Academic literature on the topic 'Suppressive soils'

In disease-suppressive soils, microbiota protect plants from root infections. Bacterial members of this microbiota have been shown to produce specific molecules that mediate this phenotype. To date, however, studies have focused on individual suppressive soils and the degree of natural variability of soil suppressiveness remains unclear. Here, we screened a large collection of field soils for suppressiveness to Fusarium culmorum using wheat ( Triticum aestivum ) as a model host plant. A high variation of disease suppressiveness was observed, with 14% showing a clear suppressive phenotype. The microbiological basis of suppressiveness to F. culmorum was confirmed by gamma sterilization and soil transplantation. Amplicon sequencing revealed diverse bacterial taxonomic compositions and no specific taxa were found exclusively enriched in all suppressive soils. Nonetheless, co-occurrence network analysis revealed that two suppressive soils shared an overrepresented bacterial guild dominated by various Acidobacteria. In addition, our study revealed that volatile emission may contribute to suppression, but not for all suppressive soils. Our study raises new questions regarding the possible mechanistic variability of disease-suppressive phenotypes across physico-chemically different soils. Accordingly, we anticipate that larger-scale soil profiling, along with functional studies, will enable a deeper understanding of disease-suppressive microbiomes.

Diseases remain a yield-limiting factor for crops despite the availability of control measures for many pathogens. Indigenous soil microorganisms can suppress some plant pathogens, yet there is little systematic information on the effects of cropping systems on disease-suppressive populations in soil. Streptomyces have been associated with suppression of plant diseases in several naturally occurring disease-suppressive soils. Pathogen-suppressive activity of Streptomyces communities is correlated with higher bacterial densities and with inhibitory phenotypes, driven by competition among indigenous soil bacteria. We sought to characterize relationships between cropping practices and pathogen suppression among soil Streptomyces. We evaluated bacterial and Streptomyces densities and inhibitory activities in soils from a long-term crop rotation experiment. Signaling interactions that altered inhibitory phenotypes among sympatric populations were also evaluated for a subset of samples. Soils from longer rotations, which had a higher number of plant species over time, had larger bacterial and Streptomyces densities, and more inhibitors than soils from shorter rotations. In addition, signaling occurred more frequently among isolates from higher-density communities. Our work shows that bacterial density, pathogen suppression and signaling are interrelated and are affected by crop rotation, suggesting the potential for management to optimize suppressive populations.

Soils suppressive to soilborne pathogens have been identified worldwide for almost 60 years and attributed mainly to suppressive or antagonistic microorganisms. Rather than identifying, testing and applying potential biocontrol agents in an inundative fashion, research into suppressive soils has attempted to understand how indigenous microbiomes can reduce disease, even in the presence of the pathogen, susceptible host, and favorable environment. Recent advances in next-generation sequencing of microbiomes have provided new tools to reexamine and further characterize the nature of these soils. Two general types of suppression have been described: specific and general suppression, and theories have been developed around these two models. In this review, we will present three examples of currently-studied model systems with features representative of specific and general suppressiveness: suppression to take-all (Gaeumannomyces graminis var. tritici), Rhizoctonia bare patch of wheat (Rhizoctonia solani AG-8), and Streptomyces. To compare and contrast the two models of general versus specific suppression, we propose a number of hypotheses about the nature and ecology of microbial populations and communities of suppressive soils. We outline the potential and limitations of new molecular techniques that can provide novel ways of testing these hypotheses. Finally, we consider how this greater understanding of the phytobiome can facilitate sustainable disease management in agriculture by harnessing the potential of indigenous soil microbes.

Banana Fusarium wilt-suppressive soils are effective against pathogen invasion, yet soil physicochemical factors responsible for conducive or suppressive behavior have not been reported. Here, we investigated the changes in banana biomass, disease incidence (DI), soil culturable microbes and physicochemical properties by incorporating pepper and banana residues into conducive and suppressive soils. Before the incorporation of any residues, the suppressive soil significantly increased banana biomass and decreased DI compared to the conducive soil. The biomass of the suppressive soil was significantly higher than that of the conducive soil after the incorporation of either pepper or banana residues. Compared with the control (CK), the incorporation of pepper residues to both soils significantly reduced DI, while banana residues had the opposite effect. Additionally, both conducive and suppressive soils supplemented with pepper residues significantly reduced the amounts of culturable Fusarium oxysporum and increased the amounts of beneficial Pseudomonas and Bacillus. The pepper residue extracts significantly inhibited the growth of F. oxysporum mycelium. Soil alkali-hydrolyzable nitrogen (AN) responded most strongly to residue application to suppressive soil. The AN factor was significantly and positively correlated with banana biomass; however, there was no direct and significant negative correlation with DI. Further analysis of the results showed that elevated AN content could stimulate the amounts of culturable Bacillus in the soil, and Bacillus antagonized the proliferation of pathogen and thus indirectly and effectively reduced banana DI. In conclusion, soil AN content can indirectly improve the disease suppression ability of pepper-residue-mediated suppressive soil by manipulating the soil microbiome.

A soil acidified by ammonium sulphate following annual application of the fertilizer for 9 years was suppressive of the saprophytic growth of Gaeumannomyces graminis var. tritici in soil (pathogen suppressive). The same soil amended with lime was pathogen conducive. In natural field soil microbial respiration and the 'total' number of aerobic microorganisms were greater in the conducive than in the suppressive soil. In a soil-sandwich bioassay of the transferable suppression of saprophytic growth of the pathogen there were higher numbers of 'total' aerobic microorganisms, fluorescent pseudomonads, and Gram-negative organisms, but lower numbers of filamentous fungi and yeasts in the conducive than in the suppressive soil. It was estimated that Trichoderma spp. made up 71 and 34% of the total numbers of fungi counted in the suppressive and conducive soils, respectively. It is proposed that Trichoderma spp. played a major role in the transferable pathogen suppression in the suppressive soil.

Soils in which disease fails to develop despite pathogen presence are considered disease-suppressive. They offer sustainable, effective protection to plants against infection by soil-borne pathogens. Naturally disease-suppressive soils have been reported for diseases of a diverse range of agricultural crops worldwide yet the underlying mechanisms of disease suppression are still not completely understood. Two large greenhouse experiments, conducted during 2017/18 (Year 1) and 2018/19 (Year 2), determined that soils naturally suppressive to stem canker and black scurf of potato (caused by Rhizoctonia solani) are present in vegetable-arable cropping soils of the Auckland and Waikato regions of New Zealand. Soil was pre-treated with heat prior to inoculation with R. solani and compared with untreated and uninoculated controls to ascertain if stem canker and black scurf suppression was ‘general’, or ‘specific’ (i.e. transferable; possibly involving specific microorganisms). Rhizoctonia solani inoculation was also combined with transfer of one part test soil to nine parts of a known disease-conducive soil. Abiotic factors such as soil texture and organic matter content influenced black scurf incidence and severity. Soil microorganisms were also involved in disease suppression since black scurf incidence and severity markedly increased when they were eliminated or reduced by soil heat pre-treatment. Microbial profiling of the soils through sequencing revealed that taxa of geographically close soils of the same type had similar fungal and bacterial community structure and diversity even though they differed in their capacity to suppress black scurf. These results suggest that although the soil microbiome as a whole, was mainly responsible for soil disease suppressiveness, certain bacterial genera or species may play a role in black scurf suppression.

Weed-suppressive soils contain naturally occurring microorganisms that suppress a weed by inhibiting its growth, development, and reproductive potential. Increased knowledge of microbe–weed interactions in such soils could lead to the identification of management practices that create or enhance soil suppressiveness to weeds. Velvetleaf death and growth suppression was observed in a research field (fieldA) that was planted with high populations of velvetleaf, which may have developed via microbial mediated plant–soil feedback. Greenhouse studies were conducted with soil collected fromfieldA(soilA) to determine if it was biologically suppressive to velvetleaf. In one study, mortality of velvetleaf grown for 8 wk insoilAwas greatest (86%) and biomass was smallest (0.3 g plant−1) in comparison to soils collected from surrounding fields with similar structure and nutrient content, indicating that suppressiveness ofsoilAwas not likely caused by physical or chemical factors. WhensoilAwas autoclaved in another study, mortality of velvetleaf plants in the heat-treated soil was reduced to 4% compared to 55% for the untreated soil, thus suggesting that suppressiveness ofsoilAis biological in nature. A third set of experiments showed that suppressiveness to velvetleaf could be transferred to an autoclaved soil by amending the autoclaved soil with untreatedsoilA; this provided additional evidence for a biological basis for the effects ofsoilA.The suppressive condition in these greenhouse experiments was associated with high soil populations of fusaria.Fusarium lateritiumwas the most frequently isolated fungus from roots of diseased velvetleaf plants collected fromfieldA, and also was the most virulent when inoculated onto velvetleaf seedlings. Results of this research indicate that velvetleaf suppression can occur naturally in the field and thatF. lateritiumis an important cause of velvetleaf mortality infieldA.

