Abstract – The objective of this work was to evaluate the effect of croppingsystems and crops cultivated previously to common beans (Phaseolus vulgaris L.) on soildensity and soil populations of Rhizoctonia spp. and Fusarium spp. Previouscrops included the following legumes: Cajanus cajan, Stylosanthes guianensis cv. Mineirão and Crotalaria spectabilis; and the following grasses: Pennisetum glaucum ( cv. BN-2, millet), Sorghum bicolor (cv. BR 304), Panicum maximum cv. Mombaça, Brachiaria brizantha cv. Marandu and a consortium of corn (Zea mays) and B. brizantha. Previouscrops were planted in Brazil summer seasons (wet) of 2002, 2003 e 2004, and bean crop (cv. BRS Valente) was planted in the correspondent subsequent winters (dry) of 2003, 2004 and 2005, irrigated by central pivot. Crop residues were incorporated to the soil, in conventional tillage, and kept on the surface, in no tillage management. In general, soil populations of Fusarium spp. and Rhizoctonia spp. were higher in no tillage cropping system. Higher populations of Rhizoctonia spp. were found in heavier soils. Legume crop residue increased soil populations of Rhizoctonia spp. and Fusarium spp. and, therefore, Leguminosae should be avoided as previouscrops to common beans, in both cultivation systems. Generally, Gramineae previouscrops are supressive to soil populations of Rhizoctonia spp. and Fusarium spp. Index terms: Fusarium, Rhizoctonia, soil fungi, conventional cropping, zero tillage, root rot.
provide an op- portunity to manage soil-bornepathogens in the field following their incorporation into moist soil. Results from our bioassays also showed that wetted residues of Caliente 166 and Nemfix killed sclerotia of S. minor more ef- fectively on contact with the pathogen, than when the pathogen was only exposed to volatiles from the residues. This may suggest that other non-volatile allelochemicals from biofumigant crops also contribute to pathogen suppression (e.g. nitriles , but further research would be needed to determine and characterise these com- pounds. Further work is also required to determine the agronomic requirements and biofumigation potential of the Brassica crops tested in this study for reducing soil-borne pests and pathogens in vegetable croppingsystems. This can be achieved by evaluating Brassica green manure crops with different levels of 2-propenyl GLS in ro- tation with vegetables during cool weather to precede spring and summer vegetables. Plants from the cultivars tested in this study have a range of other GSLs that have been shown to offer other potential benefits for vegeta- ble crops. For instance, the fodder radish Addagio (R. sativus) is a useful nematode resistant cover-crop. Field trials should therefore also evaluate other soil benefits associated with the use of biofumigant crops in vegetable rotations, including increases in organic matter and beneficial soil micro-organisms.
Because the plots at all locations are chisel-plowed annually to a depth of approximately 30 cm, the long-term N rate was not expected to influence bulk density in the surface soil. This assumption was corroborated at one location by previous research [ 10 ]. Accordingly, we used bulk density measurements taken from each cropping system within each block to scale SOC to a mass per area basis for the 0–15 cm depth. Rates of change in SOC and the C/N ratio were calculated for each individual treatment plot by first calculating the difference in surface SOC or C/N ratio between sampling times and then dividing this difference by the number of years between sampling times. Although historical sampling practices restricted our analysis of SOC to the surface 15 cm, changes observed in surface SOC may be representative of changes occur- ring at greater depths. An analysis of long-term SOC change data from regional agricultural studies showed that change in surface SOC was positively correlated with change in total soil profile SOC ( S1 Fig ).
