The nitrogen status of most Zambian soils is inherently low. Nitrogen-fixing trees such as Faidherbia albida (F. albida) could have the potential to restore soil fertility. We conducted a study to examine the role of mature F. albida trees on the soil microbial communities and overall N fertility status in Zambia. Soil samples were collected under and outside the canopies of F. albida trees in representative fields from two sites namely; Chongwe (loamy sand) and Monze (sandy loam). To assess the long term canopy effects; total N, mineral N and soil organic carbon (Corg) content were directly measured from soils collected under and outside the canopy. Short term litter effects were assessed by subtracting concentrations of biochemical properties of non-amended controls from amended soils with F. albida litter during an 8 week incubation experiment. We also determined N mineralization rates, microbial community structure—Phospholipid fatty acids, microbial biomass carbon, and labile organic carbon (\({\text{C}}_{{{\text{org[K}}_{ 2} {\text{SO}}_{ 4} ]}}\)) during incubation. For the long term canopy effect, average N mineralization rate, Corg, total N and mineral N content of non-amended soils under the canopy were (all significant at p < 0.05) greater than soils outside the canopy on both sites. In the short term, amending soils with litter significantly increased N mineralization rates by an average of 0.52 mg N kg−1 soil day−1 on soil from Monze. Microbial biomass carbon measured after 4 weeks of incubation was on average significantly higher on amended soils by 193 and 334 mg C kg−1 soil compared with non-amended soils in Chongwe and Monze soils, respectively. After 6 weeks of incubation, the concentration of all selected biomarkers for major microbial groups concentrations in non-amended soils were significantly higher (all p < 0.05) under the canopy than outside in Monze soil. Using principal component analysis, we found that the segregation of the samples under and outside the canopy by the first principal component (PC1) could be attributed to a proportional increase in abundances of all microbial groups. Uniform loadings on PC1 indicated that no single microbial group dominated the microbial community. The second principal component separated samples based on incubation time and location. It was mainly loaded with G-positive bacteria, and partly with G-negative bacteria, indicating that microbial composition was dominated by these bacterial groups probably at the beginning of the incubation on Monze soils. Our results show that the improvement of soil fertility status by F. albida could be attributed to a combination of both long term modifications of the soil biological and chemical properties under the canopy as well as short term litter fall addition.

Seven farms (two state, two cooperatives, and three private farms) were selected for assessing effects of farm management on the microbial biomass and the structure of the microbial community, as well as, the responses to seasonality on these two bio-indicators in these three representative farming systems. All farms are located on brown calcareous soil. Soil samples from the 0-20 cm depth were collected from two fields of each farm. Soil microbial community was assessed through two analyses: microbial biomass carbon and phospholipid fatty acid. The technological differences in soil management, among the three farming systems, affected both microbial biomass carbon and the microbial community composition. The differences were most pronounced between the private and the state farms. The statistical analyses demonstrated that the total of phospholipid fatty-acid were significantly higher in cooperative farms. The use of fallow in these farms seems to have positive effects on soil microbial communities. Seasonality has a clear effect on both indicators. Summarizing, both indicators demonstrated sensible responses to disturbances caused by farm management and seasonality in the conditions of Cuban agriculture. Keywords: farming systems, microbial biomass carbon, phospholipid fatty-acid analysis (PLFA), soil quality

