[Truncated abstract] Weeds are a major limitation to agricultural and horticultural production and the main method of control is the use of herbicides. In addition to the resulting chemical pollution of the environment, the wide spread and continues use of herbicides have resulted in many weeds developing resistance to commonly used herbicides. This study investigated the potential of using green manures as a cultural method of control of weed invasion in agricultural fields. To understand the general mechanisms involved in the suppression of seed germination in green manure amended soils, seeds of crop species with little or no dormancy requirements were used in certain studies. Lettuce (Lactuca sativa) and cress (Lepidium sativum) seeds were sown to a sandy soil amended with green manures of lupin (Lupinus angustifolius), Brassica juncea, or oats (Avena sativa) to determine if the amendments affected seed germination and/or decay. It was hypothesised that the addition of plant material would increase the microbial activity of the soil thereby increasing seed decay, under laboratory and greenhouse conditions. Initial experiments used lettuce, cress and lupin seeds. Lettuce and cress are commonly used as standard test species for seed viability studies. Subsequent experiments used seeds of annual ryegrass (Lolium rigidum), silver grass (Vulpia bromoides), wild radish (Raphanus raphanistrum) and wild oat (Avena fatua) as these weed species are commonly found throughout agricultural regions in Western Australia. Amending the soil with lupin or Brassica green manure was established as treatments capable of developing environments suppressive to seed germination. Lupin residues as green manure showed the strongest inhibition of seed germination and seed decay. The decay of certain seeds was enhanced with changes to soil microbial activity, dissolved organic carbon and carbon and nitrogen amounts in lupin amended soil. Seeds of weed species were decayed in lupin amended soil, but showed varied degree of decay. Annual ryegrass and silver grass were severely decayed and wild oat and wild radish were less decayed, in lupin amended soil.

Submitted by Izabel Franco (izabel-franco@ufscar.br) on 2016-10-03T17:39:45Z No. of bitstreams: 1 DissLCDS.pdf: 1437971 bytes, checksum: b520fddddb51565a19856b3d8f57911f (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-10-20T18:29:08Z (GMT) No. of bitstreams: 1 DissLCDS.pdf: 1437971 bytes, checksum: b520fddddb51565a19856b3d8f57911f (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-10-20T18:29:22Z (GMT) No. of bitstreams: 1 DissLCDS.pdf: 1437971 bytes, checksum: b520fddddb51565a19856b3d8f57911f (MD5) / Made available in DSpace on 2016-10-20T18:29:30Z (GMT). No. of bitstreams: 1 DissLCDS.pdf: 1437971 bytes, checksum: b520fddddb51565a19856b3d8f57911f (MD5) Previous issue date: 2016-06-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Insect symbionts may have unknown functions in the interaction between insect-plant and insect with microorganisms that co-inhabit the same space. The objective of this study was to investigate the antagonism potential of symbiont microbiota from oral secretion D. saccharalis collected in the field, against Fusarium verticillioides and Colletotrichum falcatum pathogens commonly found inside the cane. For this, 4° and 5° instar caterpillars were collected inside sugarcane varieties RB-835 054 and SP- 813 250, and brought to the lab inside the cane stalks. The microbiota of oral secretion was transferred to two selective media, NA (nutrient agar) for bacteria and DRBC (dicloran Rose Bengal Chloramphenicol) for yeast. Based on morphology and coloration of the colonies twenty colonies of bacteria and yeast were selected. Four culture media were tested in co-cultivation of F. verticillioides and C. falcatum versus bacteria or yeast isolates: PDA (potato, dextrose, agar), YEPD (yeast extract, peptone, dextrose), CCS (supplemented cane broth) and NA (Nutrient Agar). The most suitable culture medium for growth of most microorganisms was BDA. Antagonism potential of 82 bacterial isolates and 87 yeast isolates to C. falcatum and F. verticillioides was assessed using a visual scale of categories 1 to 4, with 4 being the maximum degree of antagonism. Isolates that allocated category greater than or equal to 2 were evaluated in co-culture with C. falcatum and F. verticillioides as the percentage of growth inhibition. It was possible to identify four isolates of bacteria which have the potential to inhibit growth of pathogens and 9 isolates with the same potential