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In the highlands of Madagascar, agricultural expansion gained on grasslands and cropping systems based on direct seeding with permanent vegetation cover are emerging as a means to sustain upland crop production. The objective of this study was to examine how such agricultural practices affect greenhouse-gas emissions from a loamy Ferralsol previously used as a pasture. We conducted an experiment under controlled laboratory conditions combining cattle manure, crop residues (rice straw), and mineral fertilizers (urea plus NPK or di-NH4-phosphate) to mimic on-field inputs and examined soil CO2 and N2O emissions during a 28-d incubation at low and high water-filled pore space (40% and 90% WFPS). Emissions of N2O from the control soil , i.e., soil receiving no input, were extremely small (< 5 ng N2O-N (g soil)-1 h-1) even under anaerobic conditions. Soil moisture did not affect the order of magnitude of CO2 emissions while N2O fluxes were up to 46 times larger at high soil WFPS, indicating the potential influence of denitrification under these conditions. Both CO2 and N2O emissions were affected by treatments, incubation time, and their interactions. Crop-residue application resulted in larger fluxes of CO2 but reduced N2O emissions probably due to N immobilization. The use of di-NH4-phosphate was a better option than NPK to reduce N2O emissions without increasing CO2 fluxes when soil received mineral fertilizers. Further studies are needed to translate the findings to field conditions and relate greenhouse-gas budgets to crop production. [ABSTRACT FROM AUTHOR]

Priming effect (PE) is defined as a stimulation of the mineralization of soil organic matter (SOM) following a supply of fresh organic matter. This process can have important consequences on the fate of SOM and on the management of residues in agricultural soils, especially in tropical regions where soil fertility is essentially based on the management of organic matter. Earthworms are ecosystem engineers known to affect the dynamics of SOM. Endogeic earthworms ingest large amounts of soil and assimilate a part of organic matter it contains. During gut transit, microorganisms are transported to new substrates and their activity is stimulated by (i) the production of readily assimilable organic matter (mucus) and (ii) the possible presence of fresh organic residues in the ingested soil. The objective of our study was to see (i) whether earthworms impact the PE intensity when a fresh residue is added to a tropical soil and (ii) whether this impact is linked to a stimulation/inhibition of bacterial taxa, and which taxa are affected. A tropical soil from Madagascar was incubated in the laboratory, with a 13C wheat straw residue, in the presence or absence of a peregrine endogeic tropical earthworm, Pontoscolex corethrurus. Emissions of 12CO2 and 13CO2 were followed during 16 days. The coupling between DNA-SIP (stable isotope probing) and pyrosequencing showed that stimulation of both the mineralization of wheat residues and the PE can be linked to the stimulation of several groups especially belonging to the Bacteroidetes phylum. [ABSTRACT FROM AUTHOR]

Soils are the main sources of the greenhouse gas nitrous oxide (N2O). The N2O emission at the soil surface is the result of production and consumption processes. So far, research has concentrated on net N2O production. However, in the literature, there are numerous reports of net negative fluxes of N2O, (i. E. Fluxes from the atmosphere to the soil). Such fluxes are frequent and substantial and cannot simply be dismissed as experimental noise. Net N2O consumption has been measured under various conditions from the tropics to temperate areas, in natural and agricultural systems. Low mineral N and large moisture contents have sometimes been found to favour N2O consumption. This fits in with denitrification as the responsible process, reducing N2O to N2. However, it has also been reported that nitrifiers consume N2O in nitrifier denitrification. A contribution of various processes could explain the wide range of conditions found to allow N2O consumption, ranging from low to high temperatures, wet to dry soils, and fertilized to unfertilized plots. Generally, conditions interfering with N2O diffusion in the soil seem to enhance N2O consumption. However, the factors regulating N2O consumption are not yet well understood and merit further study. Frequent literature reports of net N2O consumption suggest that a soil sink could help account for the current imbalance in estimated global budgets of N2O. Therefore, a systematic investigation into N2O consumption is necessary. This should concentrate on the organisms, reactions, and environmental factors involved. [ABSTRACT FROM AUTHOR]