Sustainable agriculture requires the careful optimization of the use of organic amendments to improve soil fertility while minimizing any harmful environmental effects. To understand the events that occur in soil after the addition of different organic amendments, we evaluated the nitrogen (N) mineralization dynamics in soil after adding organic amendments, and evaluated changes in the microbial population. The four organic amendments were fresh dairy cattle manure, fresh white clover, vegetable, fruit, and yard waste compost, and poplar tree compost. The N mineralization potential of each organic amendment was determined by analyzing total mineral nitrogen during a 97-day laboratory incubation experiment. Soils amended with clover released 240 mu g N g(-1) soil during the 97-day incubation, more than twice as much as that released from soils amended with manure or composts (76-100 mu g N g(-1) soil). At the end of the incubation, the net N mineralization in clover-amended soils was 54%, more than five times higher than that in soils amended with composts or manure (4%-9%). Nitrogen was mineralized faster in clover-amended soil (1.056 mu g N g(-1) soil day(-1)) than in soil amended with composts (0.361-0.417 mu g N g(-1) soil day(-1)). The microbial biomass carbon content was higher in clover-amended soil than in the soils amended with manure or composts. We monitored changes in the microbial population in amended soils by a phospholipid fatty acid (PLFA) analysis. On day 97, there were higher concentrations of total PLFAs in soils with organic amendments (e.g., 14.41 nmol g(-1) in clover-amended soil) than in control soil without amendments (9.84 nmol g(-1)). Bacteria (Gram-positive and Gram-negative), actinomycetes, and fungi were more abundant in clover-amended soils than soils amended with manure or composts. The N mineralization potential varied among the four organic amendments. Therefore, the timing of application and the type of organic amendment should be matched to the nutrient needs of the crop. (C) 2016 The Authors. Published by Elsevier B.V.

The role of soil fauna in crucial ecosystem services such as nutrient cycling remains poorly quantified, mainly because of the overly reductionistic approach adopted in most experimental studies. Given that increasing nitrogen inputs in various ecosystems influence the structure and functioning of soil microbes and the activity of fauna, we aimed to quantify the role of the entire soil nematode community in nutrient mineralization in an experimental set-up emulating nutrient-rich field conditions and accounting for crucial interactions amongst the soil microbial communities and plants. To this end, we reconstructed a complex soil foodweb in mesocosms that comprised largely undisturbed native microflora and the entire nematode community added into defaunated soil, planted with Lolium perenne as a model plant, and amended with fresh grass-clover residues. We determined N and P availability and plant uptake, plant biomass and abundance and structure of the microbial and nematode communities during a three-month incubation. The presence of nematodes significantly increased plant biomass production (+9%), net N (+25%) and net P (+23%) availability compared to their absence, demonstrating that nematodes link below- and above-ground processes, primarily through increasing nutrient availability. The experimental set-up presented allows to realistically quantify the crucial ecosystem services provided by the soil biota.

Seven farms (two state, two cooperatives, and three private farms) were selected for assessing effects of farm management on the microbial biomass and the structure of the microbial community, as well as, the responses to seasonality on these two bio-indicators in these three representative farming systems. All farms are located on brown calcareous soil. Soil samples from the 0-20 cm depth were collected from two fields of each farm. Soil microbial community was assessed through two analyses: microbial biomass carbon and phospholipid fatty acid. The technological differences in soil management, among the three farming systems, affected both microbial biomass carbon and the microbial community composition. The differences were most pronounced between the private and the state farms. The statistical analyses demonstrated that the total of phospholipid fatty-acid were significantly higher in cooperative farms. The use of fallow in these farms seems to have positive effects on soil microbial communities. Seasonality has a clear effect on both indicators. Summarizing, both indicators demonstrated sensible responses to disturbances caused by farm management and seasonality in the conditions of Cuban agriculture. Keywords : farming systems, microbial biomass carbon, phospholipid fatty-acid analysis (PLFA), soil quality