but with much lower percentages. These results demonstrate that some isolates of bacteria and yeast may influence the relationship between the bit-rot complex and sugarcane plant, may in future be used as a biological control of these pathogens or have some molecules of biotechnological interest extracted and purified. / Simbiontes de insetos podem ter funções desconhecidas na interação entre insetoplanta e do inseto com microrganismos que co-habitam o mesmo espaço. O objetivo desse estudo foi investigar o potencial de antagonismo da microbiota simbionte, presentes na secreção oral de Diatraea saccharalis, com os fitopatógenos Fusarium verticillioides e Colletotrichum falcatum que habitam o colmo de cana-de-açúcar. Para isso, foram coletadas, nas variedades de cana RB-835054 e SP-813250, lagartas de 4° e 5° instar e trazidas para o laboratório junto aos toletes de cana. A microbiota da secreção oral foi transferida para dois meios de cultura seletivos, NA (nutrient agar) para bactérias e DRBC (Dicloran Rosa-de-Bengala Cloranfenicol) para leveduras. Baseado na morfologia e coloração das colônias, foram selecionadas, vinte colônias de bactéria e também de levedura de 5 lagartas. Foram testados quatro meios de cultura: BDA (batata, dextrose, agar), YEPD (yeast extract, peptone, dextrose), CCS (caldo-de-cana suplementado) e NA para os testes de cultivo pareado. O meio de cultura mais adequado para o crescimento da maioria dos microrganismos foi o BDA. O potencial de antagonismo de 82 isolados de bactéria e 87 isolados de levedura a C. falcatum e F. verticillioides foi avaliado através de uma escala visual de categorias de 1 a 4, sendo 4 o grau máximo de antagonismo. Os isolados a que foi atribuída categoria maior ou igual a dois foram avaliados em co-cultivo com C. falcatum e F. verticillioides quanto à porcentagem de inibição do crescimento. Foi possível identificar 4 isolados de bactéria que tem o potencial de inibir o crescimento dos fitopatógenos e 9 isolados com o mesmo potencial, porém com porcentagens menores. Esses resultados demonstram que alguns isolados de bactérias e leveduras podem influenciar na relação existente entre o complexo broca-podridão e a planta de cana-de-açúcar, podendo, futuramente, serem utilizados como controle biológico desses fitopatógenos ou terem algumas moléculas de interesse biotecnológico extraída e purificada.

Made available in DSpace on 2015-03-26T13:52:00Z (GMT). No. of bitstreams: 1 texto completo.pdf: 1252953 bytes, checksum: 5c4901cfbd21633e7c02d3de0ad4790a (MD5) Previous issue date: 2014-02-20 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Endophytic fungi are those living at least a part of their life cycle within plant tissue, apparently without causing any damage to their hosts. These microorganisms have been studied for their capacity to produce secondary metabolites of biotechnological interest, and also for their ability for biological control of phytopathogens. Endophytic fungi have been isolated from a wide variety of plant species, including crops such as common bean (Phaseolus vulgaris L.). Fungi from the genus Diaporthe were abundant in the endophytic community of this legume. The objectives of this study were to evaluate the antimicrobial activity and the potential use of endophytic fungi of P. vulgaris in the control of phytopathogens of bean, and to analyze phylogenetic relationships and genetic variability of endophytic fungi of the genus Diaporthe isolated from P. vulgaris. Dual culture assays were performed between ninety endophytic fungi and four phytopathogenic fungi (Colletotrichum lindemuthianum, Fusarium oxysporum, Rhizoctonia solani and Sclerotinia sclerotiorum) to assess for the ability of endophytic fungi inhibit the growth of phytopathogens. The isolates that were able to inhibit the four phytopathogens tested were selected for cultivation and obtention of metabolites crude extracts. These extracts were evaluated for antibacterial and antifungal activity. The sequences of the ITS region of rDNA of the isolates of the genus Diaporthe from common bean, along with the partial sequences of the genes encoding translation elongation factor 1-α, β-tubulin and calmodulin were used for the study of the phylogenetic relationships of these isolates. Molecular markers based on sequences of retrotransposons, IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism), were used for the analysis of genetic variability. It was found that endophytic fungi of common bean are able to inhibit the in vitro growth of phytopathogenic fungi and that metabolites crude