Peas are growing all over the world as a leguminous crop due to high nutrients value. Fusarium wilt of peas is a destructive disease and causing deleterious loses in pea growing regions of the world. The fields were surveyed with disease incidence of Fusarium wilt in major pea growing areas. Fields with heavy pathogen infestation and natural disease suppressive were observed at District Sahiwal, Pakistan. The samples were collected to diagnose the disease and factors responsible in the suppression of disease. The results of soil physio-chemical properties showed no significant differences between diseased and suppressive soils. Pathogenicity assays both in-vitro and pot trial showed that suppressive soil has natural ability to suppress the disease. Furthermore, in-vitro and pot assays were designed with different soil treatments to investigate the factors responsible in the natural disease suppressiveness in suppressive soil. The results demonstrated that the mechanism involved in disease suppressive soil is biotic in nature. All isolated fungal strains from diseased and healthy roots of pea were subjected to biological assays to evaluate the virulence. The assays showed that isolate SAH09 is non-pathogenic Fusarium oxysporum which was isolated from the pea roots of suppressive soil. Isolate SAH09 was used in dual culturing technique and pot trial to evaluate the mycoparastism behavior against virulent pathogenic isolates SAH03, SAH05 and SAH10. Results concluded that isolate SAH09 of non-pathogenic Fusarium oxysporum has potential to suppress the growth of all isolates of pathogenic Fusarium and possibly play the role in natural disease suppression in suppressive soils

The induction of disease-suppressive soils in response to specific cropping sequences has been demonstrated for numerous plant-pathogen systems. The role of host genotype in elicitation of the essential transformations in soil microbial community structure that lead to disease suppression has not been fully recognized. Apple orchard soils were planted with three successive 28-day cycles of specific wheat cultivars in the greenhouse prior to infestation with Rhizoctonia solani anastomosis group (AG)-5 or AG-8. Suppressiveness to Rhizoctonia root rot of apple caused by the introduced isolate of R. solani AG-5 was induced in a wheat cultivar-specific manner. Pasteurization of soils after wheat cultivation and prior to pathogen introduction eliminated the disease suppressive potential of the soil. Wheat cultivars that induced disease suppression enhanced populations of specific fluorescent pseudomonad genotypes with antagonistic activity toward R. solani AG-5 and AG-8, but cultivars that did not elicit a disease suppressive soil did not modify the antagonistic capacity of this bacterial community. When soils were infested prior to the initial wheat planting, all cultivars were uniformly susceptible to R. solani AG-8. However, when pathogen inoculum was added after three growth-cycles, wheat root infection during the fourth growth-cycle varied in a cultivar specific manner. The same wheat cultivar-specific response in terms of transformation of the fluorescent pseudomonad community and subsequent suppression of Rhizoctonia root rot of apple was observed in three different orchard soils. These results demonstrate the importance of host genotype in modification of indigenous saprophytic microbial communities and suggest an important role for host genotype in the success of biological control.