In recent years, an increasing body of knowledge showed that the introduction of trees into temperate croplands and pasturelands such as occurs with the implementation of agroforestry practices, improves C sequestration both in above ground biomass and in the soil (Haile et al 2010). Nair et al. (2010) showed that tree-based agricultural systems, compared to treeless systems, stored more C in deeper soil layers near the tree than away from the tree, and higher soil organic C content was associated with higher species richness and tree density. In addition trees have also other added values, providing shade and shelter for workers and livestock, and combat wind and water erosion processes (Eichorn et al., 2006). Therefore, it is important to quantify the strength and longevity of the C sink in tree-based pasture systems to understand the mechanisms and processes associated with C transformation and storage. SOM has a very complex and heterogeneous composition, and is associated with mineral soil constituents to form soil aggregates (Haile et al 2010). The nature and extent of turnover of soil organic carbon (SOC) is intimately linked to organic matter size fractions as well as to soil structure and extent of aggregation (Martens, 2000). Different pools of SOC have different residence times, ranging from labile to stable forms, different effects on soil quality and respond differently to management practices (Chan, 2001)
Yield decline of oilseed rape (OSR) is a complex and multifaceted problem, with many contributing components. This is further compounded by soil-bornepathogens which are becoming an increasing concern, with shortened and species poor rotations implicated in their increase in recent decades. As a consequence, this thesis aimed to utilise molecular techniques to observe for pathogenic species within commercial crops of OSR, relating their occurrence to possible agronomic factors, whilst elucidating their role in yield decline through glasshouse experiments. Chapter 3 utilised real-time PCR (qPCR) to examine the occurrence of Rhizoctonia solani, Pythium ultimum and Gibellulopsis nigrescens. However this proved difficult as many of the assays available were not well designed or validated. Instead high throughput sequencing was utilised in Chapter 4 to examine the fungal communities within OSR roots, aiming to elucidate any pathogenic species present, along with their relation to potential agronomic factors. From this it was found that fungal communities were relatively simple, comprising of a few main phyla, genera and species; although this varied drastically with analysis technique used. Similarly, no relationship was observed between these species and the agronomic factors associated with the samples. However, both techniques used suggested that R. solani was a prominent pathogen within all of the samples, and as such warranted further study. Rhizoctonia solani is a diverse and variable pathogen comprising of 13 known sub-groups or anastomosis groups (AG), with Chapter 5 aiming to characterise these utilising AG specific qPCR assays. From this it was found that AG 2-1 was the main AG present within the samples, followed by AG 8 and 5. This was also confirmed by pathogenicity testing of UK isolates in chapter 6, where only AG 2-1 caused significant disease on OSR seedlings. Glasshouse experiments examined the role of pathogen inoculum in causing disease, and to clarify the mechanism by which yield loss occurred. Whilst the results varied between experiments as a consequence of inoculum preparation, they suggested that no sub-clinical disease symptoms occurred at the doses tested. In addition to this, the mechanism of yield loss appeared to be restricted to pre- and post-emergence damping off of seedlings which impacted on plant emergence and stand evenness. Further experiments in Chapter 6 examined the variability in a collection of UK isolates comprising primarily of AG 2-1 and other OSR non-pathogenic AG. Utilising an in vitro pathogenicity test it was found that AG 2-1 resulted in the most severe disease followed by AG 8 and 4 further supporting the qPCR results in Chapter 5 and the literature; although this was limited by the number of isolates. Interestingly, variation also existed within the AG 2-1 isolates with some being non-pathogenic in this system.
Soil ecologists have long studied the beneficial con- tributions of microbial communities, as opposed to in- dividual species, within the soil substrate and the plant rhizosphere. When microbial diversity is high, the over- all soil health is regarded as good (Hillel 2007 ). Ap- proaching the soil-borne pathogen complex by redirecting the focus on communities rather than a single species has improved our understanding of associations between soil edaphic properties, the recovery of certain pathogenic microbial communities and disease inci- dence. Previous research has indicated that host resis- tance to a single pathogen identified in one site may not be effective across geography or environments (Abdullah et al. 2017 ; Hamon et al. 2011 ). In France, quantitative trait loci for resistance were determined to be effective, but when these resistant lines were planted in U.S. they were not resistant to the native A. euteiches population (Hamon et al. 2011 ). The authors concluded that the combination of a differing A. euteiches popula- tion and the presence of other soil microorganisms, mainly Fusarium spp., explained the site-specific resis- tance. To develop genetic resistance effective across environments, it is necessary to develop and optimize previously developed screening systems by incorporat- ing interactions among multiple organisms within a community (Abdullah et al. 2017 ). While single organ- isms in screening methods produce valuable results, identifying the soil-borne pathogen communities
Soil survey information related to the Central Altiplano region of Bolivia is limited and this lack of information is a critical problem for resource management. Some important information about the soils of this region includes publications by Clapperton (1993) and Blodgett et al. (1997). These publications indicate that during the Quaternary Period, there was a vast high lake stage of the Titicaca Lake called Ballivian Lake that covered what is now the Altiplano in the Andes Mountains of South America. The fact that the highland Andean was once an ocean floor made this region to be subject to high salt accumulation during bedrock formation, and the current soil salinity of some areas of the Altiplano is a function of the high concentrations of salts in soil parent materials (Jetté et al., 2001). According to Ruthsatz and Fiseln (1984) mentioned by Jetté et al. (2001), the mountain slopes of the Andean Cordilleras are sheltered by unweathered rock, the foothills at the bottom are still covered with fresh rock, and in the downslope there are alluvian fans, small plateaus and central plains. The soil textural gradient in this highland region ranges from sandy-silty to clay-silty and heavy clay, and there are also sandy soils resulting from eolian deposition which apparently has contributed to stabilize sand dunes over the Altiplano.