Gamma irradiation is becoming a potential tool in soil ecological studies as it gives a possibility to vary a dose that selectively kills the target organism. It makes minimum changes in soil biochemical properties as compared to autoclaving and freezing. Although gamma irradiation has often been used in studying the roles of nematodes on nutrient cycling, the recommended doses to eliminate nematodes still lead to a nutrient flush, and are less reproducible. Given that the indirect effect of gamma irradiation is through radiolysis, the same dose might have a different effect on the soil biochemical properties as the soil moisture content changes. Thus, an optimal dose that eliminates nematodes needs to be determined taking the moisture content of the soil sample at the time of irradiation into consideration. We conducted an incubation experiment for about three months during which the effects of a range of low gamma irradiation doses (0, 1, 3 and 5 kGy) at different moisture content (air dried, 50% water filled pore space (WFPS), 80% WFPS) were tested on nematode abundance and selected soil biochemical properties. Leaching with water immediately after irradiation at 50% WFPS, was used to assess to what extent it would remove N from the flush. The results showed that as the moisture content of the soil increases from 50% WFPS to 80% WFPS, nematode abundance, enzyme activities and total mineral N concentrations decreased during most of the incubation period at each irradiation dose. Increasing the moisture content, however, did not make significant changes in total phospholipid fatty acid concentrations in all levels of irradiations except at 3 kGy. These findings indicate the effects of gamma irradiation on soil biological and chemical properties vary depending on the moisture content of the soil at the time irradiation. Moreover, the moisture content of the soil at the time of gamma irradiation need to be considered during optimizing gamma irradiation as a tool in selective sterilization or defaunation. In the current experimental set up, the application of 3 kGy at 80% WFPS at the time of irradiation eradicated nematodes and left a comparable microbial abundance and community structure to the unirradiated CTR. Leaching the 50% WFPS samples irradiated at 5 kGy dose immediately after irradiation generally significantly reduced both NH4+-N and NO3 -N concentrations, but NH4+-N concentration remained higher compared to the unirradiated CTR. This indicates that leaching with water only partly reduced the nutrient flush and underlines the need to test additional methods to reduce the nutrient flush further. (C) 2015 Elsevier B.V. All rights reserved.

The present study examines the effects of different fertilization treatments (chemical fertilization, farmyard manure, plant compost, and mycorrhiza-inoculated compost) on the soil fungi under a crop rotation of wheat (Triticum aestivum L.) and corn (Zea mays L.) in a long-term field experiment established in Mediterranean Turkey in 1996. Soil samples were collected in May, August, and October 2009. Soil pH, organic carbon, plant-available nitrogen and phosphorus, mycorrhizal colonization, and a series of biochemical markers (phospholipid and neutral lipid fatty acid [PLFA and NLFA] profiles, soil ergosterol content, and glomalin related soil protein [GRSP] as indicators of abundance of bacteria, saprotrophic, and arbuscular mycorrhizal [AM] fungi) were assessed. No significant difference was observed in soil organic C and plant available N in relation to long-term fertilization treatments, but plant available P in soil changed significantly in relation to the fertilization treatment used and the sampling season (between 11.5–33.8 mg · kg−1 in spring, 10.4–28.6 mg · kg−1 in summer, and 10.5–33.2 mg · kg−1 in autumn). Mycorrhizal colonization patterns were similar for both plants. However, mycorrhiza-inoculated compost treatment exhibited higher root colonization (77.3%) over control (16.3%), chemical fertilization (10.0%), farmyard manure (19.3%), and plant compost (20.0%). No statistically significant change was observed in ergosterol content. The effect of long-term organic treatments on soil PLFA structure was statistically prominent; whereas seasonality only affected bacterial PLFAs. Organic fertilization increased GRSP (mean annual ranging from 0.91 to 2.46 mg · g−1 total GRSP) but long-term annual mycorrhizal inoculation had no significant effect on the soil GRSP pool.

Soil quality in vegetable cropping systems is seriously threatened by intensive tillage and fertilization practices and by limited crop rotations. Inclusion of cover crops, compost application and reduced tillage may help to sustain soil quality. A three-year field trial was set up on horticultural land to explore the combined effects of compost amendment at three rates (0,15 and 45 Mg ha (1) year (1)) and tillage practices (reduced tillage versus conventional ploughing) on soil quality. Cover crop was not a factor in the experiment, but cover crops were included in the rotation for reasons of good agricultural practice. The highest compost dose supported the initial level of total organic carbon in the arable layer. The decrease in pH in the arable layer was considerably limited by compost application, irrespective of the dose applied. Reduced tillage resulted in a favorable stratification for different soil quality indicators both by placement of organic inputs near the soil surface and by a reduction of leaching of base cations and organic carbon compounds. Differences between tillage practices and compost doses were most striking in the 0-10 cm soil layer. Compost application at the highest rate enhanced organic C content by 16% compared to the content in the non-amended soil. Reduced tillage induced a 13% higher organic C content in the 0-10 cm soil layer than that in the underlying 10-30 cm layer. Combining reduced tillage and recurrent compost application resulted in a different soil microbial community structure in the 0-10 cm surface layer, as revealed by phospholipid fatty acids analysis. Total microbial biomass was 44% higher under reduced compared to conventional tillage and increased by 27% due to compost application at a rate of 45 Mg ha (1) year (1). Fungal biomass doubled in the surface layer by reduced tillage. Actinomycetes and arbuscular mycorrhizal fungi were favored by both reduced tillage and compost application. Conversion to reduced tillage allowed for sustaining crop production in this intensive vegetable cropping system. Compost application and reduced tillage counteracted soil degradation. (C) 2014 Elsevier B.V. All rights reserved.