extracts of endophytic exhibit significant antimicrobial activity especially regarding the inhibitory activity against Gram-positive bacteria (Listeria monocytogenes, Bacillus cereus, B. subtilis and Staphylococcus aureus). Diaporthe sp., D. infecunda, D. melonis and D. phaseolorum are members of the endophytic fungal community in the common bean as verified by multilocus phylogenetic analysis. Cluster analysis, conducted with pooled data from IRAP and REMAP markers, was consistent regarding what was observed in multilocus phylogeny and revealed the existence of high genetic variability, particularly among isolates of D. infecunda. It was concluded that the metabolites crude extracts of endophytic fungi of common bean exhibit promising antimicrobial activity; that endophytic fungi used in this study have the potential to control phytopathogens that affect the bean crop; the multilocus phylogenetic approach was more effective than individual analysis of ITS sequences in the study of phylogenetic relationships of endophytic fungi of the genus Diaporthe from common bean and that IRAP and REMAP markers can be employed in the study of genetic variability of this genus of fungi. / Fungos endofíticos são aqueles que vivem, em pelo menos uma parte de seu ciclo de vida, no interior de tecidos vegetais, sem causar aparentemente qualquer dano a seus hospedeiros. Esses micro-organismos têm sido estudados em relação à capacidade de produzirem metabólitos secundários de interesse biotecnológico e quanto ao potencial de controle biológico de fitopatógenos. Fungos endofíticos já foram isolados de uma ampla variedade de espécies vegetais, incluindo culturas agrícolas como o feijoeiro comum (Phaseolus vulgaris L.). O gênero Diaporthe foi um dos mais abundantes na comunidade endofítica dessa leguminosa. Os objetivos do presente estudo foram avaliar a atividade antimicrobiana e o potencial de uso de fungos endofíticos de P. vulgaris no controle de fitopatógenos da cultura do feijoeiro e analisar as relações filogenéticas e a variabilidade genética de fungos endofíticos do gênero Diaporthe isolados de P. vulgaris. Ensaios de cultura dupla entre 90 isolados endofíticos e quatro fungos fitopatogênicos (Colletotrichum lindemuthianum, Fusarium oxysporum, Rhizoctonia solani e Sclerotinia sclerotiorum) foram realizados para verificar a capacidade dos isolados endofíticos inibirem o crescimento dos fitopatógenos. Os isolados que foram capazes de inibir os quatro fitopatógenos testados foram selecionados para cultivo e obtenção de extratos brutos de metabólitos. Esses extratos foram avaliados quanto à atividade antibacteriana e antifúngica. As sequências da região ITS do rDNA dos isolados do gênero Diaporthe do feijoeiro, juntamente com as sequências parciais dos genes codificam o fator de elongação da tradução 1-α, β-tubulina e calmodulina, foram utilizadas para o estudo das relações filogenéticas desses isolados. Marcadores moleculares baseados em sequências de retrotransposons, IRAP (Inter-Retrotransposon Amplified Polymorphism) e REMAP (Retrotransposon-Microsatellite Amplified Polymorphism), foram utilizados para a análise de variabilidade genética. Foi constatado que os fungos endofíticos do feijoeiro comum são capazes de inibir o crescimento in vitro de fungos fitopatogênicos e, que extratos brutos de metabólitos de isolados endofíticos exibem atividade antimicrobiana significativa, principalmente em relação à atividade inibitória sobre bactérias Gram-positivas (Listeria monocytogenes, Bacillus cereus, B. subtilis e Staphylococcus aureus). Por meio de análise filogenética multilocus, verificou-se que Diaporthe sp., D. infecunda, D. melonis e D. phaseolorum são integrantes da comunidade fúngica endofítica do feijoeiro comum. A análise de agrupamento, realizada com os dados dos marcadores IRAP e REMAP em conjunto, foi coerente em relação ao que foi verificado na filogenia multilocus e, revelou a existência de grande variabilidade genética, sobretudo entre os isolados de D. infecunda. Concluiu-se que extratos brutos de metabólitos de fungos endofíticos do feijoeiro exibem atividade antimicrobiana promissora; que fungos endofíticos utilizados neste estudo apresentam potencial para controle de fitopatógenos que acometem a cultura do feijoeiro; que a abordagem filogenética multilocus foi mais efetiva que análise individual de sequências de ITS no estudo das relações filogenéticas de fungos endofíticos do gênero Diaporthe do feijoeiro e que marcadores IRAP e REMAP podem ser empregados no estudo de variabilidade genética de fungos desse gênero.