The comparative impact of the two most representative species of termites ( Cubitermes niokoloensis and Macrotermes bellicosus) on the monosaccharide (glucose, galactose, mannose, rhamnose, arabinose, and xylose) content of soil from a semi-arid tropical savanna (Senegal) was investigated. Two complementary procedures for soil fractionation (particle-size fractionation vs. aggregate-size fractionation) were carried out on a control soil (not subjected to the influence of termites) and on the soil of the internal wall (IW) of the termite mounds. Irrespective of the termite species and the soil (control vs. IW), glucose and galactose were the most abundant sugars, representing respectively 28–44%, and 21–28% of the total amount of monosaccharides. The impact of the two termite species on the sugar content differed. For the fungus-growing termite, M. bellicosus, the total monosaccharide content in the IW was about half that of the control soil. Most of this decrease was due to the decline of glucose (34% and 14% of the total decrease) and galactose (14% and 12%) associated with the particle size of the sand (i.e. >200 µm and 50–200 µm), respectively. In contrast, the total sugar content was 4 times higher in the IW of C. niokoloensis mounds than in the control soil. At the particle-size level, this accumulation of monosaccharides was mainly due to the increase in glucose and galactose in the particle-size fractions 20–50 µm and 2–20 µm. The aggregate-size fractionation indicated that the accumulation of glucose was particularly evident in the aggregate-size fraction 20–50 µm isolated from the IW of the mounds of C. niokoloensis. [ABSTRACT FROM AUTHOR]

The effects of 3 and 19 yr natural fallows on soil structure and soil bacteria were assessed by aggregate size fractionation of a tropical sandy soil (0–10 cm). Bulk unfractionated soil and fractions including particulate coarse organic residues (COR), and four fractions (>2000, 50–2000, 2–50 and <2 μm) from each treatment were analysed for total heterotrophic bacteria, free N-fixers and the diversity of Azospirillum species. The potential N2 fixation (acetylene reduction activity, ARA) was also measured using unfractionated soil and soil fractions. Long-term fallow (19 yr) under Pennisetum was found to stimulate aggregation, while all clay particles were easily dispersed from the 3 yr fallow soil. Hot spots of potential N2 fixation were observed in coarse soil fractions (>50 μm), suggesting that these microhabitats were favourable to active N2 fixers. In contrast, more than 70% of the N2 fixing microorganisms and 90% of the recovered Azospirillum were isolated from the dispersible clay fraction (0–2 μm). Diversity of Azospirillum species was assessed by hybridisation with specific genetic probes on colonies within each fraction. This approach revealed the abundance of Azospirillum irakense in the 3 yr fallow soil fractions only and a selective effect of fallow on Azospirillum brasilense/Azospirillum amazonense genomic species in the 19 yr fallow soil. These changes would remain hidden, if the investigation had been restricted to the unfractionated soil. [Copyright &y& Elsevier]

New developments in the estimation of free spores of Pasteuria penetrans, a hyperparasite of plant-parasitic nematodes, including Meloidogyne spp., have been tested in contrasted textured soils. They were dedicated to improving the recovery of spores. Different methods of increasing energy of aggregate dispersion were compared in their efficiency in recovering spores inoculated in a sandy clay soil and a clay soil. The dispersion of the soils by the less energetic method (method A) allowed only 50% and 20% of the spore inoculum to be recovered from the sandy clay soil and clay soil, respectively. For these soils, 76% and 81% of the particle-size fraction (0–20 µm) isolated by this method were still aggregated in coarser structures. With increasing energy (methods B and C), these coarse aggregates disappeared entirely in both soils. At the same time, the recovery of spores increased sharply, representing about 87% and 75% of the inoculum of the sandy clay soil and clay soil, respectively. Therefore, at most 25% of the pool of spores remained undetectable. The formation of artificial aggregates during the enumeration procedure could not be advocated to explain this result, since the dispersion of the fraction collected for the enumeration did not improve spore recovery. [ABSTRACT FROM AUTHOR]