Several ecosystem processes such as nitrogen mineralization are mainly controlled by complex multitrophic interactions in which nematodes play major roles. Despite the abundance and diversity of these nematodes, studies on their contribution to N mineralization have been limited to a few selected species and often in completely sterilized media. Such simplified experiments are unrealistic and usually give inaccurate results as part of the interaction is missed. Therefore the contributions of nematodes to N mineralization need to be quantified more accurately in realistic conditions where native microbes, nematodes and plants interact. To do this, we set up a microcosm incubation experiment in which the whole nematode communities were extracted from fresh soil and reinoculated into the soil defaunated by 5 kGy dose gamma irradiation that leaves the microbial community largely intact. Three treatments namely control, +Nem (with nematodes) and -Nem (without nematodes), with or without plants were incubated for 86 days. In bare microcosms, +Nem cores increased total mineral nitrogen with 32% compared to -Nem. However, no significant (p > 0.05) differences were observed on total mineral nitrogen and plant N uptake between +Nem and -Nem treatments in planted microcosms. Nematode abundances and community structures were significantly changed over time and differed in bare and planted microcosms. Bacterivores dominated in bare, while herbivores dominated in planted soils throughout the incubation period. This could explain the contrasting effects of nematodes in N mineralization in bare and planted microcosms. Optimization of gamma irradiation technique is required to further reduce its side effects on nutrient flush and non-targeted organisms. (C) 2014 Elsevier Ltd. All rights reserved.

Soil fauna, particularly nematodes, are considered to strongly contribute to nitrogen mineralisation through grazing on microflora during decomposition. Demonstration of this effect has mostly relied on calculation-based soil food web analyses or experiments involving simplified and artificially constructed food webs. We carried out an incubation experiment in which defaunated soil cores were reinoculated with entire soil nematode populations extracted from bulk soil and during which nitrogen mineralisation was measured. Both undisturbed and disturbed cores were prepared to investigate whether a representative pore structure influences the effect of entire free-living nematode populations on nitrogen mineralisation. Cores were subjected to a 5 kGy gamma irradiation dose sufficient to eliminate all soil fauna while leaving the microbial biomass largely intact. Half of the irradiated cores were reinoculated with nematodes extracted from a corresponding volume of bulk soil and incubated for 82 days. The microbial biomass was not strongly affected by gamma irradiation or nematode addition but declined strongly in all treatments during incubation. Reinoculation of nematodes was successful in establishing populations of a similar size and composition as in the control samples. Net nitrogen mineralisation from indigenous soil organic matter was observed in all treatments throughout the incubation, but was always more pronounced in irradiated cores. Total mineral nitrogen concentrations did not differ significantly between simply irradiated and irradiated then reinoculated cores. However by the end of the incubation period nematode addition resulted in 87% and 23% more NO3--N g(-1) dry soil in undisturbed and disturbed cores respectively, while NH4+-N g(-1) dry soil decreased by 50% in both core types. We found no convincing evidence for a contribution of free-living nematodes on total nitrogen mineralisation, but the activity of nitrifying organisms was clearly stimulated by nematode grazing. (C) 2013 Elsevier Ltd. All rights reserved.