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2015-12-04T10:24:50Z No. of bitstreams: 2 Dissertação - Paulo Roberto da Mota - 2015.pdf: 1806908 bytes, checksum: d6798b75ceeef2f456ddde6fbf387e77 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2015-12-04T10:27:57Z (GMT) No. of bitstreams: 2 Dissertação - Paulo Roberto da Mota - 2015.pdf: 1806908 bytes, checksum: d6798b75ceeef2f456ddde6fbf387e77 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2015-12-04T10:27:57Z (GMT). No. of bitstreams: 2 Dissertação - Paulo Roberto da Mota - 2015.pdf: 1806908 bytes, checksum: d6798b75ceeef2f456ddde6fbf387e77 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2015-08-28 / Fungi of the genus Trichoderma have emerged as biological control agents, especially those belonging to the species Trichoderma harzianum with various mechanisms involved include production of antibiotics, mycoparasitism, competition for nutrients and host plant resistance induction. Mycoparasitism is a sequential process that involves recognition of the host contact, adhesion, expression of specific genes and secretion of secondary metabolites. Several hydrolytic enzymes are involved in this process among them chitinases, beta-glucanases and proteases. Recent studies of T. harzianum interaction with some pathogens have shown that other enzymes may also be involved in this mechanism, among which alphamannosidase. Alpha-mannosidase has an essential role in the recycling of glycoproteins in filamentous fungi, but little is known about the role of these enzymes in mycoparasitism. This study aims to characterize the expression of T. alphamannosidase gene harzianum after growth in cell wall of Sclerotinia sclerotiorum (SS), Fusarium solani (FS) and Fusarium oxysporum (FO) as well as during the interaction in vivo . It was used as a control cell wall T. harzianum (TH). Also, jobs obtaining mutants of this gene in T. harzianum were performed. Our data show that alpha-mannosidase gene was highly expressed as T. harzianum grown in the presence of cell wall SS (4.5X), FS (18X) and FO (75X) compared to the control TH (1X). In comparison situation it was noticed a 75X greater expression in TH x FO state during contact as compared with the control (TH x TH). In other situations of confrontation did not observe a significant increase in expression. The promoter region, the selection mark and the terminator region of the alpha-mannosidase of T. harzianum gene was cloned into the pRS426 vector, and the deletion cassette was assembled by the recombination technique in Saccharomyces cerevisiae. Then, these vectors were used for transformation of T. harzianum and transformants were obtained by selection on plates containing hygromycin b. Approximately 50 transformants were obtained, but none of the alpha-mannosidase gene was successfully deleted. Obtaining more transformants is necessary for us to have a mutant alpha-mannosidase gene deleted. / Fungos do gênero Trichoderma têm se destacado como agentes de controle biológico, principalmente aqueles pertencentes à espécie Trichoderma harzianumcom vários mecanismos envolvidos incluem produção de antibióticos, micoparasitismo, competição por nutrientes e indução de resistência da planta hospedeira. Micoparasitismo é um processo sequencial que envolve reconhecimento do hospedeiro, contato, adesão, expressão de genes específicos e secreção de metabólitos secundários. Várias enzimas hidrolíticas estão envolvidas neste processo dentre elas quitinases, beta-glucanases e proteases. Estudos recentes de interação de T. harzianum com alguns fitopatógenos tem demonstrado que outras enzimas podem também estar envolvidas neste mecanismo, dentre elas as alfamanosidases. As alfa-manosidases tem um papel fundamental na reciclagem de glicoproteínas em fungos filamentosos, mas pouco se sabe sobre o papel destas enzimas no micoparasitismo. Este trabalho tem como objetivo a caracterização da expressão do gene de alfa-manosidase de T. harzianumapós crescimento em parede celular de Sclerotinia sclerotiorum (SS), Fusarium solani (FS) e Fusarium