Availability of a soluble phosphorus source applied to soil samples with different acidicity levels

Considerations on the interactions of P in the soil-plant system have a long history, but are still topical and not yet satisfactorily understood. One concern is the effect of liming before or after application of soluble sources on the crop yield and efficiency of available P under these conditions. The aim of this study was to evaluate the effect of soil acidity on availability of P from a soluble source, based on plant growth and chemical extractants. Nine soil samples were incubated with a dose of 200 mg kg-1 P in soil with different levels of previously adjusted acidity (pH H2O 4.5; 5.0; 5.5; 6.0 and 6.5) and compared to soils without P application. After 40 days of soil incubation with a P source, each treatment was limed again so that all pH values were adjusted to 6.5 and then sorghum was planted. After the first and second liming the P levels were determined by the extractants Mehlich-1, Bray-1 and Resin, and the fractionated inorganic P forms. In general, the different acidity levels did not influence the P availability measured by plant growth and P uptake at the studied P dose. For some soils however these values increased or decreased according to the initial soil pH (from 4.5 to 6.5). Plant growth, P uptake and P extractable by Mehlich-1 and Bray-1 were significantly correlated, unlike resin-extractable P, at pH values raised to 6.5. These latter correlations were however significant before the second liming. The P contents extracted by Mehlich-1 and Bray-1 were significantly correlated with each other in the entire test range of soil acidity, even after adjusting pH to 6.5, besides depending on the soil buffering capacity for P. Resin was also sensitive to the properties that express the soil buffering capacity for P, but less clearly than Mehlich-1 and Bray-1. The application of triple superphosphate tended to increase the levels of P-Al, P-Fe and P-Ca and the highest P levels extracted by Bray-1 were due to a higher occurrence of P-Al and P-Fe in the soils.

Liming influence on soil chemical properties, nutritional status and yield of alfalfa grown in acid soil

Alfalfa is an important forage crop with high nutritive value, although highly susceptible to soil acidity. Liming is one of the most efficient and prevailing practices to correct soil acidity and improve alfalfa yield. The objective of this study was to evaluate response to liming of alfalfa grown in a greenhouse on a Typic Quartzipsamment soil. The treatments consisted of four lime rates (0, 3.8, 6.6 and 10.3 Mg ha-1) and two cuts. Alfalfa dry matter increased quadratically with increasing lime rates. In general, dry matter yield was maximized by a lime rate of 8.0 Mg ha-1. Except for the control, the dry matter nutrient contents in the treatments were adequate. The positive linear correlation between root and nodule dry matter with lime rates indicated improvement of these plant traits with decreasing soil acidity. The soil acidity indices pH, base saturation, Ca2+ concentration, Mg2+ concentration, and H + Al were relevant factors in the assessment of alfalfa yield. The magnitude of influence of these soil acidity indices on yield as determined by the coefficient of determination (R²) varied and decreased in the order: base saturation, H + Al, pH, Ca and Mg concentrations. Optimum values of selected soil chemical properties were defined for maximum shoot dry matter; these values can serve as a guideline for alfalfa liming to improve the yield of this forage on acid soils.

Study of the regulation of antifungal activity in plant-associated pseudomas fluorescens