Root-knot nematodes (RKN), Meloidogyne spp., are the most economically important genus of plant parasitic nematodes that cause considerable damage and yield losses of horticultural crops worldwide. RKN management strategies tend to reduce chemical nematicides by encouraging alternative control methods like the use of plants bearing resistance genes (R-genes) and/or by microbe-inducing plant resistance, and the antagonistic potential of soils. In the thesis, two biological control approaches of Meloidogyne spp. were evaluated: 1) the application of selected nematode antagonists, the fungus Pochonia chlamydosporia and the bacteria Bacillus firmus I-1582 (Bf I-1582), to know its ability to induce plant resistance, and 2) the level of soil suppressiveness of vegetable production sites conducted under organic or integrated standards. Regarding the ability of P. chlamydosporia and Bf I-1582 to induce plant resistance, the results of this thesis provide evidence that two out of five P. chlamydosporia isolates (M10.43.21 and M10.55.6) and Bf I-1582 are able to induce systemic resistance against M. incognita in the susceptible tomato (Solanum lycopersicum) cv. Durinta but not in the cucumber (Cucumis sativus) cv. Dasher II in split-root experiments. In addition, the cardinal temperatures for the Bf I-1582 growth and biofilm formation were determined in order to improve its use in field conditions. Moreover, Bf I-1582 was transformed with GFP to study its effect on nematode eggs and on tomato and cucumber root colonization. In tomato, the number of egg masses and the number of eggs per plant were reduced by M10.43.21 and M10.55.6 P. chlamydosporia isolates and by Bf I-1582. P. chlamydosporia isolates colonized both tomato and cucumber roots, being the M10.43.21 and the M10.55.6 isolates the best root colonizers in tomato and cucumber, respectively. In the case of Bf I-1582, the bacteria colonized endophytically roots of both plants, but highest values were recorded in tomato. The dynamic regulation of genes related to jasmonic acid (JA) and salicylic acid (SA) was determined by RT-qPCR at three different times after nematode inoculation (dani). Bf I-1582 primed tomato plants by both SA and JA at all the times in tomato, but only SA at 7 dani in cucumber. Regarding P. chlamydosporia, isolate M10.43.21, induced the expression of the SA pathway in tomato at 0, 7 and 42 dani. The JA pathway was also up regulated at 7 dani. These results show the similar model of dynamic regulation of these plant hormone pathways related to plant defense mechanisms against the nematode. Also, Bf I-1582 grew and formed biofilm between 15 and 45 ºC, being 35 ºC the optimal temperature. Bf I-1582GFP was adhered to the egg shell and inside the eggs. Also, Bf I-1582GFP colonized root hairs and epidermal cells and some bacteria were found inside the tomato root. In cucumber, few bacteria were observed on epidermal cells and the bacteria were no found inside the root. In relation to the level of soil suppressiveness of vegetable production it was carried out a study in four organic and two integrated vegetables production standards sites located in north-eastern Spain. The fluctuation both of Meloidogyne population density and fungal egg parasitism were determined during the rotation sequences in two years (2015-2016). Five out of six of these sites were suppressive soils to Meloidogyne spp. The percentage of fungal egg parasitism ranged from 11.2 to 55 % and P. chlamydosporia was the only fungal species isolated from the eggs. In parallel, two tomato pots experiments were carried out using sterilized and non-sterilized soils from each site and inoculated with second-stage juveniles (J2) to achieve a rate of 1 J2 cm-3 of soil. In both, in five of them the number of nematode eggs per plant was reduced in all nonsterilized soils compared to the sterilizes ones. Also, P. chlamydosporia was the only fungal species isolated from parasitized nematode eggs.
Meloidogyne spp. (RKN) es el género de nematodos fitopatógenos que causan las mayores pérdidas económicas y que más afectan al rendimiento de cultivos hortícolas a nivel mundial. Las estrategias de manejo de RKN tienden a sustituir la utilización de nematicidas químicos por medidas de control alternativas como son el uso de plantas con genes de resistencia (genes R) y/o mediante la utilización de microorganismos inductores de resistencia, y el potencial antagónico del suelo. En esta tesis, se han evaluado dos enfoques de control biológico: 1) la aplicación de microorganismos antagónicos, el hongo Pochonia chlamydosporia (Pc) y la bacteria Bacillus firmus I-1582 (Bf I-1582) para evaluar su capacidad de inducir mecanismos de resistencia, y 2) el nivel de supresividad del suelo de diferentes lugares bajo estándares de producción orgánica e integrada. Con respecto a la capacidad de Pc y Bf I-1582 para inducir resistencia, los resultados de esta tesis muestran que dos (M10.43.21 y M10.55.6) de los cinco aislados de Pc utilizados y la bacteria Bf I-1582 inducen resistencia sistémica frente a M. incognita en el tomate susceptible (Solanum lycopersicum) cv. Durinta pero no en el pepino (Cucumis sativus) cv. Dasher II usando el modelo split-root. En el caso de Bf I-1582, se determinaron las temperaturas cardinales para el crecimiento y la formación de biofilms de Bf I-1582 con el fin de mejorar su utilización en condiciones de campo y se transformó con la GFP para estudiar su efecto sobre los huevos de RKN y sobre la colonización radicular. Los aislados M10.43.21 y M10.55.6 de Pc y Bf I-1582 redujeron el número de masas de huevos y el número de huevos por planta en tomate. Todos los aislados de Pc colonizaron raíces de tomate y pepino, siendo los aislados M10.43.21 y M10.55.6 los mejores colonizadores en tomate y pepino, respectivamente. En el caso de Bf I-1582, la bacteria colonizó endofíticamente las raíces de ambas plantas, pero los valores más altos se registraron en tomate. La expresión de los genes relacionados con el ácido jasmónico (JA) y el ácido salicílico (SA) se determinó a tres tiempos tras la inoculación de nematodos (dani). En plantas de tomate inoculadas con Bf I-1582 la expresión de los genes relacionados con SA y JA aumentaron en los tres puntos, pero en pepino solo se observó un incremento de expresión en el gen relacionado con la ruta de SA a los 7 dani. Con respecto a Pc, el aislado M10.43.21, indujo la expresión de la vía SA en tomate a los 0, 7 y 42 dani. La vía JA también aumentó su expresión a los 7 dani. Además, Bf I-1582 creció y formó biofilms entre 15 y 45 ºC, siendo 35 ºC la temperatura óptima. Bf I-1582GFP se adhirió a la cubierta y al interior de los huevo de M. incognita. Además, Bf I-1582GFP en tomate colonizó los pelos radiculares, así como las células epidérmicas y se encontraron algunas bacterias en el interior radicular. En el pepino, se observó un menor número de bacterias en las células epidérmicas y no se encontraron bacterias en el interior radicular. En relación con el nivel de supresión del suelo, se realizó un estudio en cuatro lugares de producción hortícola orgánica y dos de producción integrada en el noreste de España. Durante la secuencias de rotación en 2015-2016 se determinó la fluctuación tanto de la densidad de población de Meloidogyne en suelo como del parasitismo de huevos de nematodos. Cinco de estos sitios resultaron ser supresivos a Meloidogyne spp. Paralelamente, se llevaron a cabo dos experimentos en macetas con suelo esterilizado y no esterilizado de cada sitio donde las plantas de tomate se inocularon con juveniles (J2) para lograr una tasa de 1 J2 cm-3 de suelo. En cinco de ellos, el número de huevos de nematodos por planta se redujo en todos los suelos no esterilizados en comparación con los esterilizados. Respecto al parasitismo, Pc fue la única especie aislada de los huevos de Meloidogyne spp. p
Els nematodes formadors de gal·les, Meloidogyne spp., és el gènere més important nematodes fitoparàsits que causen danys considerables i generen pèrdues econòmiques en cultius hortícoles arreu del món. Les estratègies actuals de gestió de Meloidogyne solen reduir l’ús dels nematicides químics fomentant mètodes de control alternatius com l’ús de plantes amb gens de resistència (gens R) i/o l’ús de la resistència vegetal induïda per microorganismes, i el potencial antagonista dels sòls. En la present tesis, dos aproximacions al control biològic de Meloidogyne spp. van ser estudiades: 1) l’aplicació d’antagonistes dels nematodes: el fong Pochonia chlamydosporia i el bacteri Bacillus firmus aïllat I-1582 i es a avaluar la seva capacitat per induir resistència vegetal, i 2) el nivell de supressivitat de sòls de producció vegetal orgànica o integrada. Respecte a la capacitat de P. chlamydosporia i B. firmus I-1582 (Bf I-1582) a induir resistència vegetal, els resultats d’aquesta tesis van donar evidències que dos de cinc aïllats de P. chlamydosporia (M10.43.21 i M10.55.6) i Bf I-1582 induien resistència sistèmica enfront M. incognita en tomàquet susceptible (Solanum lycopersicum) cv. Durinta però no en cogombre (Cucumis sativus) cv. Dasher II en experiments “split-root”. A més, les temperatures cardinals de creixement i de formació de biofilm de Bf I-1582 van ser determinades per tal de millorar el seu ús en condicions de camp. A més, el bacteri va ser transformat amb GFP per estudiar el seu efecte sobre els ous del nematode i la seva colonització sobre les arrels de tomàquet i cogombre per microscopia de rastreig làser confocal. En tomàquet, tant el nombre de masses d'ou com el nombre d'ous per planta es va veure reduït quan s’aplicaven tant els aïllats fúngics com el bacteri. Els aïllats de P. chlamydosporia colonitzaven les arrels de tomàquet i cogombre, però diferien en el nivell de colonització. L’aïllat M10.43.21 va ser el millor colonitzador de les arrels de tomàquet mentre que l’aïllat M10.55.6 ho va ser per cogombre. En el cas de Bf I-1582, el bacteri va ser capaç de colonitzar endofíticament les arrels de les dues plantes, però es va trobar un 61% més de densitat d’ADN de bacteri en arrels de tomàquet. La regulació dinàmica dels gens relacionats amb l’àcid jasmònic (JA) i l’àcid salicílic (SA) a tres temps diferents van ser avaluats: 7 dies després de la inoculació de l’antagonista i just després de la inoculació del nematode (0 dani), 7 dies desprès de la inoculació del nematode (7 dani) i 40 dies desprès de la inoculació del nematode (40 dani). Les dues vies SA (gen PR-1) i JA (gen Lox D) van ser sobre-expressades plantes de tomàquet a 0 dani, reduint el nombre de masses d’ou al final de l’experiment “split-root” quan es va inocular amb Bf I-1582. No obstant, no hi va haver diferencies en l’expressió dels gens relacionats SA (PR 1) i JA (Lox D) en cogombre inoculat amb el bacteri com tampoc en el nombre de masses d’ou produïdes en les arrels de cogombre. A 7 dani, el gen relacionat amb el JA (Lox D) estava sobre-expressat en tomàquet i podria afectar el desenvolupament del nematode i la seva reproducció. En cogombre, la via del SA (Pal I) estava sobre-expressada tant en les plantes inoculades amb M. incognita com en les co-inoculades amb el bacteri i el nematode. A 40 dani, quan va començar l’eclosió dels ous i es van produir noves infeccions a l’arrel, les plantes de tomàquet co-inoculades amb els nematode 2 i Bf I-1582 tenia reprimit el gen relacionat amb el JA (Lox D), mentre que el gen relacionat amb la via del SA (PR 1) estava sobre-expressat en plantes co-inoculades i també amb només Bf I-1582, però va ser reprimit en plantes inoculades només amb el nematode. En cogombre, les dues vies, JA i SA, van ser reprimides en plantes inoculades amb M. incognita però només la JA en plantes co-inoculades. Respecte l’aïllat de P. chlamydosporia M10.43.21, va induir l’expressió de la via del SA en arrels de tomàquet a 0, 7 i 42 dani. La via del JA va ser també sobre-expressada a 7 dani. Per tant, alguns aïllats de P. chlamydosporia i l’aïllat Bf I-1582 poden induir resistència sistèmica envers al nematode, encara que depèn de l’espècie vegetal. Aquests resultats han demostrat el model similar de regulació dinàmica d’aquestes vies d’hormones vegetals relacionades amb mecanismes de defensa de les plantes contra el nematode. El bacteri Bf I-1582 va créixer en el rang de temperatures des de 15 ºC a 45 ºC, sent 35 ºC la temperatura òptima de creixement tant en medi sòlid com en líquid, però no a 10 ºC i 50 ºC. Igualment, es va observar la formació de biofilm entre 15 ºC i 45 ºC però tampoc a 10 ºC ni a 50 ºC, sent més gruixut i uniforme a 35 ºC. La degradació de la closca del nematode i la colonització dels ous per Bf I-1582 GFP va mostrar que a 3 dies desprès de la seva inoculació (dai) el bacteri estava envoltant i degradant l'ou del nematode; a 5 dai, colònies de bacteri es van adherir a la closca de l’ou i es van trobar alguns bacteris dins de l’ou; a 10 dai, el bacteri era completament adherit a la closca de l’ou i dins de l’ou. A més, Bf I-1582GFP va colonitzar les pèls radiculars i cèl·lules epidèrmiques a 5 dai; es van observar colònies de bacteris en pèls radiculars de tomàquet i alguns bacteris dins de l’arrel a 10 dai. En cogombre, es van observar pocs bacteris a les cèl·lules epidèrmiques a 5 dai i no es va trobar el bacteri dins de l’arrel a 10 dai. En relació al nivell de supressivitat del sòl, es va realitzar un estudi a sis parcel·les de producció d’hortalisses localitzades al nord-est d’Espanya. Quatre realitzaven producció orgànica (M10. 16, M10.41, M10.55, i M10.56) i dues (M10.43 i M10.45) producció integrada. La fluctuació de la densitat de població de Meloidogyne i el parasitisme d’ous per part de fongs van ser determinats durant la seqüència de rotació de cultius durant dos anys (2015-2016). Cinc dels sols estudiats eren sòls supressius a Meloidogyne spp. El percentatge de parasitisme d’ous va variar de 11.2 a 55 % i P. chlamydosporia va ser l'única espècie fúngica aïllada dels ous. En paral·lel, dos experiments es van dur a terme utilitzant sòl de cada parcel·la. Una part de cada sòl es va esterilitzar i es va barrejar amb sorra estèril, i una altre part no es va esterilitzar i es va barrejar també amb sorra estèril amb una relació 1:1 i es va col·locar en testos de 3-l. El cultivar susceptible de tomàquet Durinta es va trasplantar en cada test i es va inocular amb juvenils de segon estadi (J2) amb un nivell de 1 J2 cm-3 de sòl. En els dos experiments en testos, els nombre d’ous per planta es va reduir (P<0.05) en tots els sòls no esterilitzats comparats amb els estèrils, excepte en el M10.45. També, P. chlamydosporia va la única espècie fúngica aïllada d’ous parasitats de nematodes. P. chlamydosporia és el fong més freqüent i més prevalent amb una alta plasticitat capaç d’adaptar-se a les pràctiques agronòmiques en un sistema de producció vegetal molt pertorbat.