Most of the C and N models published over past decades are based on parameters not always linked to the environment and underestimate the role of microorganisms. They are often over-parameterized, which can give multiple solutions for flow calculations between state variables. This work proposes a modelling method centred on the functioning of living organisms in order to calculate flow parameters using data on N stocks in decomposers, plant organs, symbiotic microorganisms, and the soil compartments. The model was settled via a complex N fixing and intercropping system of durum wheat/faba bean compared to the cropping of pure durum wheat and pure faba bean, all in the context of organic farming invaded by weeds and weeded by hand just before flowering. To avoid perturbation of natural exchanges of C and N, no fertilizer was added from 1997 to 2011. The equation system defined for the association of any number of plants, as well as parameters previously published for C-flow calculations were used, and only a few parameters specific to N flows were added, and are discussed. The results showed the strong link between N and C in the environment. The calculations converge toward an unique set of solutions that is consistent with literature data when available. The labile organic N of microbial origin was modelled as the main potentially available stock. Living microorganisms stored about 1% of total N, which was close to the N stock in faba bean and four times more than stock in durum wheat. Inorganic N was immobilized before flowering in competition with N requirement of durum wheat roots. Net N mineralization, mainly from decomposition of faba bean roots, started too late to improve wheat production. During the cropping period, weeds accounted for losses of 20 kg N ha −1 , while the atmospheric N 2 fixation of 90 kg N ha −1 was close to the total microbial immobilization. The model associating microbial and plant flows of C and N in complex plant covers, appears as a robust tool to quantify the exchanges of the earth organisms with the soil and atmosphere. It enables to propose essential recommendations to improve as well agro-ecology as predictions of global changes of C and N stocks. [ABSTRACT FROM AUTHOR]

Soil organic carbon (SOC) balance is an important component of the terrestrial carbon (C) budget. However, effect of cropland management changes on SOC dynamics has not been recently assessed in the tropics. Studies were compiled in the tropics where SOC stocks were measured in the topsoil (0–20 or 0–30 cm depth) after the adoption of management practices that are expected to enhance SOC stocks, including tillage reduction, crop rotation, exogenous organic amendments, restitution of crop residues, mineral amendments, and combinations of these practices. Random forest regression was used to identify the determinants of SOC accumulation rates (ΔSOC) depending on the climate, soil characteristics and changes in management practices. 214 cases were identified in 48 studies in 13 different countries. The average ΔSOC was 0.41 ± 0.03 Mg C ha −1  yr −1 (significantly greater than zero), for an average experiment duration of 13.6 ± 0.6 years. Although a large part of the variability remained unexplained due to methodological bias in the studies or a lack of relevant predictors. The strongest predictors of ΔSOC were C inputs, duration of the experiments, and the management practices, whereas neither soil characteristics (soil type, clay content, and initial SOC stock) nor climate variables (mean annual temperature and rainfall, aridity index) affected ΔSOC. The SOC accumulation rates increased linearly with C inputs, and the conversion rate of C inputs to SOC was 8.2 ± 0.8%. Given the competing uses of organic matter on many tropical farms, the benefits of using changes in management practices for climate change mitigation might be overrated. As ΔSOC decreased with the duration of the experiments, ΔSOC would probably be smaller if a period of 20 years were considered, as recommended by the IPCC guidelines. The management practice with the greatest ΔSOC was diversified crop rotation. Cropping systems where diverse practices were combined resulted in higher ΔSOC than individual practices such as reduced tillage and mineral fertilization on their own. The adoption of improved management practices that increase C inputs is still relevant for meeting the challenges of food security and adaptation to climate change. [ABSTRACT FROM AUTHOR]

Organic carbon saturation in soils refers to the theoretical maximum soil organic carbon (SOC) that can be associated with and stabilized on fine silt plus clay particles (F < 20 μm). We reviewed the literature dealing with SOC distribution between soil fractions to evaluate carbon saturation for tropical soils and estimate the C storage potential of cropland. We collected 258 data points on SOC distribution between soil fractions in tropical soils from 84 sites in 27 countries. We used boundary line analysis to estimate the maximum stabilized SOC depending on soil group, clay type and land use. SOC storage potential was calculated as the SOC saturation deficit, the difference between the actual SOC content and the maximum stabilized SOC content. We found that the maximum SOC in the fine fraction of tropical soils (53 g C kg − 1 fine fraction) was lower than previous assessments of global SOC storage scale based mainly on temperate soils. The F < 20 μm fractions were closer to SOC saturation in forest soils than in croplands. The cropland had a higher soil C storage potential, but changing agricultural management practices did not fill the deficit that is calculated using the whole dataset. The deficit was much lower when it was estimated with grassland or cropland data only: this provides a more realistic estimate for SOC storage potential for croplands. The SOC content in the coarser fraction (F > 50 μm) did not depend on soil texture and significantly contributed to the total SOC, especially in sandy soils (41.3%). This is affected by changes in agricultural management practices. We concluded that, although the aim of increasing SOC stabilization originally arose from climate change mitigation strategies, it must now be more viewed as being more relevant to food security and local adaptation to climate change. [ABSTRACT FROM AUTHOR]