RésuméEn agriculture d'énormes pertes sont causées par des champignons telluriques pathogènes tels que Thielaviopsis, Fusarium, Gaeumannomyces et Rhizoctonia ou encore l'oomycète Pythium. Certaines bactéries dites bénéfiques, comme Pseudomonas fluorescens, ont la capacité de protéger les plantes de ces pathogènes par la colonisation de leur racines, par la production de métabolites secondaires possédants des propriétés antifongiques et par l'induction des mécanismes de défenses de la plante colonisée. P. fluorescens CHAO, une bactérie biocontrôle isolée d'un champ de tabac à Payerne, a la faculté de produire un large spectre de métabolites antifongiques, en particulier le 2,4- diacétylphloroglucinol (DAPG), la pyolutéorine (PLT), le cyanure d'hydrogène (HCN), la pyrrolnitrine (PRN) ainsi que des chélateurs de fer.La plante, par sécrétion racinaire, produit des rhizodéposites, source de carbone et d'azote, qui profitent aux populations bactériennes vivant dans la rhizosphere. De plus, certains stresses biotiques et abiotiques modifient cette sécrétion racinaire, en terme quantitatif et qualitatif. De leur côté, les bactéries bénéfiques, améliorent, de façon direct et/ou indirect, la croissance de la plante hôte. De nombreux facteurs biotiques et abiotiques sont connus pour réguler la production de métabolites secondaires chez les bactéries. Des études récentes ont démontré l'importance de la communication entre la plante et les bactéries bénéfiques afin que s'établisse une interaction profitant à chacun des deux partis. Il est ainsi vraisemblable que les populations bactériennes associées aux racines soient capables d'intégrer ces signaux et d'adapter spécifiquement leur comportement en conséquence.La première partie de ce travail de thèse a été la mise au point d'outils basés sur la cytométrie permettant de mesurer l'activité antifongique de cellules bactériennes individuelles dans un environnent naturel, les racines des plantes. Nous avons démontré, grâce à un double marquage aux protéines autofluorescentes GFP et mCherry, que les niveaux d'expression des gènes impliqués dans la biosynthèse des substances antifongiques DAPG, PLT, PRN et HCN ne sont pas les mêmes dans des milieux de cultures liquides que sur les racines de céréales. Par exemple, l'expression de pltA (impliqué dans la biosynthèse du PLT) est quasiment abolie sur les racines de blé mais atteint un niveau relativement haut in vitro. De plus cette étude a mis en avant l'influence du génotype céréalien sur l'expression du gène phlA qui est impliqué dans la biosynthèse du DAPG.Une seconde étude a révélé la communication existant entre une céréale (orge) infectée par le pathogène tellurique Pythium ultimum et P. fluorescens CHAO. Un système de partage des racines nous a permis de séparer physiquement le pathogène et la bactérie bénéfique sur la plante. Cette méthode a donné la possibilité d'évaluer l'effet systémique, causé par l'attaque du pathogène, de la plante sur la bactérie biocontrôle. En effet, l'infection par le phytopathogène modifie la concentration de certains composés phénoliques dans les exsudats racinaires stimulant ainsi l'expression de phi A chez P.fluorescens CHAO.Une troisième partie de ce travail focalise sur l'effet des amibes qui sont des micro-prédateurs présents dans la rhizosphere. Leur présence diminue l'expression des gènes impliqués dans la biosynthèse du DAPG, PLT, PRN et HCN chez P.fluorescens CHAO, ceci en culture liquide et sur des racines d'orge. De plus, des molécules provenant du surnageant d'amibes, influencent l'expression des gènes requis pour la biosynthèse de ces antifongiques. Ces résultats illustrent que les amibes et les bactéries de la rhizosphere ont développé des stratégies pour se reconnaître et adapter leur comportement.La dernière section de ce travail est consacrée à l'acide indole-acétique (LA.A), une phytohormone connue pour son effet stimulateur sur phlA. Une étude moléculaire détaillée nous a démontré que cet effet de l'IAA est notamment modulé par une pompe à efflux (FusPl) et de son régulateur transcriptionnel (MarRl). De plus, les gènes fusPl et marRl sont régulés par d'autres composés phénoliques tels que le salicylate (un signal végétal) et l'acide fusarique (une phytotoxine du pathogène Fusarium).En résumé, ce travail de thèse illustre la complexité des interactions entre les eucaryotes et procaryotes de la rhizosphère. La reconnaissance mutuelle et