk and rhizosphere soils. The results indicated that the most effective co-inoculation was the dual inoculation with Mortierella sp. and G. mosseae, which may help in alleviating the deleterious effects of salt on plants growth and soil enzyme activities.

Crop residues and fertilizer nitrogen influence residue decomposition and nitrous oxide emission from a Vertisol

Abstract: Crop residues with high C/N ratio immobilize N released during decomposition in soil, thus reducing N losses through leaching, denitrification, and nitrous oxide (N2O) emission. A laboratory incubation experiment was conducted for 84 days under controlled conditions (24°C and moisture content 55% of water-holding capacity) to study the influence of sugarcane, maize, sorghum, cotton and lucerne residues, and mineral N addition, on N mineralization–immobilization and N2O emission. Residues were added at the rate of 3 t C ha−1 to soil with, and without, 150 kg urea N ha−1. The addition of sugarcane, maize, and sorghum residues without N fertilizer resulted in a significant immobilization of soil N. Amended soil had significantly (P < 0.05) lower NO 3 − –N, which reached minimum values of 2.8 mg N kg−1 for sugarcane (at day 28), 10.3 mg N kg−1 for maize (day 7), and 5.9 mg N kg−1 for sorghum (day 7), compared to 22.7 mg N kg−1 for the unamended soil (day 7). During 84 days of incubation, the total mineral N in the residues + N treatments were decreased by 45 mg N kg−1 in sugarcane, 34 mg kg−1 in maize, 29 mg kg−1 in sorghum, and 16 mg kg−1 in cotton amended soil compared to soil + N fertilizer, although soil NO 3 − –N increased by 7 mg kg−1 in lucerne amended soil. The addition of residues also significantly increased amended soil microbial biomass C and N. Maximum emissions of N2O from crop residue amended soils occurred in the first 4–5 days of incubation. Overall, after 84 days of incubation, the cumulative N2O emission was 25% lower with cotton + N fertilizer, compared to soil + N fertilizer. The cumulative N2O emission was significantly and positively correlated with NO 3 − –N (r = 0.92, P < 0.01) and total mineral N (r = 0.93, P < 0.01) after 84 days of incubation, and had a weak but significant positive correlation with cumulative CO2 in the first 3 and 5 days of incubation (r = 0.59, P < 0.05).

Bacteria able to control foot and root rot and to promote growth of cucumber in salinated soils

Abstract: The aim of the present work was to test known bacterial plant growth-promoting strains for their ability to promote cucumber plant growth in salinated soil and to improve cucumber fruit yield by protecting these plants against soil-borne pathogens. Fifty-two plant-beneficial bacterial strains were evaluated for their ability to protect plants against cucumber foot and root rot after bacterization of the seeds and infestation of salinated soil with the isolated Fusarium solani pathogen. Based on the results of initial screenings, five efficient strains were selected, namely Serratia plymuthica RR-2-5-10, Stenotrophomonas rhizophila e-p10, Pseudomonas fluorescens SPB2145, Pseudomonas extremorientalis TSAU20, and P. fluorescens PCL1751. All five strains are salt tolerant since they grow well in a medium to which 3% NaCl was added. Infestation of the soil with F. solani resulted in an increase of the percentage of diseased plants from 17 to 54. Priming of seedlings with the five selected bacterial strains reduced this proportion to as low as 10%. In addition, in the absence of an added pathogen, all five strains showed a significant stimulatory effect on cucumber plant growth, increasing the dry weight of whole cucumber plants up to 62% in comparison to the non-bacterized control. The strains also increased cucumber fruit yield in greenhouse varying from 9% to 32%. We conclude that seed priming with the selected microbes is a very promising approach for improving horticulture in salinated soils. Moreover, allochthonous strains isolated from non-salinated soil, from a moderate or even cold climate, and from other plants than cucumber, functioned as well as autochthonous strains as cucumber-beneficial bacteria in salinated Uzbek soils. These results show that these plant-beneficial strains are robust and they strongly suggest they can also be used successfully in case the climate gets warmer and the soils will become more salinated. Finally, the mechanisms by which they may exert their plant-beneficial action are discussed.