Soil degradation and salinization caused by inappropriate cultivation practices and high levels of saltwater intrusion are having an adverse effect on agriculture in Central Senegal. The residues of Piliostigma reticulatum , a local shrub that coexists with crops, were recently shown to increase particulate organic matter and improve soil quality and may be a promising means of alleviating the effects of salinization. This study compared the effects of inorganic fertilizer and P. reticulatum residues on microbial properties and the ability of soil to withstand salinity stress. We hypothesized that soils amended with P. reticulatum would be less affected by salinity stress than soils amended with inorganic fertilizer and control soil. Salinity stress was applied to soil from a field site that had been cultivated for 5 years under a millet/peanut crop rotation when microbial biomass, phospholipid fatty acid (PLFA) community profile, catabolic diversity, microbial activities were determined. Microbial biomass, nitrification potential and dehydrogenase activity were higher by 20%, 56% and 69% respectively in soil with the organic amendment. With salinity stress, the structure and activities of the microbial community were significantly affected. Although the biomass of actinobacteria community increased with salinity stress, there was a substantial reduction in microbial activity in all soils. The soil organically amended was, however, less affected by salinity stress than the control or inorganic fertilizer treatment. This suggests that amendment using P. reticulatum residues may improve the ability of soils to respond to saline conditions. [ABSTRACT FROM AUTHOR]

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, farmyard manure (FYM) at 10 t ha) and inorganic fertilizers 120 kg N, 52.8 kg P (NP), NP + MS, NP + 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 NP 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 NP was different than the effect on bacterial diversity since the fungal diversity was similar to that of the NP + FYM and NP + 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. [ABSTRACT FROM AUTHOR]

Soil degradation has led crop yield to decline in many Sahelian countries and is a fundamental agricultural and economical threat for local populations. In Saria, Burkina Faso, long-term experiments are being performed to find efficient soil management practices that could improve soil fertility. A randomized block experiment comprising organic amendment (unamended control, straw at 8.3 t ha−1, manure at 10 t ha−1) coupled with mineral fertilization (no urea, urea at 60 kg ha−1) was started in 1980 with a continuous sorghum ( Sorghum bicolor) cropping system. Twenty-six years after the settlement of the treatments, we compared their effects on nematode populations, community structure, and ecological indices, as well as soil physical and chemical properties at three stages of sorghum’s cropping cycle. The addition of manure led to significantly higher soil C, N, and P content and produced a higher sorghum grain yield in comparison to unamended or straw-amended soils. The number of plant-parasitic nematodes (mainly Pratylenchus and Tylenchorhynchus) was significantly higher in plots fertilized with manure in comparison to unamended or straw-amended plots. They were also significantly more abundant when urea was added. Mineral nitrogen fertilization had little impact on free-living nematodes, regardless of S. bicolor development stage, whereas organic amendment significantly raised the abundance of bacterivorous and fungivorous nematodes. Moreover, microphagous nematodes were significantly more numerous in plots amended with straw than with manure. Our results show that, on the long-term, only manure amendment seemed able both to store C and nutrients whereas both manure and straw led to greater microphagous nematode communities. [ABSTRACT FROM AUTHOR]