Soil extracts were prepared by placing 200 g m . of soil in a flask with 1.5 1. of glass distilled water, thoroughly mixing and then allowing it to incubate at 25°C. for 24 h. The super natant in each flask was filtered under suction through Whatman No. 1 filter paper.
vegetation as reference. In 2005, 60 days after cutting the cover crops, BRS Valente bean cultivar, under irrigation, was cultivated. Sowing was performed on June 16, 2005 and the harvest on September 19, 2005. Soil samples were collected to a depth of 0–10 cm, in November 2004 (before cover crops planting), June 2005 (before dry bean planting) and July 2005 (at dry bean flowering). Evaluations of basal respiration, carbon and nitrogen of microbial biomass, microbial/organic carbon ratio, microbial/total nitrogen ratio and metabolic quotient were performed. Soil biological attributes were influenced by cover crops, soil management and sampling time. Index terms: microbial biomass carbon, microbial biomass nitrogen, basal respiration, metabolic quotient, microbial quotient, cover crops.
The soil microbial biomass (SMB) indicates the ecological and biological quality and fertility of the soil, and is affected by organic/inorganic fertilizer application . The SMB is involved in soil biogeochemical processes in soil-water-plant systems  , not only driving the nutrient cycle in agro-ecosystems, but also playing a vital role in soil nutrient transformations and acting as a labile nutrient pool that is available to plants  . Several studies have emphasized the effects of organic manures such as soil organic carbon (SOC) on soil physicochemical properties. However, SOC may take a very long time to increase   and ob- servation of SOC changes alone may not explain the effect of organic matter on nutrient availability via microbiological activities. Alternatively, soil microbial biomass, which measures changes in both SOC and total soil nitrogen (TSN), can be used as a management indicator for soil fertility and crop productivity . However, the effects of the various influencing factors, such as climatic and edaphic factors, fertilizer use, and crop establishment practices, on SMB are dif- ficult to quantify due to their interactions; and estimation of the spatial and temporal distribution of SMB on the basis of limited field observations are even more difficult  .
Little is known about how croppingsystems influence soil quality and fertility in Uganda. Some croppingsystems are more valued and as a result are given more nutrients and planted in certain soils, all of which leads to varying soil quality and fertility. This study compared soil quality (soil pH, cation exchange capacity (CEC), electric conductivity (EC), total N, and depth to restrictive layer (DRL)) and fertility (extractable P, K, Ca, Mg, and Na, and base saturation (BS) from five croppingsystems (banana (Musa × paradisiaca L.)- dominant (B), coffee [Coffea robusta (L.) Linden]-dominant (C), banana-coffee (BC), annual with no crop rotation (ANR), and annual with crop rotation (AR); fertilized and unfertilized soils; and three soil types (black (Phaeozem), red (Ferralsol), and black-stony) in south-central Uganda. The analysis included farm assessments to establish management history of studied fields and soil sampling from 52 fields in Masaka District, Uganda. Main-effects ANOVA was employed to determine differences in means in soil under different croppingsystems, soil types, and fertilizer use. Soil quality (pH at depths of 0 to 10 and 20 to 30 cm, CEC, and EC) and fertility (extractable Ca and Mg) varied by cropping system. The AR and B systems had higher soil quality and fertility compared to other croppingsystems. Soil quality (pH at depths of 0 to 10 and 0 to 15 cm and DRL) and soil fertility (extractable P and K) varied by soil type. Black and black-stony soils had higher soil quality and fertility than red soils. Soil quality and fertility did not vary by fertilizer use. The results of this study indicate that both cropping system and soil type are associated with soil quality and fertility in south-central Uganda.