Effect of long-term fertilizers and manure application on microbial biomass and microbial activity of a tropical agricultural soil

Abstract: We investigated some aspects of soil quality and community-level physiological profiles (CLPP) of bacteria in soil under a long-term (37 years) trial with either exclusive inorganic fertilizers or fertilizers combined with farmyard manure cultivated with jute–rice–wheat system The treatments consisted of 100% recommended dose (RD) of NPK, 150% RD of NPK, 100% RD of N, 100% RD of NPK + FYM (10 t ha−1 year−1), and untreated control Long-term application of 150% RD of NPK lowered the soil pH considerably while the soils in the other treatments remained near neutral The 100% RD of NPK + FYM treated plot showed significantly highest accumulation of organic carbon, total nitrogen, microbial biomass carbon, basal soil respiration, and fluorescein diacetate hydrolyzing activity among the treatments CLPP analysis in Biolog Ecoplates revealed that utilization of carbohydrates was enhanced in all input treated regimes, while the same for polymers, carboxylic acids, amino acids, and amines/amides were similar or less than the untreated control However, within these groups of carbon sources, heterogeneity of individual substrate utilization between treatments was also noted Taken together, addition of organic supplements showed significantly increased microbial biomass carbon and microbial activity, but input of nutrient supplements, both inorganic and organic, only marginally affected the overall substrate utilization pattern of soil microorganisms

Effects of poultry manure amendment on phosphorus uptake by ryegrass, soil phosphorus fractions and phosphatase activity

Abstract: Poultry manure (PM) contains a large proportion of phosphorus (P) in mineral-associated forms that may not be readily available for plant uptake. In addition, PM application influences both chemical and biotic processes, and can affect the lability of native soil P. To investigate the effects of PM on soil P availability, we grew ryegrass (Lolium perenne) in greenhouse pots amended with poultry manure. Biomass was harvested at 4, 8, and 16 weeks following PM application, with soil separated into rhizosphere and bulk fractions. Soil was sequentially extracted by H2O, 0.5 M NaHCO3, 0.1 M NaOH, and 1 M HCl, and inorganic P (Pi) and enzymatically hydrolyzable organic P (Poe) were quantitated. Root P concentrations were 37% higher and total P uptake 59% higher with PM application than Control. At week 16, there was 30% more labile-Pi (H2O- plus NaHCO3-Pi) in the rhizosphere with PM than in Control. Phosphodiesterase activity increased with PM application. Furthermore, acid phosphomonoesterase, alkaline phosphomonoesterase, and phosphodiesterase activities were all higher in the rhizosphere than in bulk soil at week 16 with PM, indicating that increased labile-Pi was due primarily to stimulation of soil phosphatases to mineralize NaOH-Poe. Soil pH increased with PM application and plant growth, and may have promoted P availability by decreasing sorption of Al- and Fe-associated inorganic and organic phosphates. These results demonstrate that whereas PM application may initially increase NaOH and HCl-Pi, these fractions can be readily changed into labile-P and do not necessarily accumulate as stable or recalcitrant P in soil.

Soil microbial recolonisation after a fire in a Mediterranean forest

Abstract: The capacity of different microbial groups to recolonise soil after a fire event will be decisive in determining the microbial community after the fire. Microbial recovery after a wildfire that occurred in Sierra la Grana (Alicante province, southeast Spain) was tracked for 32 months after the fire. Colony forming units (CFUs) of different microbial groups, microbial biomass, soil respiration, bacterial growth (leucine incorporation) and changes in the microbial community structure (phospholipid fatty acid (PLFA) analysis) were determined directly after the fire and four times during the recovery period. Direct effects were reflected by low values of most microbiological variables measured immediately after the fire. Microbial biomass increased during the first year after the fire but was below the unburned reference site 32 months after the fire. Bacterial activity and soil respiration showed the highest values immediately after the fire, but decreased to values similar to that of the unburned reference site or even lower (respiration) 32 months after the fire. Colony forming units of bacterial groups estimated by the plate count method peaked 8 months after the fire, but then decreased, showing values similar to the unburned reference site at the end of the study, with the exception of spore formers, which were 20 times higher than the reference site 32 months after the fire. Fungal CFUs were more sensitive to the fire and recovered more slowly than bacteria. Fungi recovering less rapidly than bacteria were also indicated by the PLFA pattern, with PLFAs indicative of fungi being less common after the fire. The recovery of microbial biomass and activity was mirrored by the initially very high levels of dissolved organic carbon being consumed and decreasing within 8 months after the fire. The wildfire event had thus resulted in a decrease in microbial biomass, with a more bacteria-dominated microbial community.