oxysporum (FO), bem como durante a interação in vivo. Como controle foi utilizado parede celular de T. harzianum (TH). Além disto, trabalhos de obtenção de mutantes deste gene em T. harzianum foram realizados. Nossos dados mostraram que o gene de alfa-manosidase foi altamente expresso quando T. harzianum cresceu na presença de parede celular de SS (4.5X), FS (18X) e FO (75X) quando comparado com o controle TH (1X). Em situação de confronto foi observado uma expressão de 75X maior na situação TH x FO durante o contato, quando comparado com o controle (TH x TH). Na outras situações de confronto não observamos um aumento significativo de expressão. A região promotora, a marca de seleção e a região terminadora do gene da alfa-manosidase de T. harzianumfoi clonado no vetor pRS426 e o cassete de deleção foi montado através da técnica de recombinação em Saccharomyces cerevisiae . Em seguida, estes vetores foram utilizados para a transformação de T. harzianume os transformantes foram obtidos por seleção em placas contendo higromicina b. Aproximadamente 50 transformantes foram obtidos, mas em nenhum deles o gene da alfa-manosidase foi deletado com sucesso. A obtenção de mais transformantes se faz necessário para que possamos ter um mutante com o gene da alfa-manosidase deletado.

Until now little attention has been paid to the development of military capabilities designed to target food crops with biological warfare agents. This book represents the first substantive study of state-run activities in this field. It shows that all biological warfare programmes have included a component concerned with the development of anti-crop biological warfare agents and munitions. Current concern over the proliferation of biological weapons is placed in the context of the initiative to strengthen the Biological and Toxin Weapons Convention. The book concludes by arguing that the risks posed by this form of warfare can be minimised, but that this would depend largely on the effective and efficient implementation of regimes concerning the peaceful use and control of plant pathogens that pose a risk to human health and the environment.

Submitted by (lucia.rodrigues@ufrpe.br) on 2017-02-20T14:59:48Z No. of bitstreams: 1 Albaneyde Leite Lopes.pdf: 563588 bytes, checksum: 42574d0f1d68741b58e267ad9448a570 (MD5) / Made available in DSpace on 2017-02-20T14:59:48Z (GMT). No. of bitstreams: 1 Albaneyde Leite Lopes.pdf: 563588 bytes, checksum: 42574d0f1d68741b58e267ad9448a570 (MD5) Previous issue date: 2009-03-20 / Papaya rot resulting from fungal infections causes high post-harvest losses. The influence of temperature (5, 10, 15, 20, 25, 30 and 35 oC) and wetting period (0, 12, 24, 36, 48, 60 and 72 h) in the incidence and severity of post-harvest rot in papaya caused by Alteraria alternata, Cladosporium herbarum, Colletotrichum gloeosporioides, Fusarium verticillioides, Geotrichum candidum and Lasiodiplodia theobromae, and their influence on physicochemical characteristics . The temperature significantly influenced the incidence and severity of rot. There was a higher incidence and severity in fruits incubated in the range of 25 to 35 ºC. The temperature in the range of 5 to 10 ºC did not allow the development of A. alternata, C. herbarum, C. gloeosporioides and L. theobromae. Analyzes of pH, titratable total acidity (TTA) and total soluble solid (TSS) showed no significant differences when compared to the control. A second experiment was carried out to verify the possibility of control through the use of gamma radiation (0, 0.6, 0.8, 1.0, 1.2, 1.4, 1.8, 2.4 And 2.8 kGy), with Cobalt 60 as a source. The parameters evaluated were: comic growth, sporulation, pathogenicity of fungi after irradiation and the physicochemical characteristics of papaya. For C. herbarum and F. verticillioides a decrease in mycelial growth occurred as the doses were increased. However, C. gloeosporioides and L. theobromae at doses of 0.6 to 1.4 kGy and G. candidum at doses of 1.4 to 2.2 kGy were more efficient in reducing the mycelial growth of these fungi. However, all the