Les bactéries du sol produisant des antifongiques comme le 2,4-diacétylphloroglucinol(DAPG) protègent les racines des plantes vis-à-vis des champignons phytopathogènes. Néanmoins, les conditions de fonctionnement de ces populations bactériennes dans le sol restent très mal connues. Dans certains sols, dits résistants aux maladies, ces bactéries phytoprotectrices sont présentes à des effectifs importants et leur activité est suffisante pour protéger la plante malgré la présence du pathogène. L'objectif de cette thèse a été de comprendre la relation entre la résistance des sols à la maladie de la pourriture noire des racines de tabac, et la fonction de synthèse du DAPG chez les bactéries du genre Pseudomonas. Dans la situation de référence de Morens (Suisse), les sols résistants diffèrent des sols sensibles par la présence de vermiculite, argile capable de relarguer du fer. On sait que la présence de vermiculite améliore la phytoprotection assurée par les Pseudomonas producteurs de DAPG, mais les mécanismes moléculaires sous-jacents restent inconnus. Dans un premier temps, la quantification de ces bactéries par une nouvelle méthode de PCR quantitative développée ici, a confirmé que leurs effectifs sont élevés dans les sols résistants, mais aussi dans les sols sensibles, suggérant que la résistance puise plutôt dépendre d'une plus forte expression de la fonction de synthèse du DAPG. Dans un second temps, l'étude de l'expression des gènes de synthèse du DAPG en système de sol artificiel, à l'aide de la souche rapportrice P. protegens phlA-gfp, a montré que la présence de vermiculite dans le sol se traduit par une plus forte biodisponibilité du fer pour les Pseudomonas, induisant une plus forte expression des gènes de synthèse du DAPG et la protection du tabac. En conclusion, la résistance des sols de Morens à la maladie de la pourriture noire des racines est conditionnée par plusieurs facteurs abiotiques et biotiques, dont la biodisponibilité du fer qui régule l'expression des gènes de synthèse du DAPG chez Pseudomonas
Soil bacteria producing antimicrobial compounds like 2,4-diacetylphloroglucinol (DAPG) protect plants from soil-borne phytopathogens. Nevertheless, the functioning of these bacterial populations in the soil is largely unknown. In certain soils, termed disease- suppressive soils, these bacteria are present at high numbers and their activity is sufficient to assure effective plant protection in the presence of the pathogen. The aim of this thesis was to understand the relation between soil suppressiveness towards black root rot of tobacco, and the 2,4-diacetylphloroglucinol synthesis ability of certain Pseudomonas. In Morens region (Switzerland), suppressive soils differ from conducive soil by the presence of vermiculite, an iron-releasing clay. It is known that DAPG-producing Pseudomonas provide better plant protection in the presence of vermiculite, but the molecular basis of this interaction is still unknown. First, the quantification of these bacteria, through a new real-time PCR method developed here, confirmed that high numbers of DAPG-producing Pseudomonas occur in suppressive soils, as well as in conducive ones, raising the possibility that suppressiveness depends rather on a higher expression of DAPG synthetic genes. Second, expression studies of DAPG synthetic genes using a P. protegens ph/A- gfp reporter strain and artificial soil systems, confirmed that the presence of vermiculite in the soil can translate into higher iron bioavailability for Pseudomonas, triggering higher expression of DAPG synthetic genes and effective plant protection. In conclusion, black root rot suppressiveness of Morens soils is determined by several abiotic and biotic factors, among which iron bioavailability regulating the expression of DAPG synthetic genes in plant-protecting Pseudomonas

Take-all, caused by the soilborne fungus, Gaeumannomyces graminis var. tritici (Ggt), is an important root disease of wheat that can be reduced by take-all decline (TAD) in successive wheat crops, due to general and/or specific suppression. A study of 112 New Zealand wheat soils in 2003 had shown that Ggt DNA concentrations (analysed using real-time PCR) increased with successive years of wheat crops (1-3 y) and generally reflected take-all severity in subsequent crops. However, some wheat soils with high Ggt DNA concentrations had low take-all, suggesting presence of TAD. This study investigated 26 such soils for presence of TAD and possible suppressive mechanisms, and characterised the microorganisms from wheat roots and rhizosphere using polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE). A preliminary pot trial of 29 soils (including three from ryegrass fields) amended with 12.5% w/w Ggt inoculum, screened their suppressiveness against take-all in a growth chamber. Results indicated that the inoculum level was too high to detect the differences between soils and that the environmental conditions used were unsuitable. Comparison between the Ggt DNA concentrations of the same soils collected in 2003 and in 2004 (collected for the pot trial), showed that most soils cropped with 2, 3 and 4 y of successive wheat had reduced Ggt DNA concentrations (by 195-2911 pg g-1 soil), and their disease incidences revealed 11 of the 29 test soils with potential take-all suppressiveness. Further pot trials improved the protocols, such that they were able to differentiate the magnitudes of suppressiveness among the soils. The first of the subsequent trials, using 4% w/w Ggt inoculum level, controlled conditions at 16°C, 80% RH with alternate 12 h light/dark conditions, and watering the plants twice weekly to field capacity (FC), screened 13 soils for their suppressiveness against take-all. The 13 soils consisted of 11 from the preliminary trial, one wheat soil that had been cropped with 9 y of wheat (considered likely to be suppressive), and a conducive ryegrass soil. The results revealed that 10 of these soils were suppressive to take-all. However, in only four of them were the effects related to high levels of microbial/biological involvement in the suppression, which were assessed in an experiment that first sterilised the soils. In a repeat trial using five of the soils H1, H3, M2, P7 (previously cropped with 3, 3, 4 and 9 y successive wheat, respectively) and H15 (previously cropped with 5 y of ryegrass), three of them (H1, H3 and M2) had reduced Ggt DNA concentrations (>1000 pg g-1 soil reductions), and were confirmed to be suppressive to take-all. A pot trial, in which 1% of each soil was transferred into a γ-irradiated base soil amended with 0.1% Ggt inoculum, indicated that soils H1 and H3 (3 y wheat) were specific in their suppressiveness, and M2 (4 y wheat) was general in its suppressiveness. The microbial communities within the rhizosphere and roots of plants grown in the soils, which demonstrated conduciveness, specific or general suppressiveness to take-all, were characterised using PCR-DGGE, and identities of the distinguishing microorganisms (which differentiated the soils) identified by sequence analysis. Results showed similar clusters of microorganisms associated with conducive and suppressive soils, both for specific and general suppression. Further excision, re-amplification, cloning and sequencing of the distinguishing bands showed that some actinomycetes (Streptomyces bingchengensis, Terrabacter sp. and Nocardioides sp.), ascomycetes (Fusarium lateritium and Microdochium bolleyi) and an unidentified fungus, were associated with the suppressive soils (specific and general). Others, such as the proteobacteria (Pseudomonas putida and P. fluorescens), an actinomycete (Nocardioides oleivorans), ascomycete (Gibberella zeae), and basidiomycete (Penicillium allii), were unique in the specific suppressiveness. This indicated commonality of some microorganisms in the take-all suppressive soils, with a selected distinguishing group responsible for specific suppressiveness. General suppressiveness was considered to be due to no specific microorganisms, as seen in soil M2. An attempt to induce TAD by growing successive wheat crops in pots of Ggt-infested soils was unsuccessful with no TAD effects shown, possibly due to variable Ggt DNA concentrations in the soils and addition of nutrients during the experiment. Increasing numbers of Pseudomonas fluorescens CFU in the rhizosphere of plants, during successive wheat crops was independent of the Ggt DNA concentrations and disease incidence, suggesting that increases in P. fluorescens numbers were associated with wheat monoculture. This study has demonstrated that TAD in New Zealand was due to both specific and general suppressiveness, and has identified the distinguishing microorganisms associated with the suppression. Since most of these distinguishing microorganisms are known to show antagonistic activities against Ggt or other soilborne pathogens, they are likely to act as antagonists of Ggt in the field. Future work should focus on validating their effects either individually, or interactively, on Ggt in plate and pot assays and under field conditions.