l'instauration d'un dialogue moléculaire entre une plante hôte et ses bactéries bénéfiques associées? sont indispensables à la survie des deux protagonistes et semblent être hautement spécifiques.SummaryIn agriculture important crop losses result from the attack of soil-borne phytopathogenic fungi, including Thielaviopsis, Fusarium, Gaeumannomyces and Rhizoctonia, as well as from the oomycete Pythium. Certain beneficial microorganisms of the rhizosphere, in particular Pseudomonas fluorescens, have the ability to protect plants against phytopathogens by the intense colonisation of roots, by the production of antifungal exoproducts, and by induction of plant host defences. P. fluorescens strain CHAO, isolated from a tobacco field near Payerne, produces a large array of antifungal exoproducts, including 2,4-diacetylphloroglucinol (DAPG), pyoluteorin (PLT), hydrogen cyanide (HCN), pyrrolnitrin (PRN) and iron chelators. Plants produce rhizodeposites via root secretion and these represent a relevant source of carbon and nitrogen for rhizosphere microorganisms. Various biotic and abiotic stresses influence the quantity and the quality of released exudates. One the other hand, beneficial bacteria directly or indirectly promote plant growth. Biotic and abiotic factors regulate exoproduct production in biocontrol microorganisms. Recent studies have highlighted the importance of communication in establishing a fine-tuned mutualist interaction between plants and their associated beneficial bacteria. Bacteria may be able to integrate rhizosphere signals and adapt subsequently their behaviour.In a first part of the thesis, we developed a new method to monitor directly antifungal activity of individual bacterial cells in a natural environment, i.e. on roots of crop plants. We were able to demonstrate, via a dual-labelling system involving green and red fluorescent proteins (GFP, mCherry) and FACS-based flow cytometry, that expression levels of biosynthetic genes for the antifungal compounds DAPG, PLT, PRN, and HCN are highly different in liquid culture and on roots of cereals. For instance, expression of pltA (involved in PLT biosynthesis) was nearly abolished on wheat roots whereas it attained a relatively high level under in vitro conditions. In addition, we established the importance of the cereal genotype in the expression of phi A (involved in DAPG biosynthesis) in P. fluorescens CHAO.A second part of this work highlighted the systemic communication that exists between biocontrol pseudomonads and plants following attack by a root pathogen. A split-root system, allowing physical separation between the soil-borne oomycete pathogen Phytium ultimum and P. fluorescens CHAO on barley roots, was set up. Root infection by the pathogen triggered a modification of the concentration of certain phenolic root exudates in the healthy root part, resulting in an induction ofphlA expression in P. fluorescens CHAO.Amoebas are micro-predators of the rhizosphere that feed notably on bacteria. In the third part of the thesis, co-habitation of Acanthamoeba castellanii with P. fluorescens CHAO in culture media and on barley roots was found to significantly reduce bacterial expression of genes involved in the biosynthesis of DAPG, PLT, HCN and PRN. Interestingly, molecular cues present in supernatant of A. castelanii induced the expression of these antifungal genes. These findings illustrate the strategies of mutual recognition developed by amoeba and rhizosphere bacteria triggering responses that allow specific adaptations of their behaviour.The last section of the work focuses on indole-3-acetic acid (IAA), a phytohormone that stimulates the expression of phi A. A detailed molecular study revealed that the IAA-mediated effect on phi A is notably modulated by an efflux pump (FusPl) and its transcriptional regulator (MarRl). Remarkably, transcription of fusPl and marRl was strongly upregulated in presence of other phenolic compounds such as salicylate (a plant signal) and fusaric acid (a phytotoxin of the pathogenic fungus Fusarium).To sum up, this work illustrates the great complexity of interactions between eukaryotes and prokaryotes taking place in the rhizosphere niche. The mutual recognition and the establishment of a molecular cross-talk between the host plant and its associated beneficial bacteria are essential for the survival of the two partners and these interactions appear to be highly specific.