doses used stimulated the mycelial growth of A. alternata. The results demonstrated that in general, as the doses increased, there was a reduction in the number of conidia. Regarding the effect of radiation on the pathogenicity of fungal species, only L. theobromae at the doses tested, did not lose pathogenicity in relation to the other fungi. The physico-chemical characteristics of the fruits subjected to radiation did not compromise the commercialization and consumption 'in natura'. / As podridões em mamão resultantes de infecções de fungos causam perdas elevadas em pós-colheita. Diante da necessidade do conhecimento de fatores ambientais que favorecem a infecção por esses agentes, foi avaliada a influência da temperatura (5, 10, 15, 20, 25, 30 e 35 oC), e período de molhamento (0, 12, 24, 36, 48, 60 e 72 h) na incidência e severidade de podridões pós-colheita em mamão causada por Alteraria alternata, Cladosporium herbarum, Colletotrichum gloeosporioides, Fusarium verticillioides, Geotrichum candidum e Lasiodiplodia theobromae, e a influência desses sobre as características físico-químicas. A temperatura influenciou significativamente a incidência e a severidade de podridões. Ocorreu maior incidência e severidade em frutas incubadas na faixa em torno de 25 a 35 ºC. A temperatura na faixa de 5 a 10 ºC não permitiu o desenvolvimento de A. alternata, C. herbarum, C. gloeosporioides e L. theobromae. Análises de pH, acidez total titulável (ATT) e sólido solúvel total (SST) não apresentaram diferenças significativas quando comparados com a testemunha. Um segundo experimento foi realizado com o objetivo de verificar a possibilidade de controle através do uso da radiação gama (0; 0,6; 0,8; 1,0; 1,2; 1,4; 1,8; 2,4 e 2,8 kGy), tendo como fonte o Cobalto 60. Os parâmetros avaliados foram: crescimentomicelial, esporulação, patogenicidade dos fungos após irradiação e as características físico-químicas do mamão. Para C. herbarum e F. verticillioides ocorreu uma diminuição do crescimento micelial à medida que se aumentaram as doses. Já o C. gloeosporioides e L. theobromae nas doses de 0,6 a 1,4 kGy, e G. candidum nas doses de 1,4 a 2,2 kGy foram mais eficientes na redução do crescimento micelial destes fungos. Entretanto, todas as doses utilizadas estimularam o crescimento micelial de A. alternata. Os resultados demonstraram que, de modo geral, à medida que as doses foram aumentando, houve uma redução no número de conídios. Em relação ao efeito da radiação sobre a patogenicidade das espécies fúngicas, apenas L. theobromae nas doses testadas, não perdeu a patogenicidade em relação aos demais fungos. As características físico-químicas das frutas submetidas à radiação não comprometeram a comercialização e o consumo ‘in natura’.

5 Absctract Environment and demographic characteristics of host population are important factors affecting incidence and severity of plant diseases. The aim of this study was to reveal possible effects of microclimatic and edaphic characteristics and host population demographic factors on the biotrophic pathogen Puccinia cribrata, microcyclic rust parasitising clonal evergreen plant Vinca minor. I studied the ecology of this pathosystem in natural populations of V. minor in the Soča valley in the Julian Alps in Slovenia. Rugged terrain of the Soča valley with different bedrocks allowed to study pathogen distribution at topographically diverse forest and scrub sites, greatly differing in soil depth and canopy structure. P. cribrata was significantly more likely to occur in the themophilous forest with shallow calcareous soils and open canopy than in the mesophilous forest types. Its prevalence (proportion of diseased stems in population) was also highest in this type of vegetation. Most important host population factors were population size and population density positively affecting incidence and prevalence respectively. Additionally, I tested various vegetation and topographic indexes derived from remote sensing for usability in prediction models. It appears that vegetation indexes connected with canopy...