Effects of 17-year fertilization on soil microbial biomass C and N and soluble organic C and N in loessial soil during maize growth

Abstract: As labile organic pools, soluble organic matter and soil microbial biomass are sensitive to changes in soil management and therefore good indicators of soil quality. Effects of a 17-year long-term fertilization on soil microbial biomass C (SMBC) and N (SMBN), soluble organic C, and soluble organic N during the maize growing season were evaluated in a loess soil (Eum-Orthic Anthrosol) in northwest China. The fertilization treatments included no fertilizer (CK), inorganic N, P, and K fertilizer (NPK), cattle manure plus NPK fertilizer (MNPK), and straw plus NPK fertilizer (SNPK). Our results showed that C storage in the 0–20 cm soil layer was 28% to 81% higher in the fertilized treatments compared to the unfertilized treatment. In the 0–10 cm soil layer, SMBC and SMBN in the three fertilized treatments were higher than in the unfertilized treatment on all sampling dates, while microbial biomass C and N in the 0−10 cm soil layers were the highest at grain filling. In the same soil layer, soil-soluble organic C generally decreased in the order MNPK > SNPK > NPK > CK, while soluble organic N was the highest in the MNPK followed by the SNPK treatment. There was no significant difference in soluble organic N in the NPK and CK treatments throughout most of the maize growing season. Changes in soluble organic N occurred along the growing season and were more significant than those for soluble organic C. Soluble organic N was the highest at grain filling and the lowest at harvest. Overall, our results indicated that microbial biomass and soluble organic N in the surface soil were generally the highest at grain filling when maize growth was most vigorous. Significant positive relationships were found between soluble organic C and SMBC and between soluble organic N and SMBN.

Impact of urease and nitrification inhibitors on nitrous oxide emissions from fluvo-aquic soil in the North China Plain

Abstract: Little information is available on the effects of urease inhibitor, N-(n-butyl)thiophosphoric triamide (NBPT), and nitrification inhibitor, dicyandiamide (DCD), on nitrous oxide (N2O) emissions from fluvo-aquic soil in the North China Plain. A field experiment was conducted at the Fengqiu State Key Agro-Ecological Experimental Station, Henan Province, China, to study the influence of urea added with NBPT, DCD, and combination of both NBPT and DCD on N2O emissions during the maize growing season in 2009. Two peaks of N2O fluxes occurred during the maize growing season: the small one following irrigation and the big one after nitrogen (N) fertilizer application. There was a significant positive relationship between ln [N2O flux] and soil moisture during the maize growing season excluding the 11-day datasets after N fertilizer application, indicating that N2O flux was affected by soil moisture. Mean N2O flux was the highest in the control with urea alone, while the application of urea together with NBPT, DCD, and NBPT + DCD significantly lowered the mean N2O flux. Total N2O emission in the NBPT + DCD, DCD, NBPT, and urea alone treatments during the experimental period was 0.41, 0.47, 0.48, and 0.77 kg N2O–N ha−1, respectively. Application of urea with NBPT, DCD, and NBPT + DCD reduced N2O emission by 37.7%, 39.0%, and 46.8%, respectively, over urea alone. Based on our findings, the combination of DCD and NBPT together with urea may reduce N2O emission and improve the maize yield from fluvo-aquic soil in the North China Plain.

Soil organic C variability and microbial functions in a Mediterranean agro-forest ecosystem

Abstract: Five soils characterised by different agro-forest managements, typical of Mediterranean environment and with increasing human impact were chosen in Sardinia (Italy): two vineyards with different management systems, a rotation hay crop-pasture and a forest (Quercus suber L.). The study aimed to investigate the relationships between C storage and microbial functionality in soil under different managements. Pools of total organic C and microbial biomass C were determined, as well as the loss of organic C due to microbial respiration (basal and cumulative) and several microbial indices (metabolic, mineralization, and microbial quotient) as indicators of the microbial efficiency in the use of energy and the degree of substrate limitation for soil microbes. Enzymes were chosen on their relevance in the C (β-cellobiohydrolase, N-acetyl-β-glucosaminidase, β-glucosidase, α-glucosidase), N (leucine aminopeptidase), S (arylsulphatase) and P (acid phosphatase) cycling and were used as indicators of functional diversity in soil. Organic C pools and enzyme activities on average increased noticeably in soils with a lower human impact showing the highest values in forest and the lowest in the vineyards, following the trend of organic matter availability. The trend in functional diversity reflected the increase of microbial pool and organic C availability: the vineyards showed a lower Shannon’s diversity index, whilst pasture and forest sites reached the maximum levels of functional diversity. These soils showed an increase of microbial efficiency in the use of available resources and the decrease of substrate limitation for soil microbes.