Leguminous cover crops are promising as Meloidogyne spp. suppressants but where populations of mixed species occur, their potential remains uncertain. When inoculated with a Meloidogyne arenaria-incognita-javanica complex in a glasshouse experiment, Mucuna pruriens and Crotalaria spectabilis, were poor or non-hosts, did not gall and plant height and shoot biomass were not affected. However, Dolichos lablab was highly susceptible. The root system of D. lablab stimulated population increase but the leaf eluant proved lethal. Thus, different parts of a plant contain different active ingredients or concentrations of compounds. In ancillary experiments, M. pruriens, C. retusa and C spectabilis inhibited hatching of eggs, caused juvenile mortality, decreased population density and roots were either not invaded by juveniles or invasion was minimal.

Use of known antagonists and antagonistic, endophytic bacteria was investigated to screen a successful antagonist for the fungal strains R. solani AG 2-1, R. solani AG 4 and R. solani AGSL01.   Reputed antagonists used in the study; Bacillus subtilis MBI 205,  B. subtilis MBI 600, Pseudomonas fluorescens B5 and P. corrugate R. 117 were capable of suppressing the fungus in dual cultures. Manipulation of soil factors to reduce pre-plant density of R. solani sclerotia involved a laboratory experiment followed by two field experiments.  In the laboratory study, the effect of constant soil temperatures was investigated by incubating sclerotia at 30, 35, 40, 45 and 50°C.  Sclerotia were counted into lots of 100, placed in polyester mesh bags (85 μm pore size, 10 x 10 cm dimension) at depths of 5 and 10 cm in rice field soils contained in plastic containers (20x20x18 cm).  Total loss of viability was observed on day 1, day 8 and day 28 at 45°C, 40°C and 35°C, respectively.  Loss was even detected within 6.00 h at 50oC. Field experiments of soil solarization (carried out at The Regional Agricultural Research Institute (RARI), Bombuwela, Sri Lanka) were conducted during the fallow periods between the two main cropping seasons in 2003.  During the trials, the effect of polythene mulching, straw incorporation and their combined effect on the viability of sclerotia were investigated.  Sclerotia (lots of 100) were buried at depths of 5 and 10 cm and the soil temperature was recorded at 8.00, 11.00, 14.00 and 17.00h daily at both depths.  During the field trials, at both depths, the effect of treatment over time was noted on percentage recovery and viability of sclerotia (p<0.001).  The results showed a drop in mean percentage recovery of less than 50% during the first week of both trials.  Germination was markedly reduced to less than 10% by the first week in all the treatments.  Depth of burial and straw incorporation had no effect.  In solarized plots, a significant increase in soil temperature at both soil depths was observed between 14.00 and 17.00h.  Average temperatures of 40°C and 34°C were observed for solarized and non-solarized plots, respectively.  The study therefore has identified a practical, low cost and environmentally friendly method of control, and the use of polythene five weeks prior to rice seed sowing is recommended to minimise sheath blight and other diseases caused by similar soil-borne fungal pathogens.

The objective of this study was to evaluate the effect of various organic amendment on weed suppression, soil content and yield components of sweet com (Zea mays L.) grown under organic or sustainable agriculture regimes. Field experiments were conducted during 2004, 2005 and 2006 to study the effect poultry manure, cow manure and barley mulch, used at three rates (half, recommended. double). Sweet com ({Zea mays L.) was planted. Two experiments were conducted each year. Experiment I was in combination with nitrogen fertilization (nitrogen was added in each treatment according to the nitrogen content of each amendment; the amount added was equal to that needed to bring all treatments to the rate of 240 kg N/ha). Experiment II was purely organic.

This thesis includes two studies. The first study examined changes in soil characteristics as a result of prolonged conifer dominance in successional aspen-conifer forests. Changing disturbance patterns in aspen-conifer forests appear to be altering successional dynamics that favors conifer expansion in aspen forests. The primary objective of this paper was to identify how increasing conifer dominance that develops in later successional stages alters forest soil characteristics. Soil measurements were collected along a stand composition gradient: aspen dominated, aspen-conifer mix, conifer dominated and open meadow, which includes the range of conditions that exists through the stages of secondary succession in aspen-conifer forests. Soil chemistry, moisture content, respiration, and temperature were measured. There was a consistent trend in which aspen stands demonstrated higher mean soil nutrient concentrations than adjacent meadows, mixed or conifer stands. Soil moisture was significantly higher in aspen stands and meadows in early summer. Soil respiration was significantly higher in aspen stands than conifer stands or meadows throughout the summer. The results indicate that soil resource availability and respiration peak within aspen dominated stands that are present during early succession and then decrease as conifer abundance increases along our stand composition gradient, representative of stand characteristics present in mid to late successional stages. Emerging evidence from other studies suggest that these observed changes in soil characteristics with increasing conifer dominance may have negative feedbacks on aspen growth and vigor. The second study examined the facilitation effect between aspen and subalpine fir establishment. In subalpine forests, conifer species are often found intermixed with broadleaf species. However, few if any studies have explored the existence and influence of facilitation between broadleaf tree species and conifers. We have observed the general establishment of subalpine fir seedlings at the base of aspen trees in a subalpine forest, indicating that a facilitative relationship may exist. To explore the potential facilitative relationship during secondary succession in subalpine forests, subalpine fir seeds were planted across a stand composition gradient (aspen dominated → mixed → conifer dominated stands) at six study sites in the Fishlake National Forest. Seeds were placed during the fall of 2010, at distances of 0 cm and 25 cm in each cardinal direction at the base of mature aspen and subalpine fir trees in each of the three stand types. Seeds were also planted within stand interspaces and in adjacent meadows. Seedling emergence was recorded at the beginning of the summer of 2011 and seedling mortality was recorded in October 2011. Soil moisture content was measured at the position that seeds were placed during the summers of 2009 and 2011. Aspen dominated stands had subalpine fir germination that was on average 11 times greater than mixed or conifer dominated stands. Germination was 2.3 fold greater at the base of aspen trees than fir trees and two fold greater at the base of aspen trees than interspaces. Seedling mortality was lower in aspen stands but was not significantly influenced by position relative to mature trees. Soil moisture was highest in aspen dominated stands, with better soil moisture conditions at the base of aspen trees and in interspaces compared to the base of fir trees. Few if any studies regarding conifer facilitation have provided evidence for facilitation at the germination life stage, rather they focus on seedling survival. However, our study illustrates a strong facilitative interaction in which both aspen dominated stands and aspen trees increase the likelihood of subalpine fir seedling establishment by drastically increasing rates of subalpine fir germination. Because of aspen's primary role in initiating secondary succession through post-disturbance sucker regeneration, and the subsequent dependence of conifers on aspen for establishment, aspen mortality via competition with conifers under longer fire cycles, droughts, or intensive ungulate browsing may result in a loss of aspen-conifer forest communities in some locales.