Les mécanismes expliquant le maintien de la diversité végétale dans les forêts tropicales sont mal connus. Une hypothèse particulièrement étudiée est l’hypothèse Janzen-Connell qui postule que ces mécanismes sont essentiellement causés par les interactions entre les plantes et leurs ennemis naturels, en particulier les organismes pathogènes. Dans cette thèse, nous nous sommes donc intéressés aux agents pathogènes présents dans les sols d’une forêt guyanaise et à leur lien de spécificité avec les plantes. Dans le cas où l’hypothèse Janzen-Connell serait vérifiée, on peut s’attendre à ce que les plantes structurent les communautés de micro-organismes pathogènes. Nos travaux se sont focalisés sur les Oomycètes et en particulier les Phytophthora, pathogènes des arbres très importants, mais nous nous sommes aussi intéressés aux champignons pathogènes. Ainsi, nous avons développé et comparé des jeux d’amorces PCR spécifiques des Phytophthora et des Péronosporomycètes afin d’étudier ces organismes par metabarcoding. Ces amorces ont ensuite servi à étudier la diversité des communautés de Phytophthora dans des échantillons de sols de deux sites forestiers de Guyane Française prélevés au pied d’arbres appartenant à 10 familles végétales. Une faible diversité a été retrouvée, avec seulement 8 taxons en tout, et la très large dominance d’un complexe d’espèces Phytophthora heveae. La structuration par la plante-hôte de ces communautés est plutôt faible. Dans une étude complémentaire, nous avons analysé la diversité des Oomycètes et des champignons pathogènes dans les sols et les litières de six plantations monospécifiques et au sein d’une forêt naturelle de Guyane. La structuration par l’hôte s’est avérée nulle pour les Oomycètes et faible pour les champignons pathogènes. Enfin, nous n’avons pas réussi à déclencher expérimentalement des mortalités ou dépérissements par des Oomycètes sur le wacapou, une espèce d’arbre guyanaise, via des inoculations de sols de forêt. Au final, les résultats de cette thèse ne supportent pas l’hypothèse selon laquelle les Oomycètes seraient d’importants acteurs du maintien de la diversité végétale dans les forêts tropicales. Par ailleurs, ils nous interrogent sur la faible diversité de ce groupe de microorganismes dans les sols et litières dans un hotspot de diversité végétale. / The mecanisms implied in the maintenance of plant diversity in tropical forests are still poorly known. One particularly studied hypothesis is the Janzen-Connell hypothesis, which posits that these mecanisms are essentially caused by the interactions between plant and their natural enemies, including pathogenic organisms. In this thesis, we looked at the pathogenic organisms present in the soils of a Guyanese forest, and the specificity of their interactions withplants. In the case where the Janzen-Connell hypothesis would be verified, we could expect that pathogenic micro-organisms communities would be structured by plants. Our works focused on Oomycetes and especially the Phytophthora, which are very important pathogens of trees, but we also took an interest on pathogenic Fungi. Thus, we developed PCR primer sets specific of the Phytophthora and Peronosporomycete groups, in order to study these organismsthroughmetabarcoding. These primers were then used to investigate the community of Phytophthora in soils sampled from two French Guiana sites, near trees belonging to 10 families. A low diversity was described, with a total of only 8 taxas, and the overwhelming dominance of the species complex P. heveae. A weak host effect was detected. In a complementary study, we looked at the diversity of Oomycetes and Fungi in soils and litters of six monospecific tree plantations and a Guianese natural forest. Structuration by host appeared to be null for Oomycetes and weak for pathogenic Fungi. Finally, we did not success in trying to experimentally provoke, through forest soil inoculations, Janzen-Connell mortalities due to Oomycetes on the Wacapou, a Guianese tree species. In the end, the results of this thesis do not support the hypothesis that Oomycetes may be important agents of the maintenance of tree diversity in tropical forests. Moreover, they bring some questions about the low diversity of this group of micro-organisms in a tree diversity hotspot.