Community level functional diversity and enzyme activities in paddy soils under different long-term fertilizer management practices

Abstract: Soil microbial community structure and function are commonly used as indicators for soil quality and fertility. The present study deals with the effect of different long-term fertilizer management practices on community-level physiological profiles (CLPP) and soil enzyme activities of paddy soils. Since 1954, chemical fertilizers have been applied in the fields as N–P2O5–K2O, and compost has been added as rice straw at 0, 7.5, 22.5, and 30.0 Mg ha−1 in NPK, NPKC750, NPKC2250, and NPKC3000 treatments, respectively. Community-level functional diversity was significantly enhanced in the plots treated with both chemical fertilizer and compost as compared to only chemical fertilizer and untreated control plots. Average well color development (AWCD) obtained by the Biolog Eco plate indicates that there were few differences among soil samples. Shannon diversity and evenness indices were the highest in NPKC750-treated soil and the lowest in chemically fertilized soil. Dehydrogenase, cellulose, β-glucosidase, and acid and alkaline phosphomonoesterase activities were significantly increased depending on the amount of added compost with inorganic fertilizers; the alkaline phosphomonoesterase activity was the most sensitive to treatments. Our results demonstrated that enzyme activities can be used as sensitive and liable indicators in long-term managed rice-paddy ecosystems.

Formulations can affect rhizosphere colonization and biocontrol efficiency of Trichoderma harzianum SQR-T037 against Fusarium wilt of cucumbers

Abstract: Pot experiments were carried out over two growing periods to assay the biocontrol efficacy and rhizosphere colonization of Trichoderma harzianum SQR-T037 (SQR-T037) applied as SQR-T037 conidia suspension (TCS), SQR-T037 conidia suspension blended with organic fertilizer (TBF), or SQR-T037 fermented organic fertilizer (TFF). Each formulation had three T. harzianum numbers. In two experiments, Percent Disease Indexes (PDIs) decreased with the increase of SQR-T037 number added to soils. The TFF treatment consistently exhibited the lowest PDIs at same amendment rate of SQR-T037 and 0–8.9%, 25.6–78.9%, and 4.4–50.0% of PDIs were found in TFF, TCS, and TBF treatment, respectively. Soils treated with TFF showed the highest SQR-T037 population in rhizosphere and bulk soil. Decrease of Fusarium oxysporum population in both bulk and rhizosphere soils occurred in the treatment SQR-T037 at 105 and 106 cfug−1 soil rate. The TFF treatment at the SQR-T037 rate of 103 cfug−1 soil significantly (p < 0.05) increased SQR-T037 population within the rhizoplane but had no effect on F. oxysporum population when compared to TCS and TBF. Generally, TFF treatments were superior to TCS and TBF treatments on disease control by sustaining colonization of SQR-T037 and decreasing F. oxysporum abundance in the rhizosphere soil. We propose that TFF treatment at SQR-T037 rate of 107 cfug−1 (i.e., 105 cfug−1 soil after applied to soil) was the best formulation for controlling Fusarium wilt of cucumber.

Abundance and community structure of ammonia-oxidizing archaea and bacteria in an acid paddy soil

Abstract: Nitrification is essential to the nitrogen cycle in paddy soils. However, it is still not clear which group of ammonia-oxidizing microorganisms plays more important roles in nitrification in the paddy soils. The changes in the abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated by real-time PCR, terminal restriction fragment length polymorphism, and clone library approaches in an acid red paddy soil subjected to long-term fertilization treatments, including treatment without fertilizers (CT); chemical fertilizer nitrogen (N); N and potassium (NK); N and phosphorus (NP); N, P, and K (NPK); and NPK plus recycled crop residues (NPK+C). The AOA population size in NPK+C was higher than those in CT, while minor changes in AOB population sizes were detected among the treatments. There were also some changes in AOA community composition responding to different fertilization treatments. Still few differences were detected in AOB community composition among the treatments. Phylogenetic analysis showed that the AOA sequences fell into two main clusters: cluster A and cluster soil/sediment. The AOB composition in this paddy soil was dominated by Nitrosospira cluster 12. These results suggested that the AOA were more sensitive than AOB to different fertilization treatments in the acid red paddy soil.