Our capacity to maintain world food production depends heavily on the thin layer of soil covering the Earth's surface. The health of this soil determines whether crops can grow successfully, whether a farm business is profitable and whether an enterprise is sustainable in the long term. Farmers are generally aware of the physical and chemical factors that limit the productivity of their soils but often do not recognise that soil microbes and the soil fauna play a major role in achieving healthy soils and healthy crops. Soil Health, Soil Biology, Soilborne Diseases and Sustainable Agriculture provides readily understandable information about the bacteria, fungi, nematodes and other soil organisms that not only harm food crops but also help them take up water and nutrients and protect them from root diseases. Complete with illustrations and practical case studies, it provides growers and their consultants with holistic solutions for building an active and diverse soil biological community capable of improving soil structure, enhancing plant nutrient uptake and suppressing root pests and pathogens. The book is written by scientists with many years' experience developing sustainable crop production practices in the grains, vegetable, sugarcane, grazing and horticultural industries. This book will be useful for: growers, consultants, agronomists and soil chemists, extension personnel working in the grains, livestock, sugarcane and horticultural industries, professionals running courses in soil health/biological farming, and students taking university courses in soil science, ecology, microbiology, plant pathology and other biological sciences.

AbstractAmong the diversity of plant diseases occurring in aquaponics, soil-borne pathogens, such as Fusarium spp., Phytophthora spp. and Pythium spp., are the most problematic due to their preference for humid/aquatic environment conditions. Phytophthora spp. and Pythium spp. which belong to the Oomycetes pseudo-fungi require special attention because of their mobile form of dispersion, the so-called zoospores that can move freely and actively in liquid water. In coupled aquaponics, curative methods are still limited because of the possible toxicity of pesticides and chemical agents for fish and beneficial bacteria (e.g. nitrifying bacteria of the biofilter). Furthermore, the development of biocontrol agents for aquaponic use is still at its beginning. Consequently, ways to control the initial infection and the progression of a disease are mainly based on preventive actions and water physical treatments. However, suppressive action (suppression) could happen in aquaponic environment considering recent papers and the suppressive activity already highlighted in hydroponics. In addition, aquaponic water contains organic matter that could promote establishment and growth of heterotrophic bacteria in the system or even improve plant growth and viability directly. With regards to organic hydroponics (i.e. use of organic fertilisation and organic plant media), these bacteria could act as antagonist agents or as plant defence elicitors to protect plants from diseases. In the future, research on the disease suppressive ability of the aquaponic biotope must be increased, as well as isolation, characterisation and formulation of microbial plant pathogen antagonists. Finally, a good knowledge in the rapid identification of pathogens, combined with control methods and diseases monitoring, as recommended in integrated plant pest management, is the key to an efficient control of plant diseases in aquaponics.

Biochar application to agriculture soil has been recommended as a strategy to reduce increasing atmospheric carbon dioxide (CO2) concentrations and mitigate climate change. Significant suppression of soil CO2 emissions following biochar amendments has been demonstrated in short-term laboratory incubations by several authors, yet evidence from long-term field trials has been contradictory. This study investigates whether biochar addition to the soil could suppress soil CO2 emission under field conditions after 6�th years following amendment. CO2 emissions were not significantly suppressed with biochar addition, although they were generally low. Biochar amendment suppressed soil cumulative CO2 emissions by 30.59%. These findings demonstrate that biochar amendment has the potential to suppress soil CO2 emissions in corn crop system after 6�th years of biochar application. We conclude that the concentration of soil CO2 emissions were depended on soil temperature measured during study period.

the article discusses the methods of uprooting (removing) stumps, depending on various situations. Particular attention is paid to the chemical destruction of stumps by introducing an arboricidal mixture. On the basis of the carried out literary and patent sources, a technical solution was proposed in the form of a device for suppressing stumps by introducing a chemical solution during reforestation work when preparing the soil for planting.

Although significant pipe-soil interaction information is now available in the industry for shallowly-embedded, cylindrical pipelines on a flat seabed, there is little information available for subsea pipelines with vortex-induced vibration (VIV) suppression strakes on a furrowed seabed. A heavily furrowed seabed may have multiple free spans that are subjected to seabed currents and potential VIV. To suppress VIV at the free spans, strakes are often applied to the pipeline over the entire length of the furrowed area. At the tops of the furrows, the pipeline will penetrate further into a soft clay seabed due to the weight of adjacent free spans. Significantly different pipe-soil interactions are possible in these areas, especially with the presence of VIV suppression strakes. Accounting for these differences is essential when assessing thermal expansion issues, such as global lateral buckling and pipeline walking. This paper presents the findings for a test case of a pipeline with strakes on a furrowed seabed and provides suggestions for a user subroutine to be used for a pipeline system with beam elements in a finite-element analysis. The CEL method is first used to assess the impact of straked-pipeline penetration into a flat, soft-clay seabed, then to assess lateral and axial pipe resistances at different penetration depths. This information is used to develop a user subroutine for beam elements to further assess the pipeline on a furrowed seabed, in which the effects of vertical pipeline load and penetration on the lateral soil resistance are included. The test case also considers a typical analysis for a pipeline subjected to elevated temperature and pressure cycles.

Abstract Subsea wells present challenges for fatigue utilisation throughout the life of these high-value assets. New wells may be constructed at seabed locations where soil properties may be unfavourable or uncertain. Existing wells may require workover and eventual abandonment. This can lead to relatively small conductors supporting higher BOP masses than was envisaged when these wells were constructed. To address such stability issues during drilling and work-over operations, a BOP stack may be tethered to seabed anchors to provide lateral retention. The increased foundation stiffness raises the BOP characteristic frequency which suppresses motion of the BOP and significantly reduces fatigue of the conductor and wellhead. Real-time monitoring of the tether tensions and BOP characteristic frequency provide on-going verification of the efficacy of this fatigue suppressing technology as well as tracking structural integrity. For example, the ability of the monitoring system to detect loss of tether tension and the success of ROV intervention to reapply tension is demonstrated.

Laboratories in traditional radiochemistry courses typically involve basic and fundamental understanding in solvent extraction, ion exchange, precipitation, etc. procedures. With the increased focus on nuclear forensics in pre- and post-detonation scenarios different skill sets are now required for the student to learn. At the University of Texas we have developed two independent graduate courses in gamma-ray spectrometry and radiochemistry. Currently, we have amalgamated these two courses to 1. better serve our nuclear engineering graduate students, many of which are involved in nuclear forensics and 2. to attract both undergraduate and graduate students from the Chemistry Department. We incorporated gamma-ray spectrometry laboratories with several others which are nuclear forensics related. The seven laboratory sessions include half-life measurement of 137mBa (the daughter produce of 137Cs) and secular equilibrium, basic gamma and beta shielding, and gamma-ray spectrometry calibration, resolution and uncertainty in statistics. These labs have been augmented with four others including uranium fission product identification, 137Cs soil profile with Compton suppression, tritium analysis in water with a liquid scintillation counter and double replacement reaction.