Soil aggregation in a crop-livestock integration system under no-tillage

Grazing intensities can influence soil aggregation, which can be temporarily and permanently affected. The objective of this study was to evaluate the aggregate stability in water at the end of a soybean cycle and during pasture development in a crop-livestock integration system under no-tillage and grazing intensities. The experiment was initiated in 2001, in a dystrophic Red Latosol, after soybean harvest. Treatments consisted of pasture (black oat + Italian ryegrass) at heights of 10, 20 and 40 cm, grazed by young cattle, and a control (no grazing), followed by soybean cultivation, in a randomized block design. Soil samples were collected at the end of the soybean cycle (May/2007), during animal grazing (September/2007) and at the end of the grazing cycle (November/2007). The grazing period influences aggregate distribution, since in the September sampling (0-5 cm layer), there was a higher proportion of aggregates > 4.76 mm at all grazing intensities. Soil aggregation is higher in no-tillage crop-livestock integration systems in grazed than in ungrazed areas.

Irrigation with domestic wastewater: a multivariate analysis of main soil changes

Irrigation with treated domestic sewage wastewater (TSE) is an agricultural practice to reduce water requirements of agroecossystems and the nutrient load impact on freshwaters, but adverse effects on soil chemical (salinization, sodification, etc.) and soil physical properties (alteration in soil porosity and hydraulic conductivity, etc.) have been reported. This study aimed to define some relationships among these changes in an Oxisol using multivariate analysis. Corn (Zea mays L.) and sunflower (Helianthus annuus L.) were grown for two years, irrigated with TSE. The following soil properties were determined: Ca2+; Mg2+; Na+; K+ and H + Al contents, cationic exchangeable capacity (CEC), sum of bases (SB), base saturation (V), texture (sand, silt and clay), macro-, micro-, and cryptoporosity (V MA, V MI and V CRI), water content at soil saturation (θS) and at field capacity (θFC), residual water content (θR), soil bulk density (d s), water dispersed clay (WDC) and saturated hydraulic conductivity (K SAT). Factor analysis revealed the following six principal factors: Fine Porosity (composed of Na+; K+; WDC, θR, θRFC, and V CRI); Large Porosity (θS, d s, V MA, Vs); Soil CEC (Ca2+; Mg2+; CEC, SB, V); Soil Acidity (H + Al); and Soil Texture (factors 5 and 6). A dual pore structure appears clearly to the factors 1 and 2, with an apparent relationship between fine porosity and the monovalent cations Na+ and K+. The irrigation (with potable sodic tap water or sewage wastewater) only had a significant effect on Fine Porosity and Large Porosity factors, while factors 3 and 4 (Soil CEC and Soil Acidity) were correlated with soil depth. The main conclusion was a shift in pore distribution (large to fine pores) during irrigation with TSE, which induces an increase of water storage and reduces the capacity of drainage of salts.

Persistence of a biocontrol Pseudomonas inoculant as high populations of culturable and non-culturable cells in 200-cm-deep soil profiles

Little is known about the ecology of soil inoculants used for pathogen biocontrol, biofertilization and bioremediation under field conditions. We investigated the persistence and the physiological states of soil-inoculated Pseudomonas protegens (previously Pseudomonas fluorescens) CHA0 (108 CFU g−1 surface soil) in different soil microbial habitats in a planted ley (Medicago sativa L.) and an uncovered field plot. At 72 days, colony counts of the inoculant were low in surface soil (uncovered plot) and earthworm guts (ley plot), whereas soil above the plow pan (uncovered plot), and the rhizosphere and worm burrows present until 1.2 m depth (ley plot) were survival hot spots (105-106 CFU g−1 soil). Interestingly, strain CHA0 was also detected in the subsoil of both plots, at 102-105 CFU g−1 soil between 1.8 and 2 m depth. However, non-cultured CHA0 cells were also evidenced based on immunofluorescence microscopy. Kogure's direct viable counts of nutrient-responsive cells showed that many more CHA0 cells were in a viable but non-culturable (VBNC) or a non-responsive (dormant) state than in a culturable state, and the proportion of cells in those non-cultured states depended on soil microbial habitat. At the most, cells in a VBNC state amounted to 34% (above the plow pan) and those in a dormant state to 89% (in bulk soil between 0.6 and 2 m) of all CHA0 cells. The results indicate that field-released Pseudomonas inoculants may persist at high cell numbers, even in deeper soil layers, and display a combination of different physiological states whose prevalence fluctuates according to soil microbial habitats.

Influence of litter layer removal on the soil thermal regime of a pine forest in a mediterranean climate

The removal of the litter layer in Portuguese pine forests would reduce fire hazard, but on the other hand this practice would influence the thermal regime of the soil, hence affecting soil biological activity, litter decomposition and nutrient dynamics. Temperature profiles of a sandy soil (Haplic Podzol) under a pine forest were measured with thermocouples at depths to 16 cm, with and without litter layer. The litter layer acted as a thermal insulator, reducing the amplitude of the periodic temperature variation in the mineral soil underneath and increasing damping depths, particularly at low soil water contents. At the mineral soil surface the reduction of amplitudes was about 2.5 ºC in the annual cycle and 5 to 6.7 ºC in the daily cycle, depending on the soil water content. When soil was both cold and wet, mean daily soil temperatures were higher (about 1 - 1.5 ºC) under the litter layer. Improved soil thermal conditions under the litter layer recommend its retention as a forest management practice to follow in general.