Effect of long-term fertilization on bacterial composition in rice paddy soil

Abstract: We investigated the effect of long-term fertilization on bacterial abundance, composition, and diversity in paddy soil. The experiment started in 1990 in Taoyuan Agro-ecosystem Research Station in China (111°33′ E, 28°55′ N). The molecular approaches including real-time quantitative PCR, terminal restriction fragment length polymorphism, and clone library construction were employed using 16S rRNA gene as genetic marker. Application of inorganic fertilizers did not affect bacterial abundance, and rice straw incorporation combined with inorganic fertilizers significantly (P < 0.05) increased bacterial abundance with shifts in bacterial community composition. Among phylogenetic groups, γ-Proteobacteria was responsive to all fertilization regimes while Acidobacteria was relatively stable to fertilization practices. Inorganic fertilizer mainly affected γ-Proteobacteria and δ-Proteobacteria, while rice straw incorporation influenced β-Proteobacteria and Verrucomicrobia. Therefore, long-term fertilization can affect abundance and composition of bacterial communities in paddy soil.

Comparative effectiveness of Pseudomonas and Serratia sp. containing ACC-deaminase for coinoculation with Rhizobium leguminosarum to improve growth, nodulation, and yield of lentil

Abstract: Three plant growth-promoting rhizobacteria strains containing ACC-deaminase (Pseudomonas jessenii, Pseudomonas fragi, and Serratia fonticola) and Rhizobium leguminosarum were selected and characterized by conducting some experiments under axenic condition. The selected isolates had the potential to improve the growth of lentil seedlings under axenic conditions. Pot and field experiments were conducted to evaluate the potential of these selected strains for improving growth and yield of lentil under natural conditions. A classical triple response (reduction of stem elongation, swelling of hypocotyle, and change in the direction of growth) bioassay was also conducted to evaluate the effect of high ethylene concentration on the growth of etiolated lentil seedlings, and the performance of coinoculation was evaluated to reduce the classical triple response in comparison with cobalt (Co2+), a chemical inhibitor of ethylene. Results showed that coinoculation of Pseudomonas and Serratia sp. with R. leguminosarum significantly increased the growth and yield of lentil. However, synergistic/coinoculation effect of P. jessenii with R. leguminosarum was more pronounced compared to that with P. fragi and S. fonticola. It increased the number of pods per plant, number of nodules per plant, dry nodule weight, grain yield, and straw yield up to 76%, 196%, 109%, 150%, and 164% under pot and up to 98%, 98%, 100%, 82%, and 78%, respectively, under field conditions as compared to uninoculated control. Similarly, combined inoculation significantly increased N concentration of grains under both pot and field conditions. The results from classical triple response assay showed that the effects of classical triple response decreased due to coinoculation in etiolated lentil seedlings and due to a decrease in the ethylene concentration. It is suggested that the strategy adopted by Pseudomonas sp. containing ACC-deaminase with Rhizobium to promote nodulation and yield by adjusting ethylene levels could be exploited as an effective tool for improving growth, nodulation, and yield of lentil.

Optimisation of amino sugar quantification by HPLC in soil and plant hydrolysates

Abstract: Amino sugars are increasingly used as indicators for the accumulation of microbial residues in soil and plant material. A reverse-phase high-performance liquid chromatography method was improved for the simultaneous determination of muramic acid, mannosamine, glucosamine and galactosamine in soil and plant hydrolysates via ortho-phthaldialdehyde (OPA) pre-column derivatisation and fluorescence detection. The retention time was reduced, and the separation of muramic acid and mannosamine was optimised by modifying the mobile phase. The effects of excitation wavelength, OPA reaction time, tetrahydrofuran concentration and pH value of the mobile phase on the amino sugar separation were tested. Quantification limits were in the range of 0.13 to 0.90 μg ml−1. No interferences exist from amino acids or other primary amines, occurring in soil and plant hydrolysates.

Urea hydrolysis and lateral and vertical movement in the soil: effects of urease inhibitor and irrigation

Abstract: A glasshouse-based study was conducted to investigate the effect of urease inhibitor N-(n-butyl) thiophosphoric triamide (‘Agrotain’) and irrigation on urea hydrolysis and its movement in a Typic Haplustept silt loam soil (in 72 repacked soil cores). Half (36) of these cores were adjusted to soil moisture contents of 80% field capacity (FC) and the remaining 36 cores to 50% FC. Granular urea with or without Agrotain was applied at a rate equivalent to 100 kg N ha−1. There were three replicates to these two sets of soil cores. After 1 day of treatment application, soil cores of the 50% FC were adjusted to 80% FC by applying surface irrigation. Twelve pots were destructively sampled at each day after 1, 2, 3, 4, 7 and 10 days of treatment application to determine urea hydrolysis and its lateral and vertical movement in different soil layers. Agrotain-treated urea delayed urea hydrolysis during the first 7 days after its application. This delay in urea hydrolysis caused by Agrotain enabled added urea, which is uncharged, to move away from the surface soil layer to the sub-surface soil layer both vertically and laterally. In contrast, most urea hydrolysed to soil NH4+ within 2 days of its application. Irrigation after 1 day resulted in further urea movement both laterally and vertically from the surface soil layer (0–10 mm) to the sub-soil layer (30–50 mm) in Agrotain-treated urea. These results suggest that Agrotain delayed urea hydrolysis and allowed more time for rainfall or irrigation to move added urea from the surface layer to sub-soil layers where it is likely to make good contact with plant roots. This distribution of urea in the rooting zone has the potential to enhance N use efficiency and minimize N losses associated with ammonia volatilization from surface-applied urea.