Humic substances (HS) are abundant in the environment. They penetrate through water, soil, and air. They have plentiful fossil and renewable resources including oxidized brown coal, peat, sapropel, spent sulphite liquor, composts, and other organic waste. HS govern many vitally important ecosystem processes like maintenance of soil fertility, nutrients delivery to plants, mitigation of abiotic stresses, etc. Numerous examples on their beneficial effects to plants and other living organisms are reported. Still, due to complexity of humic molecular assemblies, they have been very limitedly tapped for practical needs. Here we introduce a concept of ecoadaptive chemistry, which implies molecular and functional studies of life-sustaining processes in nature aimed at their further transfer into ecoadaptive technologies via rational design of nature-like chemicals, materials, and processes (Perminova 2019). We show how the disclosed mechanisms of self-purification and self-healing implied by natural systems can be applied to molecular design of humics-based products (chemicals, materials) with the tailored properties. The examples will be given for direct chemical modification of HS by incorporation of phenolic units into molecular backbone of HS, for preparation of interpolyelectrolyte complexes with aminoorganolanes , for HS assisted synthesis of nanoparticles with the needed properties (iron (hydr)oxides, silver, gold), for preparation of HS-based hybrid nanomaterials. The possibilities for practical applications of the obtained humic derivatives, polyelectrolyte complexes, HS-stabilized nanoparticles and hybrid materials will be demonstrated. They include novel humics-based biocatalytic systems for manipulation of microbial metabolism (suppression of methane synthesis by methanogens), solid HS-clay emulsion stabilizers for eliminating of oil slicks, humics-based non-lactam inhibitors of beta-lactamases, HS-based nanomaterials for wound-healing. The developed approaches open a way for broad innovative applications of humics-based chemicals and materials both in the field of environmental protection, biotechnology, human and environmental health. They also contribute to further elaboration and development of the concept of ecoadaptive chemistry and technology. References Perminova, I.V. From green chemistry and nature-like technologies towards ecoadaptive chemistry and technology. Pure and Applied Chemistry 2019, 91(5), 851-864. DOI: 10.1515/pac2018-1110 Acknowledgement: This research was supported by the Russian Science Foundation 20-63- 47070. The studies were conducted in the framework of the Interdisciplinary Scientific and Educational School of M. V. Lomonosov Moscow State University “Future Planet and Global Environ-mental Change”.

VIVA is a vortex induced vibration (VIV) analysis software that to date has not been widely used as a design tool in the offshore oil and gas industry. VIVA employs a hydrodynamic database that has been benchmarked and calibrated against test data [1]. It offers relatively few input variables reducing the risk of user induced variability of results [2]. In addition to cross flow current induced standing wave vibration, VIVA has the capability of predicting traveling waves on a subsea riser, or a combination of standing and traveling waves. Riser boundary conditions including fixed, pinned, flex joint or SCR seabed interaction can be modeled using springs and dashpots. VIVA calculates riser natural frequencies and mode shapes and also has the flexibility to import external modal solutions. In this paper, the applicability of VIVA for the design of straked steel catenary risers (SCR) and top tensioned risers (TTR) is explored. The use of linear and rotational springs provided by VIVA to model SCR soil interaction and flex joint articulation is evaluated. Comparisons of the VIV fatigue damage output with internal and external modal solution is presented in this paper. This paper includes validation of the VIVA generated modal solution by comparing the modal frequencies and curvatures against a finite element (FE) model of the risers. Fatigue life is calculated using long term Gulf of Mexico (GoM) currents and is compared against the industry standard software SHEAR7. Three different lift curve selections in SHEAR7 are used for this comparison. The differences in riser response prediction by the two software tools are discussed in detail. The sensitivity of the VIVA predicted riser response to the absence of VIV suppression devices is presented in this paper. The riser VIV response with and without external FE generated modal input is compared and the relative merits of the two modeling approaches are discussed. Finally, the recommended approach for VIVA usage for SCR and TTR design is given.

Original objectives: Our initial project objectives were to 1) Determine and compare the composition of seed-colonizing microbial communities on seeds, 2) Determine the dynamics of development of microbial communities on seeds, and 3) Determine and compare the composition of seed-colonizing microbial communities with the composition of those in the soil and rhizosphere of the plants. Revisions to objectives: Our initial work on this project was hampered by the presence of native Pythium species in the soils we were using (in the US), preventing us from getting accurate assessments of spermosphere microbial communities. In our initial work, we tried to get around this problem by focusing on water potentials that might reduce damage from native Pythium species. This also prompted some initial investigation of the oomycete communities associated seedlings in this soil. However, for this work to proceed in a way that would allow us to examine seed-colonizing communities on healthy plants, we needed to either physically treat soils or amend soils with composts to suppress damage from Pythium. In the end, we followed the compost amendment line of investigation, which took us away from our initial objectives, but led to interesting work focusing on seed-associated microbial communities and their functional significance to seed-infecting pathogens. Work done in Israel was using suppressive compost amended potting mix throughout the study and did not have such problems. Our work focused on the following objectives: 1) to determine whether different plant species support a microbial induced suppression of Pythium damping-off, 2) to determine whether compost microbes that colonize seeds during early stages of seed germination can adequately explain levels of damping-off suppression observed, 3) to characterize cucumber seed-colonizing microbial communities that give rise to the disease suppressive properties, 4) assess carbon competition between seed-colonizing microbes and Pythium sporangia as a means of explaining Pythium damping-off suppression. Background: Earlier work demonstrated that seed-colonizing microbes might explain Pythium suppression. Yet these seed-colonizing microbial communities have never been characterized and their functional significance to Pythium damping-off suppression is not known. Our work set out to confirm the disease suppressive properties of seed-colonizing microbes, to characterize communities, and begin to determine the mechanisms by which Pythium suppression occurs. Major Conclusions: Compost-induced suppression of Pythium damping-off of cucumber and wheat can be explained by the bacterial consortia colonizing seeds within 8 h of sowing. Suppression on pea was highly variable. Fungi and archaea play no role in disease suppression. Potentially significant bacterial taxa are those with affinities to Firmicutes, Actinobacteria, and Bacteroidetes. Current sequencing efforts are trying to resolve these taxa. Seed colonizing bacteria suppress Pythium by carbon competition, allowing sporangium germination by preventing the development of germ tubes. Presence of Pythium had a strong effect on microbial community on the seed.

Concentrated flow erosion in rills, pipes, ephermal gullies, and gullies is a major contributor of downstream sedimentation. When rill or gullies form in a landscape, a 3- to 5-fold increase in soil loss commonly occurs. The balance between the erosive power of the flow and the erosion resistance of the bed material determines the rate of concentrated flow erosion. The resistance of the bed material to detachment depends primarily on the magnitude of the interparticle forces or cohesion holding the particles and aggregates together. The effect of soil properties on bed material resistance and concentrated flow erosion was evaluated both in the laboratory and field. Both rill erodibility and critical hydraulic shear were greater when measured in 9.0 m long rills under field conditions compared with laboratory mini-flumes. A greater hydraulic shear was required to initiate erosion in the field compared to the mini-flume because of the greater aggregate and clod size and stability. Once erosion was initiated, however, the rate of erosion as a function of hydraulic shear was greater under field conditions because of the greater potential for slaking upon wetting and the greater soil surface area exposed to hydraulic shear. Erosion tests under controlled laboratory conditions with the mini-flume allowed individual soil variables to be studied. Attempts to relate rill erosion to a group soil properties had limited success. When individual soil properties were isolated and studied separately or grouped separately, some trends were identified. For example, the effect of organic carbon on rill erodibility was high in kaolinitic soils, low in smectitic soils, and intermediate in the soils dominated by illite. Slow prewetting and aging increased the cohesion forces between soil particles and decreased rill erodibility. Quick prewetting increased aggregate slaking and increased erodibility. The magnitude of the effect of aging depended upon soil type. The effect of clay mineralogy was evaluated on sand/clay mixtures with montmorillonite (M), Illite (I), and kaolinite (K) clays. Montmorillonite/sand mixtures were much less erodible than either illite or kaolonite sand mixtures. Na-I and Na-K sand mixtures were more erodible than Ca-I and Ca-K due to increased strength from ionic bonding and suppression of repulsive charges by Ca. Na-M was less erodiblethan Ca-M due to increased surface resulting from the accessibility of internal surfaces due to Na saturation. Erodibility decreased when salt concentration was high enough to cause flocculation. This occurred between 0.001 mole L-1 and 0.01 mole L-1. Measuring rill erodibility in mini-flumes enables the measurement of cohesive forces between particles and enhances our ability to learn more about cohesive forces resisting soil detachment under concentrated water flow.