In this study we examined the impact on soil C, total soil N and available P of six rotations namely: long season tobacco cultivar „KM10‟ grown continuously (ContKM10), medium season tobacco cultivar „RK8‟ grown continuously (ContRK8), grass-grass-grass-KM10 (G-G-G-KM10), grass-grass-grass- RK8 (G-G-G-RK8), KM10-Crotalaria juncea (KM10-Cr) and RK8-Crotalaria juncea (RK8-Cr). The experiment was established in 1990 under irrigation on a sandy loam soil at Kutsaga Research Station, Zimbabwe. Soil samples were taken from 0- to 15-cm deep, after each season. After 9 years, tobacco-grass rotations showed higher soil C than monocropping, regardless of variety. The monocropping systems, ContKM10 and ContRK8, did not differ from KM10- Cr and RK8-Cr respectively showing that when crop intensity is maintained soil C will be reduced regardless of a winter C. juncea green manure in a sandy loam soil. After 9 years, soil N was greatest in the G-G-G-KM10 rotation. Available P was lower in the grass (G-G-G-KM10, G-G-G-RK8) relative to the other rotations regardless of variety. Available P accumulated in monocropping systems (ContRK8, ContKM10) and was consistently lower in the grass-tobacco rotations. This indicated an accumulation of P in the case of monocropping systems because of continuous inorganic fertiliser input. The results reaffirmed the deleterious effect of monocropping and suggested the need for diverse rotations.
seeding conditions in the ﬁrst year, bad weather conditions in spring of year 2014, and to the succession of wheat cultivation in general. Wheat grain yield showed high response to tillage and cover crop treatments. Interestingly, in this experiment, the highest yield was observed in the minimum tillage treatment which presented yield systematically higher than in the plough treatment. The no till treatment was clearly un- successful as a whole. However, the ﬁeld pea treatment in the no till treatment allowed to reach wheat yield similar to those observed in the other tillage treatments, and, in particular, higher than in the classical plough – no cover crop control treatment. So, the presence of a good soil cover before wheat cultivation, even for a short period (only two months here) allowed to alleviate the detrimental e ﬀ ects of tillage re- duction. In tilled treatments, the positive e ﬀ ect of cover crop cultivation was less pronounced, though visible when looking at the whole three year period. This agrees with other studies showing a more important role of cover crops with reduction of tillage intensity (Abdollahi and Munkholm, 2014; Wittwer et al., 2017). Many factors can explain the beneﬁcial eﬀect of cover crops for the next crop; among these are the reduction of weed pressure, improvement of soil fertility and soil quality, and nutrient release during decomposition (Abdollahi and Munkholm, 2014; Fageria et al., 2005; Mat Hassan et al., 2013; Thorup- Kristensen et al., 2003). These di ﬀ erent mechanisms are di ﬃ cult to disentangle, and can also all be present together and interact. When looking at the correlation between wheat yield and cover crop char- acteristics, di ﬀ erences between years appeared. The ﬁ rst and second years, when cover crop growth was really low, wheat yield was corre- lated with cover crop biomass and soil cover, though it was signiﬁcant only for no till in the ﬁ rst year. The third year, when all cover crop grew reasonably well
As fast-growing microbes are less efﬁcient at substrate use than slow-growing ones, the average microbial biomass of fast-growing bacteria, such as Alpha- and Gamma- proteobacteria, tends to be smaller (33), Therefore, a shift from oligotrophs to copi- otrophs effectively reduces total microbial biomass. We consistently found that NPK fertilization decreased bacterial and fungal biomass in the Mollisol (see Table S1 in the supplemental material). In addition, our sequencing results differed from a recent study that microbial communities across global-scale grasslands revealed consistent re- sponses to N and P fertilization (25). A close examination showed that soil samples in the study of Leff et al. (25) had a narrow pH range (mostly between 5.1 and 6.7) and only slight soil acidiﬁcation by fertilization, which resulted in no correlation between soil pH and any of the major bacterial taxa. In contrast, soil pH spanned a large range from 4.9 to 8.1 in our study (Table S1). Many studies have attributed the effect of inorganic nitrogen fertilization on soil microbes to soil acidiﬁcation (18, 39). For example, addition of ammonium sulfate led to soil acidiﬁcation and an almost 10-fold decrease of a dominant bacterial phylum in an Inceptisol (18). In this study, NPK fertilization decreased the soil pH by 0.4 and 0.1 unit in the Mollisol and Ultisol, respectively, which was consistent with previous studies showing that nitrogen fertil- ization