Redox index of soil carbon stability

As an alternative to the relatively complex and expensive spectroscopic methods, the redox properties of humic acids, determined by potentiometric titrations, have been used to evaluate the stability of soil organic C. The objective of the present study was to establish a Redox Index of C Stability (RICS) and to correlate it with some properties of the humic acids extracted from different modal soils in Brazil (distinct weathering stages or management) to facilitate system comparison. The RICS was efficient for soil comparison and variations were comparable to those of the chemical and spectroscopic methods used for humic acid characterization. The values of soil pH, point of zero salt effect, sum of bases, exchangeable Ca content, weathering index, as well as the humic acid O/C ratio, quinone and semiquinone free radical contents, aromatic C and fluorescence intensity were closely related with the RICS. The RICS was higher in less weathered soils, with more active clays and higher fertility. The RICS values of soils under long-term sugarcane management were ranked in decreasing order: unburned, burned with vinasse, burned without vinasse.

Enzymatic activity and mineralization of carbon and nitrogen in soil cultivated with coffee and green manures

There are great concerns about degradation of agricultural soils. It has been suggested that cultivating different plant species intercropped with coffee plants can increase microbial diversity and enhance soil sustainability. The objective of this study was to evaluate enzyme activity (urease, arylsulfatase and phosphatase) and alterations in C and N mineralization rates as related to different legume cover crops planted between rows of coffee plants. Soil samples were collected in a field experiment conducted for 10 years in a sandy soil in the North of Paraná State, Brazil. Samples were collected from the 0-10 cm layer, both from under the tree canopy and in-between rows in the following treatments: control, Leucaena leucocephala, Crotalaria spectabilis, Crotalaria breviflora, Mucuna pruriens, Mucuna deeringiana, Arachis hypogaea and Vigna unguiculata. The soil was sampled in four stages of legume cover crops: pre-planting (September), after planting (November), flowering stage (February) and after plant residue incorporation (April), from 1997 to 1999. The green manure species influenced soil enzyme activity (urease, arylsulfatase and phosphatase) and C and N mineralization rates, both under the tree canopy and in-between rows. Cultivation of Leucaena leucocephala increased acid phosphatase and arilsulfatase activity and C and N mineralization both under the tree canopy and in-between rows. Intercropped L. leucocephala increased urease activity under the tree canopy while C. breviflora increased urease activity in-between rows.

Identification of opsA, a gene involved in solute stress mitigation and survival in soil, in the polycyclic aromatic hydrocarbon-degrading bacterium Novosphingobium sp. strain LH128.

The aim of this study was to identify genes involved in solute and matric stress mitigation in the polycyclic aromatic hydrocarbon (PAH)-degrading Novosphingobium sp. strain LH128. The genes were identified using plasposon mutagenesis and by selection of mutants that showed impaired growth in a medium containing 450 mM NaCl as a solute stress or 10% (wt/vol) polyethylene glycol (PEG) 6000 as a matric stress. Eleven and 14 mutants showed growth impairment when exposed to solute and matric stresses, respectively. The disrupted sequences were mapped on a draft genome sequence of strain LH128, and the corresponding gene functions were predicted. None of them were shared between solute and matric stress-impacted mutants. One NaCl-affected mutant (i.e., NA7E1) with a disruption in a gene encoding a putative outer membrane protein (OpsA) was susceptible to lower NaCl concentrations than the other mutants. The growth of NA7E1 was impacted by other ions and nonionic solutes and by sodium dodecyl sulfate (SDS), suggesting that opsA is involved in osmotic stress mitigation and/or outer membrane stability in strain LH128. NA7E1 was also the only mutant that showed reduced growth and less-efficient phenanthrene degradation in soil compared to the wild type. Moreover, the survival of NA7E1 in soil decreased significantly when the moisture content was decreased but was unaffected when soluble solutes from sandy soil were removed by washing. opsA appears to be important for the survival of strain LH128 in soil, especially in the case of reduced moisture content, probably by mitigating the effects of solute stress and retaining membrane stability.