PGPR bacteria include taxonomically diverse bacterial species that function for improving plant mineral nutrition, stress tolerance, and disease suppression. A number of PGPR are being developed and commercialized as soil and seed inoculants, but to date, their interactions with resident bacterial populations are still poorly understood, and-almost nothing is known about the effects of soil management practices on their population size and activities. To this end, the original objectives of this research project were: 1) To examine microbial community interactions with plant-growth-promoting rhizobacteria (PGPR) and their plant hosts. 2) To explore the factors that affect PGPR population size and activity on plant root surfaces. In our original proposal, we initially prqposed the use oflow-resolution methods mainly involving the use of PCR-DGGE and PLFA profiles of community structure. However, early in the project we recognized that the methods for studying soil microbial communities were undergoing an exponential leap forward to much more high resolution methods using high-throughput sequencing. The application of these methods for studies on rhizosphere ecology thus became a central theme in these research project. Other related research by the US team focused on identifying PGPR bacterial strains and examining their effective population si~es that are required to enhance plant growth and on developing a simulation model that examines the process of root colonization. As summarized in the following report, we characterized the rhizosphere microbiome of four host plant species to determine the impact of the host (host signature effect) on resident versus active communities. Results of our studies showed a distinct plant host specific signature among wheat, maize, tomato and cucumber, based on the following three parameters: (I) each plant promoted the activity of a unique suite of soil bacterial populations; (2) significant variations were observed in the number and the degree of dominance of active populations; and (3)the level of contribution of active (rRNA-based) populations to the resident (DNA-based) community profiles. In the rhizoplane of all four plants a significant reduction of diversity was observed, relative to the bulk soil. Moreover, an increase in DNA-RNA correspondence indicated higher representation of active bacterial populations in the residing rhizoplane community. This research demonstrates that the host plant determines the bacterial community composition in its immediate vicinity, especially with respect to the active populations. Based on the studies from the US team, we suggest that the effective population size PGPR should be maintained at approximately 105 cells per gram of rhizosphere soil in the zone of elongation to obtain plant growth promotion effects, but emphasize that it is critical to also consider differences in the activity based on DNA-RNA correspondence. The results ofthis research provide fundamental new insight into the composition ofthe bacterial communities associated with plant roots, and the factors that affect their abundance and activity on root surfaces. Virtually all PGPR are multifunctional and may be expected to have diverse levels of activity with respect to production of plant growth hormones (regulation of root growth and architecture), suppression of stress ethylene (increased tolerance to drought and salinity), production of siderophores and antibiotics (disease suppression), and solubilization of phosphorus. The application of transcriptome methods pioneered in our research will ultimately lead to better understanding of how management practices such as use of compost and soil inoculants can be used to improve plant yields, stress tolerance, and disease resistance. As we look to the future, the use of metagenomic techniques combined with quantitative methods including microarrays, and quantitative peR methods that target specific genes should allow us to better classify, monitor, and manage the plant rhizosphere to improve crop yields in agricultural ecosystems. In addition, expression of several genes in rhizospheres of both cucumber and whet roots were identified, including mostly housekeeping genes. Denitrification, chemotaxis and motility genes were preferentially expressed in wheat while in cucumber roots bacterial genes involved in catalase, a large set of polysaccharide degradation and assimilatory sulfate reduction genes were preferentially expressed.

The ability to detect and classify buried objects using thermal infrared imaging is affected by the environmental conditions at the time of imaging, which leads to an inconsistent probability of detection. For example, periods of dense overcast or recent precipitation events result in the suppression of the soil temperature difference between the buried object and soil, thus preventing detection. This work introduces an environmentally informed framework to reduce the false alarm rate in the classification of regions of interest (ROIs) in thermal IR images containing buried objects. Using a dataset that consists of thermal images containing buried objects paired with the corresponding environmental and meteorological conditions, we employ a machine learning approach to determine which environmental conditions are the most impactful on the visibility of the buried objects. We find the key environmental conditions include incoming shortwave solar radiation, soil volumetric water content, and average air temperature. For each image, ROIs are computed using a computer vision approach and these ROIs are coupled with the most important environmental conditions to form the input for the classification algorithm. The environmentally informed classification algorithm produces a decision on whether the ROI contains a buried object by simultaneously learning on the ROIs with a classification neural network and on the environmental data using a tabular neural network. On a given set of ROIs, we have shown that the environmentally informed classification approach improves the detection of buried objects within the ROIs.

The western flower thrips (WFT), Frankliniella occidentalis (Pergande), is a serious widespread pest of vegetable and ornamental crops worldwide. Chemical control for Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) on floriculture or vegetable crops can be difficult because this pest has developed resistance to many insecticides and also tends to hide within flowers, buds, and apical meristems. Predatory bugs, predatory mites, and entomopathogenic nematodes are commercially available in both the US and Israel for control of WFT. Predatory bugs, such as Orius species, can suppress high WFT densities but have limited ability to attack thrips within confined plant parts. Predatory mites can reach more confined habitats than predatory bugs, but kill primarily first-instar larvae of thrips. Entomopathogenic nematodes can directly kill or sterilize most thrips stages, but have limited mobility and are vulnerable to desiccation in certain parts of the crop canopy. However, simultaneous use of two or more agents may provide both effective and cost efficient control of WFT through complimentary predation and/or parasitism. The general goal of our project was to evaluate whether suppression of WFT could be enhanced by inundative or inoculative releases of Orius predators with either predatory mites or entomopathogenic nematodes. Whether pest suppression is best when single or multiple biological control agents are used, is an issue of importance to the practice of biological control. For our investigations in Texas, we used Orius insidiosus(Say), the predatory mite, Amblyseius degeneransBerlese, and the predatory mite, Amblyseius swirskii(Athias-Henriot). In Israel, the research focused on Orius laevigatus (Fieber) and the entomopathogenic nematode, Steinernema felpiae. Our specific objectives were to: (1) quantify the spatial distribution and population growth of WFT and WFT natural enemies on greenhouse roses (Texas) and peppers (Israel), (2) assess interspecific interactions among WFT natural enemies, (3) measure WFT population suppression resulting from single or multiple species releases. Revisions to our project after the first year were: (1) use of A. swirskiiin place of A. degeneransfor the majority of our predatory mite and Orius studies, (2) use of S. felpiaein place of Thripinema nicklewoodi for all of the nematode and Orius studies. We utilized laboratory experiments, greenhouse studies, field trials and mathematical modeling to achieve our objectives. In greenhouse trials, we found that concurrent releases of A.degeneranswith O. insidiosusdid not improve control of F. occidentalis on cut roses over releases of only O. insidiosus. Suppression of WFT by augmentative releases A. swirskiialone was superior to augmentative releases of O. insidiosusalone and similar to concurrent releases of both predator species on cut roses. In laboratory studies, we discovered that O. insidiosusis a generalist predator that ‘switches’ to the most abundant prey and will kill significant numbers of A. swirskiior A. degeneransif WFTbecome relatively less abundant. Our findings indicate that intraguild interactions between Orius and Amblyseius species could hinder suppression of thrips populations and combinations of these natural enemies may not enhance biological control on certain crops. Intraguild interactions between S. felpiaeand O. laevigatus were found to be more complex than those between O. insidiosusand predatory mites. In laboratory studies, we found that S. felpiaecould infect and kill either adult or immature O. laevigatus. Although adult O. laevigatus tended to avoid areas infested by S. felpiaein Petri dish arenas, they did not show preference between healthy WFT and WFT infected with S. felpiaein choice tests. In field cage trials, suppression of WFT on sweet-pepper was similar in treatments with only O. laevigatus or both O. laevigatus and S. felpiae. Distribution and numbers of O. laevigatus on pepper plants also did not differ between cages with or without S. felpiae. Low survivorship of S. felpiaeafter foliar applications to sweet-pepper may explain, in part, the absence of effects in the field trials. Finally, we were interested in how differential predation on different developmental stages of WFT (Orius feeding on WFT nymphs inhabiting foliage and flowers, nematodes that attack prepupae and pupae in the soil) affects community dynamics. To better understand these interactions, we constructed a model based on Lotka-Volterra predator-prey theory and our simulations showed that differential predation, where predators tend to concentrate on one WFT stage contribute to system stability and permanence while predators that tend to mix different WFT stages reduce system stability and permanence.