led to soil acidiﬁcation (24, 40). Thus, soil pH might be the main factor causing shifts in the microbial communities in these two soil types, which was conﬁrmed by the Mantel tests showing positive correlations between bacterial communities and soil pH (r ⬎ 0.34; P ⬍ 0.050) (Table 1). In contrast, when soil pH decreased from 8.1 to 7.7 in the Inceptisol (Table S1), no signiﬁcant correlation between soil pH and bacterial community (r ⫽ 0.16; P ⫽ 0.68) was detected (Table 1), verifying that a shift to neutral pH was inconsequential for most bacteria (41, 42). In addition, fungal communities were less sensitive to soil pH than bacterial communities, owing to their wider growth tolerances to pH range (43, 44). Accordingly, no signiﬁcant correlation between pH and fungal communities was detected in any soil type (Table 1).
DTPA-extractable Cu in soil (fig.2). The chelating agent DTPA has been widely used for the diagnosis of plant availability of the metals in soil at regular or even higher concentration (Singh et al., 1998). In most cases, the DTPA-extractable Cu (DTPA-Cu) was found to be correlated with the Cu concentration in crops (Obrador et al., 1997; Fuentes et al., 2004; Cattani et al., 2006). On the other in relation with copper, DOC is an important factor, because copper has a strong tendency to form complexes with organic matter and copper is known to form strong bonds with soil organic matter. This suggests that crop residues application cause increasing the organic compounds into the soil and increased copper and manganese complexation with organic matter in the soil and resulting could be to cause increasing phytoavailability of them in the soil. Therefore, Trifolium residues application decreased the amount of soil pH and consequent increase of The concentration of DOC which in turn elevated the concentrations of DTPA- extractable Cu. Trifolium was the most effective in increasing the
Microorganisms represent the countless and metabolically complex life forms in the soil. On a per gram soil basis, it is estimated that there are at least one billion bacteria, a million fungi, millions of protozoa, thousands to millions of algae and several dozen nematodes present (1). The microbiome is an integral part of almost all soil processes (21). Soil microorganisms producing extracellular enzymes are responsible for the biotransformation that provides the nutrients to plants and for maintaining the soil function (22). Soil microbial communities are particularly important to the support of ecosystems around the world, impacting nutrient cycling (22, 23), carbon cycling (24, 25), suppression of diseases (17) and enrichment and conservation of soil organic matter (SOM) (24, 26, 27). Furthermore, microbial diversity and composition are the main factors that ensure the maintenance of ecological functions (28-30). In this way, elucidating the causes and controls of the soil microbial community’s distribution and composition are necessary to reach a better understanding of sustainable agriculture (31, 32). Since soil microbiome plays a critical role in the improvement of soil from
Reasons for the increasing weed population in those croppingsystems are the stay of weed seeds in soil layers from which they can emergence and furthermore the absence of alternating growth conditions which preserves the repeated propagation of weed species with a well adapted life cycle to the occurring agronomic practice (Benvenuti et al., 2001; Liebman and Dyck, 1993). To control the increasing weed population frequent application of herbicides during vegetation of the cash crop but also during fallow periods are necessary to prevent weeds from seed dispersal (Ghosheh and Al-Hajaj, 2005). Especially the seed dispersal of weeds during fallow periods increases the weed seedbank and results in higher weed emergence in the following years (Cardina et al., 2002; Mulugeta and Stoltenberg, 1997). Even if fallow periods are too short for seed dispersion or if reduced weed growth occurs like in winter months, the application of a burn down herbicide is common practice prior seeding of the following cash crop, especially in croppingsystems with reduced tillage. Reason therefore is the fact that most herbicides are not able to control mature weeds without damaging growth or yield formation of the crop. However, also with a frequently application of herbicides, weed density is still high in such agricultural systems. Furthermore, an increased development of herbicide resistances can be observed due to the repeated application of herbicides with identical mode of action (Chauvel et al., 2009; Price et al., 2011). To avoid or at least reduce these problems of conservation tillage and low cash crop diversity, cultivation of cover crops and undersown crops can can be a possible solution to increase the sustainability of those croppingsystems.