Soil structure transformations from ferralic to nitic horizons on a toposequence in southeastern Brazil

The soil structure transformation from ferralic to nitic horizons was studied in a toposequence on quaternary red clayey sediments and diabase in Piracicaba (SP), Brazil. Morphological and micromorphological studies, image analysis, soil water characteristic curves and monitoring of (total) soil water potential head were used. The presence of polyconcave vughs, clayskins and planar voids shows that the vertical and lateral transition and structural transformation from ferralic to nitic horizons is given by the coalescence of the microaggregates, probably due to tensions created in a drier period in the past. Changes to a more humid climate with a defined dry season and alternate drying and wetting cycles resulted in the fissuration of the previously coalesced material, forming polyhedral aggregates and microaggregates. Simultaneously, clay illuviation filled the voids and together with the compacting action of the biological activity of these soils contributed to the coalescence of microaggregates.

Temporal variability of soil water content under different surface conditions in the semiarid region of the Pernambuco state

Rainfall in the semiarid region of Pernambuco is characterized by irregular distribution in time and space, which significantly hinders the rainfed agriculture in the region. This work aims to evaluate the temporal profile of soil moisture in the semiarid region of the Pernambuco State (Brazil) and the effect of different soil surface conditions on soil water content variation and the yield of rainfed beans. To monitor soil water content, five plots 4.5 m wide by 11 m long were installed in a Yellow Argisol (Ultisol). The following treatments were adopted in the experimental plots: natural vegetation, bean intercropped with cactus, beans planted down the slope, beans planted along contour lines with mulch and rock barriers, and bare soil. In each plot, eight PVC access tubes were installed for monitoring the soil water content profile at depths of 0.20 and 0.40 m using a neutron probe device. The surface condition significantly influenced the soil water content variation, both in the dry and rainy seasons. The use of mulch, associated with rock barriers, provided higher soil water content levels than the other treatments and increased the rainfed beans production.

Morphostructural characterization of soil conventionally tilled with mechanized and animal traction with and without cover crop

The structural stability and restructuring ability of a soil are related to the methods of crop management and soil preparation. A recommended strategy to reduce the effects of soil preparation is to use crop rotation and cover crops that help conserve and restore the soil structure. The aim of this study was to evaluate and quantify the homogeneous morphological units in soil under conventional mechanized tillage and animal traction, as well as to assess the effect on the soil structure of intercropping with jack bean (Canavalia ensiformis L.). Profiles were analyzed in April of 2006, in five counties in the Southern-Central region of Paraná State (Brazil), on family farms producing maize (Zea mays L.), sometimes intercropped with jack bean. The current structures in the crop profile were analyzed using Geographic Information Systems (GIS) and subsequently principal component analysis (PCA) to generate statistics. Morphostructural soil analysis showed a predominance of compact units in areas of high-intensity cultivation under mechanized traction. The cover crop did not improve the structure of the soil with low porosity and compact units that hamper the root system growth. In areas exposed to animal traction, a predominance of cracked units was observed, where roots grew around the clods and along the gaps between them.

Portable penetrometer for agricultural soil: sensitivity test to identify critical compaction depth

To express the negative effects of soil compaction, some researchers use critical values for soil mechanical strength that severely impair plant growth. The aim of this study was to identify this critical compaction depth, to test the functionality of a new, portable penetrometer developed from a spring dynamometer, and compare it to an electronic penetrometer traditionally used in compaction studies of agricultural soils. Three soils with distinct texture were conventionally tilled using a disk plow, and cultivated with different plant species. The critical soil resistance defined to establish critical compaction depth was equal to 1.5 MPa. The results of the new equipment were similar to the electronic penetrometer, indicating its viability as a tool for assessing the soil physical conditions for plant growth.

Morphological and molecular characterization of Pisolithus in soil under eucalyptus plantations in Brazil

Eighteen Pisolithus basidiomes were collected from Eucalyptus plantations in the state of Minas Gerais, Brazil. These basidiomes were characterized morphologically and molecularly. The basidiomes varied in shape, color and size. One of them was found underground, indicating a hypogeous fungus. The main morphological distinctive characteristic was spore ornamentation, which distinguished two groups. One group with short and erect spines was identified as Pisolithus microcarpus, and the other with long and curved spines as Pisolithus marmoratus, after analyzing the cladogram obtained by phylogenetic relationship based on internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA of these isolates.