Fungal degradation of chlorpyrifos by Acremonium sp. strain (GFRC-1) isolated from a laboratory-enriched red agricultural soil

Abstract: The organophosphorus insecticide, chlorpyrifos, has been widely applied in agriculture; in veterinary, against household pests; and in subterranean termite control. Due to its slow rate of degradation in soil, it can persist for extended periods in soil with a significant threat to environment and public health. The mixed and pure fungi were isolated from three soils by enrichment technique. The enriched mixed fungal cultures were capable of biodegrading chlorpyrifos (300 mg L−1) when cultivated in Czapek Dox medium. The identified pure fungal strain, Acremonium sp., utilized chlorpyrifos as a source of carbon and nitrogen. The highest chlorpyrifos degradation (83.9%) by Acremonium sp. strain GFRC-1 was found when cultivated in the nutrient medium with full nutrients. Desdiethyl chlorpyrifos was detected as a major biodegradation product of chlorpyrifos. The isolated fungal strain will be used for developing bioremediation strategy for chlorpyrifos-polluted soils.

Effects of compost input and tillage intensity on soil microbial biomass and activity under Mediterranean conditions

Abstract: Organic amendment and tillage reduction are two common practices to contrast soil organic matter decline, thus promoting sustainable cropping and carbon sequestration. In a horticultural land use system under Mediterranean climate, we evaluated the 9-year effects of two compost inputs (15 and 30 t ha−1 y−1, low and high input, respectively) and two tillage intensities (intensive and reduced) on soil macronutrients concentration, microbial biomass and activity. Total organic C, total N and POlsen were smaller in plots amended at low input, whilst intensive tillage decreased them at both compost inputs. These decreases in intensively tilled plots was ascribed to the disruption of soil aggregates, with consequent microbial degradation of the physically protected organic matter by oxidative processes. On the contrary, reduced tillage increased the extractable C, likely due to a higher protection of the most labile soil C fraction from the mineralization. Similarly, microbial biomass C and N increased following both doubling compost input and reducing tillage intensity, with a greater effect by the first factor. The higher values of cumulative 10-day basal and 20-h glucose-induced respiration, and metabolic quotient in intensively tilled plots suggested that high tillage favoured soil aggregate disruption and C accessibility. This was also confirmed by higher values of dehydrogenase activity/total organic C in those plots. Intensive tillage caused a higher soil aeration and organic substrates accessibility to microflora, thus undoing the fertility benefits provided by the high compost input. However, also a low compost input coupled to reduced tillage seemed to accomplish soil sustainability needs.

Heavy metals and arbuscular mycorrhizal (AM) fungi can alter the yield and chemical composition of volatile oil of sweet basil (Ocimum basilicum L.)

Abstract: The effects of increasing levels of metals (10 and 20 mg of Cr kg-1 and 25 and 50 mg of Cd, Pb, and Ni kg-1 soil) and arbuscular mycorrhizal (AM) fungi Glomus intraradices on the yield, chemical composition of volatile oil, and metal accumulation in sweet basil (Ocimum basilicum L.) were investigated in a pot experiment. The shoot yield, content of essential oil, and root yield of sweet basil were increased by the application of low dose of Cd, Pb, and Ni as compared to control. The application of high level of metals had deleterious effect on the yield. In soil with low dose of metal applied, AM fungi inoculation significantly enhanced the metal concentration in shoots and had adverse effect on the yield, whereas in soil with high dose of metal applied, AM fungal inoculation reduced the metal concentration in shoot and had beneficial effect on the yield. The content of linalool in basil oil was decreased and that of methyl chavicol was increased by the application of Cr, Cd, and Pb in soil as compared to control. Similarly, the level of linalool and methyl chavicol was decreased and that of methyl eugenol was increased by the application of Ni as compared to control. However, AM fungal inoculation led to maintain the content of linalool, methyl chavicol, and methyl eugenol in volatile oil, which were either increased or decreased by the application of metals. We conclude that the AM–sweet basil symbiosis could be used as a novel approach to enhance the yield and maintain the quality of volatile oil of sweet basil under metal-contaminated soils.