The effect of agricultural management practices on geochemical cycles in moderate ecosystems is by far better understood than in semiarid regions, where fertilizer availability and climatic conditions are less favorable. We studied the impact of different fertilizer regimens in an agricultural long-term observatory in Burkina Faso at three different plant development stages (early leaf development, flowering, and senescence) of sorghum cultivars. Using real-time PCR, we investigated functional microbial communities involved in key processes of the nitrogen cycle (nitrogen fixation, ammonia oxidation, and denitrification) in the rhizosphere. The results indicate that fertilizer treatments and plant development stages combined with environmental factors affected the abundance of the targeted functional genes in the rhizosphere. While nitrogen-fixing populations dominated the investigated communities when organic fertilizers (manure and straw) were applied, their numbers were comparatively reduced in urea-treated plots. In contrast, ammonia-oxidizing bacteria (AOB) increased not only in absolute numbers but also in relation to the other bacterial groups investigated in the urea-amended plots. Ammonia-oxidizing archaea exhibited higher numbers compared to AOB independent of fertilizer application. Similarly, denitrifiers were also more abundant in the urea-treated plots. Our data imply as well that, more than in moderate regions, water availability might shape microbial communities in the rhizosphere, since low gene abundance data were obtained for all tested genes at the flowering stage, when water availability was very limited. [ABSTRACT FROM AUTHOR]

Acacia holosericea seedlings were planted in 1-l pots filled with a soil collected from an Australian Acacia plantation in Southern Senegal. After 6 months of culture, mycorrhizosphere soil, roots, galls induced by root-knot nematodes and Rhizobium nodules were sampled from each pot. The diversity of this bacterial group was characterized by siderotyping (pyoverdine IsoElectric Focusing (IEF) analysis) and by restriction fragment length polymorphism (RFLP). The effect of these isolates on the establishment of the ectomycorrhizal symbiosis between an Australian Acacia (A. holosericea) and Pisolithus sp. strain IR100 was studied. In the mycorrhizosphere soil, the population of fluorescent pseudomonads was represented by strains of two different siderovars (groups of bacterial strains presenting an identical pyoverdine–IEF pattern): siderovar 1 (74%) and siderovar 2 (26%). The siderotyping of the isolates around galls of the root-knot nematodes revealed three siderovars (40% from siderovar 1, 40% from siderovar 2 and about 15% from siderovar 3). RFLP of 16S rDNA divided the isolates into four different groups with MspI, two with HhaI and two with HaeIII endonucleases. The establishment of the ectomycorrhizal symbiosis with A. holosericea was promoted by 14 bacterial strains isolated from the mycorrhizosphere soil, three isolates from the roots and four from the galls. Shoot biomass of A. holosericea seedlings was stimulated by eight bacterial isolates from soil, six isolates from galls and seven from roots. These mycorrhiza helper bacteria could have a great ecological importance in tropical areas through the reforestation programs. [Copyright &y& Elsevier]

Organic matter (OM) is both a commodity and a means of production in low-input farming systems of sub-Saharan Africa. Since this resource is becoming increasingly scarce in West African savannas (WAS), there is a need to assess OM, carbon (C), nitrogen (N), and phosphorus (P) allocation in local ecosystems related to land management. Carbon, N and P storage under semi-permanent cultivation in savannas in southern Senegal was thus measured through a chronosequence including 25 groundnut (Arachis hypogaea L.) crops and plots left to fallow for 1–26 years. The amounts of C, N and P in cropped plots were 5.5 t C, 106 kg N and 5.9 kg P ha−1, they increased to 17.7 t C, 231 kg N and 19.6 kg P ha−1 in fallow plots aged 1–9 years. A threshold was reached after 10 years of fallow. Beyond it biomass amounts remained steady. Older fallow plots stored 29 t C, 333 kg N and 33.8 kg P ha−1. Highest increases in woody components were found within the very first year following crop abandonment, and were achieved at the expense of the herbaceous layer. Carbon and nutrient allocation to woody below-ground biomass occurred only later. Massive nutrient losses were expected to occur at clearing due to both burning and wood exportation. Because storage in woody and herbaceous biomass remained steady in fallows aged more then 10 years, young fallows were found to have the highest productivity for wood and forage. However, plant productivity relied on the high resprouting capacity of local tree species, and thus on the maintenance of long breaks of fallow needed for the maintenance of perennial rooting systems. One of the aims of programs to improve the management of fallows, or to replace them with agroforestry techniques, should thus be to preserve perennial rooting systems by any means that are possible in the cropping systems of the WAS. [Copyright &y& Elsevier]