In Cuba there is a strong differentiation in types of farming systems that operate at very different levels of management intensity. The aim of this research was to characterize differences in soil quality caused by different agricultural management systems and the effects of seasonality on soil chemical and biological indicators within representative farming systems in Santa Clara municipality, Villa Clara Province, Cuba. Two state farms, two cooperative farms, and three private farms, all located on brown calcareous soils, which differed in soil management and technological complexity were selected. Soil samples from two fields of each farm were collected to a depth of 20 cm. Laboratory analysis were performed to determine physical (aggregate stability, plasticity, and permeability), chemical (pH and organic matter), and biological (dehydrogenase and β-glucosidase activities) indicators of soil quality. We found significant differences in soil quality among the three farming systems, which were most pronounced between private and state farms, with respect to physical soil properties (aggregate stability and plasticity) and the activity of enzymes. Seasonality also exerted an important influence on the activities of dehydrogenase and β-glucosidase, which were greater in the rainy season. As a conclusion, we can say that the differences in soil management between the farming systems were reflected in consistent differences in soil quality indicators, notably between the state and private farms.

Combining X-ray micro-Computed Tomography (X-ray micro-CT) analysis with measures of soil microbial functioning would provide a powerful tool for revealing the influence of soil pore structure on soil organic matter (SOM) decomposition. We investigated the impact of X-ray micro-CT scanning on soil microbial functioning for the first time by assessing C-mineralization, enzyme activities and microbial community structure by phospholipid fatty acid (PLFA) analysis 1 and 22 days after irradiation. There was no evidence for a disturbance of soil biological functioning following the X-ray micro-CT scanning, except for a small (but significant) decrease in dehydrogenase activity and a small (but significant) increase in the concentration of actinomycetes PLFA biomarkers. We conclude that X-ray micro-CT is fully compatible with soil biological experiments and that the combination of both may result in exciting new insights in the controls of soil pore architecture on soil biological experiments.

The microbial community (fungi and bacteria) is the main decomposer of organic matter during composting. Its composition is sometimes used as a proxy to assess compost maturity. Although nematodes are probably its most important grazers, only one previous study has highlighted clear shifts in nematode species composition during composting, and the assumption that nematodes reflect changes in the microbial community in compost has not yet been formally tested. Here, the microbial and nematode communities of a single composting process are analyzed together for the first time. Although both displayed broadly similar patterns, the abundance of fungal-feeding nematodes showed a distinct delay as compared to the increase in fungal PLFA. We argue that the nematode community may be a more promising tool to use in assessing compost maturity because it allows to discriminate between the three composting phases. First, during the thermophilic phase, bacterial-feeding nematodes dominate; during cooling, the bacterial-feeding/predators bloom; and during maturation, the abundance of fungal-feeding nematodes increases. Based solely on the microbial community, it was only possible to discriminate between the thermophilic phase and the rest of the process. Bacteria dominated during the thermophilic phase, while bacterial and fungal PLFA had more-or-less equal shares during cooling and maturation.

The techniques available for sterilisation or defaunation of soil in ecological experiments mostly have strongly unwanted effects on soil structure and the dynamics of major nutrients such as nitrogen. The potential for using gamma irradiation to prepare defaunated soil microcosms was investigated by subjecting undisturbed soil cores to a range of irradiation doses (0, 5, 10, 20 and 40 kGy). The absence of living nematodes at the lowest irradiation dose was confirmed by microscopic observation. The effects of irradiation dose on mineral nitrogen (as NO3- and NH4+), microbial biomass C (C-mic), and phospholipid fatty acid (PLFA) concentration and composition were determined over a 4 week incubation period. An increase in the concentration of NO occurred during the incubation period after exposure to 0, 5 and 10 kGy but was barely detectable at 20 and 40 kGy. The effect of irradiation dose on NH4+ release was complex and highly variable within treatments, with the 10 kGy dose resulting in the highest concentrations. Microbial biomass carbon was significantly reduced following a 20 kGy irradiation dose and below detection at 40 kGy. Most remarkably, the sum of all measured PLFAs did not differ significantly between most treatments and was not correlated with microbial biomass. In most cases the concentration of signature fatty acids only differed significantly between the control and the highest irradiation dose treatments. To ascertain the sensitivity of microbial taxa to acute gamma irradiation with accuracy, measures of microbial community structure other than PLFA analysis are needed. (C) 2011 Elsevier Ltd. All rights reserved.