Emission rates of N2O and CO2 from soils with different organic matter content from three long-term fertilization experiments—a laboratory study

Abstract: Increasing organic matter stocks in soils reduce atmospheric carbon dioxide (CO2), but they may also promote emissions of nitrous oxide (N2O) by providing substrates for nitrification and denitrification and by increasing microbial O2 consumption. The objectives of this study were to determine the effects of fertilization history, which had resulted in different soil organic matter stocks on (1) the emission rates of N2O and CO2 at a constant soil moisture content of 60% water-holding capacity, (2) the short-term fluxes of N2O and CO2 following the application of different fertilizers (KNO3 vs. farmyard manure from cattle) and (3) the response to a simulated heavy rainfall event, which increased soil moisture to field capacity. Soil samples from different treatments of three long-term fertilization experiments in Germany (Methau, Sproda and Bad Lauchstadt) were incubated in a laboratory experiment with continuous determination of N2O and CO2 emissions and a monitoring of soil mineral N. The long-term fertilization treatments included application of mineral N (Methau and Sproda), farmyard manure + mineral N (Methau and Sproda), farmyard manure deposition in excess (Bad Lauchstadt) and nil fertilization (Bad Lauchstadt). Long-term addition of farmyard manure increased the soil organic C (SOC) content by 55% at Methau (silt loam), by 17% at Sproda (sandy loam) and by 88% at Bad Lauchstadt (silt loam; extreme treatment which does not represent common agricultural management). Increased soil organic matter stocks induced by long-term application of farmyard manure at Methau and Sproda resulted in slightly increased N2O emissions at a soil moisture content of 60% water-holding capacity. However, the effect of fertilization history and SOC content on N2O emissions was small compared to the short-term effects induced by the current fertilizer application. At Bad Lauchstadt, high N2O emissions from the treatment without fertilization for 25 years indicate the importance of a sustainable soil organic matter management to maintain soil structure and soil aeration. Emissions of N2O following the application of nitrate and farmyard manure differed because of their specific effects on soil nitrate availability and microbial oxygen consumption. At a soil moisture content of 60% water-holding capacity, fertilizer-induced emissions were higher for farmyard manure than for nitrate. At field capacity, nitrate application induced the highest emissions. Our results indicate that feedback mechanisms of soil C sequestration on N2O emissions have to be considered when discussing options to increase soil C stocks.

Long-term straw management and N fertilizer rate effects on quantity and quality of organic C and N and some chemical properties in two contrasting soils in Western Canada

Abstract: Crop residue and fertilizer management practices alter some soil properties, but the magnitude of change depends on soil type and climatic conditions. Field experiments with mainly barley (and canola, wheat, triticale, or pea in a few years) under conventional tillage were conducted from 1983 to 2009 at Breton (Gray Luvisol (Typic Haplocryalf) loam) and Ellerslie (Black Chernozem (Albic Argicryoll) clay loam), Alberta, Canada, to determine the effects of straw management (straw removed (S Rem) and straw retained (S Ret)) and N fertilizer rate (0, 25, 50, and 75 kg N ha−1) on total organic C (TOC) and N (TON), light fraction organic C (LFOC), and N (LFON) in the 0–7.5 and 7.5–15 cm, pH in the 0–7.5, 7.5–15, and 15–20 cm and extractable P, ammonium-N, and nitrate-N in the 0–15, 15–30, 30–60, and 60–90 cm soil layers. The S Ret and N fertilizer treatments usually had higher mass of TOC, TON, LFOC, and LFON in soil at Breton, but only of LFOC and LFON in soil at Ellerslie compared with the corresponding S Rem and zero-N control treatments. The responses of soil organic C and N to management practices were more pronounced for N fertilization than straw management. There were significant correlations among most soil organic C or N fractions, especially at Breton. Linear regressions between crop residue C or N input, or rate of fertilizer N applied and soil organic C or N were significant in most cases at Breton, but only for LFOC and LFON at Ellerslie. At Breton, compared with zero-N rate, the C sequestration efficiency of additional crop residue C input was 5.8%, 20.1%, and 20.4% in S Ret and 17.2%, 28.0%, and 30.1% in S Rem treatments at the 25, 50, and 75 kg N ha−1 rates, respectively. The effects of crop residue management and N fertilization on chemical properties were generally similar for both contrasting soil types. There was no effect of crop residue management on soil pH, extractable P and residual nitrate-N. Extractable P and pH in the top 0–15 cm soil decreased significantly with N application in both soil types. Residual nitrate-N (though quite low in Breton soil) increased with application of N and also indicated some downward movement in the soil profile up to 90 cm depth in Ellerslie soil. There was generally no effect of any treatment on ammonium-N in soil. In conclusion, straw retention and N application improved organic C and N in soil, and generally differences were more pronounced for light fraction than total organic C and N, and between the most extreme treatments (S Rem0 vs. S Ret75). Application of N fertilizer reduced extractable P and pH in the surface soil, and showed accumulation and downward leaching of nitrate-N in the soil profile.