Impact of competition according to pathogen infection
The competitive environment did not modify the effects of pathogens on seedling performance, contrary to the third hypothesis of the study. Similar positive effects of fungicide on performance of Q. suber seedlings were found under the three competition treatments. Also contrary to the third hypothesis, Q. suber was a stronger competitor than O. europaea regardless of the soil type and its pathogen abundance. Even without fungicide on defoliated soil, where pathogen abundance appeared to be highest, Q. suber showed more than twice as fast growth than O. europaea, which was significantly affected by interspecific competition. These results reveal that reduced seedling performance of Q. suber as a consequence of pathogen infection is not additive with effects caused by competition and therefore, does not change the natural occurring competition pattern. Studies about the competition of Q. suber and O. europaea are commonly rare. However, in this experiment Q. suber showed rapid growth resulting in superior competitive strength over slow growing O. europaea and strong intraspecific competition with conspecific oak seedlings. These competition patterns are typical for strong competitors and highly important to maintain the coexistence of both species (Connell 1983). Even if performance of Q. suber is clearly affected by soil-bornepathogens, its competitive ability still had a negative effect on O. europaea, indicating that the species coexistence of young Q. suber and O. europaea seedlings stays unaffected by soil-bornepathogens present in declining Q. suber forests.
sure the high target yield, while reducing the soil NO 3 – -N accumulation and leaching (Ercoli et al. 2013). NO 3 – -N leaching could be further reduced by optimized irrigation management (Gheysari et al. 2009). Furthermore, the optimizations of other comprehensive agronomic measures, such as tillage and straw managements, are important options to improve the N utilization by crops and to reduce the soil NO 3 – -N accumulation and leaching (Beaudoin et al. 2005). Most recent stud- ies that address soil NO 3 – -N leaching in the NCP focus on only one or two factors (Fang et al. 2006, Wang et al. 2010). Research studies that investi- gate multiple factors and their relative impacts are few. It is suggested that current conventional intensive agriculture can be improved by an inte- grated approach, which includes optimization of N fertilization, irrigation regime, tillage method and straw management to maintain high requisite yields while reducing N fertilizer, irrigation water and minimizing NO 3 – -N leaching and subsequent groundwater contamination.
This study revealed profound but contrasting e ﬀ ects of di ﬀ erent agricultural management systems, and in particular the role of plants, on soil structure over the long-term and in the context of two soil textures. For both soil textures, perennial and annual plants (associated with organic input for the sandy soil) increased the diversity of pore sizes. In contrast, the eﬀect of plants on porosity and pore connectivity was markedly di ﬀ erent between the two soil textures: for clay soil, plants increased the porosity and the connectivity of the pore system, whereas for sandy soil, plants decreased the porosity and the pore connectivity. Hence the hypothesis that the presence of plants increases porosity requires quali ﬁ cation since plants contributed to soil porosity only in the presence of clay: for sandy soil, the presence of plants re- duced porosity and connectivity. Our results conﬁrmed the hypothesis that perennial plants invoked greater structural heterogeneity, manifest as a wider range of pore sizes. This study also showed that addition of manure to arable soil had essentially the same eﬀect as continual per- ennial plants on the maintenance of the soil structure. Incorporation of organic matter (such as root, organic carbon) can be considered as an agent which assists soil structure to reorganise from the tillage by in- creasing the diversity of the pore sizes and decreasing porosity. Diﬀerent crop/management systems create diﬀerent kinds of soil structure, and for each there are a range of consequences depending on the function under consideration.