Thesis (M.Sc. Agriculture (Soil Science)) -- University of Limpopo, 2019 / Nutritional water productivity (NWP) is an assessment tool, which describes the amount of water that has been used to produce selected mineral malnutrition (MMN) elements and micronutrient malnutrition (MNMN) substances. Therefore, it links agricultural production to human nutrition. Deficiencies in MMN elements and/or MNMN substances in human nutrition referred to as malnutrition, had been linked with fatal diseases. Agricultural soils could be affected by soil-borne pathogens such as plant-parasitic nematodes, which could limit the availability of MMN elements and MNMN substances. In some communities, vegetable crops, including chilli are regarded as a major source of MMN elements and MNMN substances. Effects of root-knot (Meloidogyne species) nematodes on NWP of chilli (Capsicum annuum L.) have not been documented. The objective of the study was to determine the effects of increasing population densities of M. incognita race 2 and M. javanica on the NWP of hot chilli plants. A microplot trial was conducted at the Green Biotechnologies Research Centre of Excellence (GBRCE), University of Limpopo, South Africa. Pots were filled with 10-L steam-pasteurised (300oC) sandy clay loam soil sourced from GBRCE and Hygromix-T (Hygrotech, Pretoria North) growth medium in the ratio 3:1 (v/v). Thereafter, three-week-old hot chilli cv. 'Serrano' seedlings were transplanted into each pot, with inoculum prepared by extracting eggs and second-stage juveniles (J2) of M. incognita race 2 and M. javanica from roots of grown nematode susceptible tomato cv. 'Floradade' (Solanum lycopersicum L.) in a 1% NaOCl solution. Fourteen days after transplanting, treatments 0, 50, 125, 250, 625, 1250 and 2000 eggs and second-stage juveniles (J2) of M. incognita race 2 and M. javanica were separately inoculated using a 20 ml plastic syringe into 5-cm-deep holes in pots. At 56 days after the initiation of the treatments, Meloidogyne species xiv decreased soil pH and increased organic carbon, contributing 29 and 43% in total treatment variation (TTV) of the respective variables. Treatment effects caused the pH to decrease. NWP variables against increasing nematode numbers exhibited quadratic relations, with coefficients of determination ranging from 59 to 86% for M. incognita race 2 trial and 80 to 98% for M. javanica trial. Meloidogyne species population densities against plant variables did not show any significant relationship, except for root galling and chlorophyll content where treatments contributed 76, 98 and 47% TTV of the respective variables. Generally, root galling increased with increase in Meloidogyne species population densities, whereas chlorophyll content decreased with increasing inoculum levels. Nematode variables against their increasing population exhibited quadratic relationship with the model explained by 44 to 95% for M. incognita race 2 and 28 to 82%, association, respectively for M. javanica. In conclusion, Meloidogyne species interfered with NWP of mineral elements in chilli plant and therefore, nematode management practices should be done to reduce the nematode population densities that would confer quality to agricultural produce for human health benefits.

Thesis (M. Tech. (Agriculture)) -- Central University of Technology, Free state, 2011 / Quality assessment of agricultural water used for fertigation in the Boland district. The study was undertaken to determine the influence of seasonal changes on the water quality (chemical and microbial analyses) of five different rivers in the Boland. The data was collected in the five most important water sources that are used for irrigation purposes in the district, i.e. Berg river, Eerste river, Klapmuts River, Klippies river and Krom river. The samples were collected from all sites once every three weeks for a period of six months. The sampling was carried out during specific periods in summer (December, 2006 to February, 2007) and winter (June to August, 2007). The results of the study showed that Klapmuts river recorded the highest levels of chloride and iron, especially in summer. However, chloride levels were far below the levels set by the Department of Water Affairs and Forestry. Results obtained from this study show the presence of pathogens in some of the rivers assessed which may have resulted from the leaching of these pathogens from nearby agricultural land, livestock watering or informal settlements in the catchment areas. The bigger rivers recorded low levels of micro-elements and this might have been affected by winter rainfall. In the Berg River, many sources of nitrate pollution seem to be present in the catchment area. The levels of iron in all the rivers assessed were far more than the levels set by the Department of Water Affairs and Forestry in all rivers assessed and these might be due to the pH levels and interaction between the rivers and seasons. Iron and manganese levels should be kept low as this may cause production problems by blocking irrigation drippers. The water samples tested for bacterial and fungal density showed Klapmuts and Eerste rivers were positive for Phytophthora cinnamomi during winter. Phytophthora citricola and Phytophthora cactorum were detected in the Klapmuts and Klippies rivers in summer. The Berg-, Klapmuts-, Krom- and Eerste rivers tested positive for species of the genera Pythium and Fusarium. Similar organisms were detected in the Eerste river mainly during summer on the fourth sampling date, while Krom river only tested positive for Pythium during summer. The total bacterial and algal density differed significantly between the seasons and was highest in winter. This might be due to high rain water influx and efflux and/or moist and aerobic conditions and air temperature. There is an increased need for farmers to sterilize feeding water (chlorination) due to high microbial count.