Dryland cropping systems influence the microbial biomass and enzyme activities in a semiarid sandy soil

Abstract: Indicators of soil quality, such as microbial biomass C and N (MBC, MBN) and enzyme activities (EAs), involved in C, P, N, and S cycling, as affected by dryland cropping systems under conventional (ct) and no tillage (nt) practices were evaluated for 5 years. The soil is sandy loam with an average of 16.4% clay, 67.6% sand, and 0.65 g kg−1 OM at 0–10 cm. The crops evaluated were rotations of grain sorghum (Sorghum bicolor L.) or forage sorghum (also called haygrazer), cotton (Gossypium hirsutum), and winter rye (Secale cereale): grain sorghum–cotton (Srg–Ct), cotton–winter rye–sorghum (Ct–Rye–Srg), and forage sorghum–winter rye (Srf–Rye). The tillage treatments did not affect soil MB and EAs of C cycling (i.e., β-glucosidase, β-glucosaminidase, α-galactosidase), P cycling (alkaline phosphatase, phosphodiesterase), and S cycling (arylsulfatase)—except for separation due to tillage for Srf–Rye and Ct–Rye–Srg observed in PCA plots when all EAs were evaluated together. After 3 years, rotations with a winter cover crop history (Ct–Rye–Srg and Srf–Rye) enhanced soil MBN (up to 63%) and EAs (21-37%) compared to Srg–Ct. After 5 years, Srg–Ct and Ct–Rye–Srg showed similar soil MBC, MBN, EAs, total carbon (TC), and organic carbon (OC). A comparison of Srg–Ct plots with nearby continuous cotton (Ct–Ct) research plots in the same soil revealed that it took 5 years to detect higher TC (12%), MBC (38%), and EAs (32–36%, depending on the enzyme) under Srg–Ct. The significant improvements in MB and EAs found, as affected by dryland cropping systems with a history of winter cover crops and/or higher biomass return crops than cotton, can represent changes in soil OM, nutrient cycling, and C sequestration for sandy soils in the semiarid Texas High Plains region. It is significant that these soil changes occurred despite summer crop failure (2003 and 2006) and lack of winter cover crops (2006) due to lack of precipitation in certain years.

Effects of organic and inorganic fertilization on soil bacterial and fungal microbial diversity in the Kabete long-term trial, Kenya

Abstract: The effects of crop manure and inorganic fertilizers on composition of microbial communities of central high land soils of Kenya are poorly known. For this reason, we have carried out a thirty-two-year-old long-term trial in Kabete, Kenya. These soils were treated with organic (maize stover (MS) at 10 t ha−1, farmyard manure (FYM) at 10 t ha−1) and inorganic fertilizers 120 kg N, 52.8 kg P (N2P2), N2P2 + MS, N2P2 + FYM, a control, and a fallow for over 30 years. We examined 16S rRNA gene and 28S rRNA gene fingerprints of bacterial and fungal diversity by PCR amplification and denaturing gradient gel electrophoresis separation, respectively. The PCR bacterial community structure and diversity were negatively affected by N2P2 and were more closely related to the bacterial structure in the soils without any addition (control) than that of soils with a combination of inorganic and organic or inorganic fertilizers alone. The effect on fungal diversity by N2P2 was different than the effect on bacterial diversity since the fungal diversity was similar to that of the N2P2 + FYM and N2P2 + MS-treated. However, soils treated with organic inputs clustered away from soils amended with inorganic inputs. Organic inputs had a positive effect on both bacterial and fungal diversity with or without chemical fertilizers. Results from this study suggested that total diversity of bacterial and fungal communities was closely related to agro-ecosystem management practices and may partially explain the yield differences observed between the different treatments.