Academic literature on the topic 'Rhizosphere competence'

The associations of Pythium oligandrum with the root cortex, rhizoplane, and rhizosphere were measured with 11 crop species. This work was expedited by the use of a semiselective technique for isolation of P. oligandrum from soil and plant material. Cortical colonization of roots by P. oligandrum was not detected, and the rhizoplanes of the roots of most crops were free of the fungus. However, P. oligandrum was detected in large quantities with every crop tested when roots with adhering soil (rhizosphere soil) were assayed. Different crop species and cultivars of cantaloupe, cauliflower, and tomato varied in rhizosphere densities of P. oligandrum, but rhizosphere population densities of the fungus were consistently higher than in nonrhizosphere soils with plants grown in P. oligandrum-infested sterilized potting mix or an unsterilized mineral soil. After transplanting tomatoes into potting mix infested with P. oligandrum, increases in CFU occurred over time in the rhizosphere but not in the nonrhizosphere soil. In trials on delivery methods of inoculum of P. oligandrum, the rhizosphere populations of tomato plants grown in potting mix were about sixfold higher compared to seed-coat treatments when ground, alginate pelleted oospores were applied to seedlings growing in plug containers prior to transplanting or to pots containing potting mix before direct seeding.

Seed treatment with conidia of rhizosphere-competent mutants of Trichoderma harzianum reduced the incidence of preemergence damping-off of barley, cucumber, pea, radish, and tomato induced by Pythium ultimum. Wild-type parents of these mutants were less effective in control. When rhizosphere-competent mutants were applied to seed or when a peat-bran preparation was added to soil, the resulting plants produced significantly higher fruit weight and higher dry weights than those treated with rhizosphere-incompetent wild types and controls. Seed treatment with mutants increased the incidence of emergence and resultant plant growth was significantly (P = 0.05) better than when mutant strains were added to soil in peat–bran. There was, however, no significant (P = 0.05) difference between the two types of application of the wild types. When cucumber seeds, treated with a T. harzianum rhizosphere-competent mutant (T-95) or its parent wild type (WT), were sown in raw soil kept under constant matric potential with no additional water added, the roots grew 8 cm in 8 days. Untreated seeds produced roots 7 cm long. Fewer colony-forming units of P. ultimum per milligram were isolated from rhizosphere soil of the T-95 treated seedlings than in the untreated controls and those treated with WT. Pythium ultimum was not detected in the 8th cm (farthest from seed) root segment of T-95 treated seeds, whereas the last centimetre of root segment from untreated and WT-treated seeds yielded 3000 colony-forming units/g rhizosphere soil. Seed treatment with rhizosphere-competent mutants of T. harzianum is an effective delivery system to achieve biocontrol and increase growth response.

Two strains of Trichoderma harzianum and one each of T. koningii, T. polysporum, and T. viride were mutated for tolerance to the fungicide benomyl. Rhizosphere competence index of several mutants of each strain and species was determined by the rhizosphere competence assay. Most of the mutants and not their wild type parents were rhizosphere competent. When the strains and species were grown in Czapek–Dox broth for 6 days with cellulose as sole carbon source, the mutants produced significantly higher dry weight than their parent wild types. Neither the mutants nor the wild types produced biomass in glucose comparable to that in cellulose. Evidence indicates that Trichoderma spp. were induced by mutation to increase their linear growth rate and to become rhizosphere competent. Tolerance to benomyl does not seem to be a necessary attribute of rhizosphere competence.

In this study, the potential of different Pseudomonas strains to utilize heterologous siderophores was compared with their competitiveness in the rhizosphere of radish. This issue was investigated in interactions between Pseudomonas putida WCS358 and Pseudomonas fluoresceins WCS374 and in interactions between strain WCS358 and eight indigenous Pseudomonas strains capable of utilizing pseudobactin 358. During four successive plant growth cycles of radish, strain WCS358 significantly reduced rhizosphere population densities of the wild-type strain WCS374 by up to 30 times, whereas derivative strain WCS374(pMR), harboring the siderophore receptor PupA for ferric pseudobactin 358, maintained its population density. Studies involving interactions between strain WCS358 and eight different indigenous Pseudomonas strains demonstrated that despite the ability of these indigenous isolates to utilize pseudobactin 358, their rhizosphere population densities were significantly reduced by strain WCS358 by up to 20 times. Moreover, rhizosphere colonization by WCS358 was not affected by any of these indigenous strains, even though siderophore-mediated growth inhibition of WCS358 by a majority of these strains was demonstrated in a plate bioassay. In conclusion, it can be stated that siderophore-mediated competition for iron is a major determinant in interactions between WCS358 and WCS374 in the rhizosphere. Moreover, our findings support the common assumption that cloning of siderophore receptor genes from one Pseudomonas strain into another can confer a competitive advantage in interactions in the rhizosphere. Interactions between WCS358 and the selected indigenous rhizosphere isolates, however, indicate that other traits also contribute to the rhizosphere competence of fluorescent Pseudomonas spp.Key words: siderophore, siderophore receptors, root colonization, fluorescent Pseudomonas.

This study emphasizes the beneficial role of rhizo-competitive Bacillus spp. isolated from rhizospheric and non-rhizospheric soil in plant growth promotion and yield improvement via nitrogen fixation and biocontrol of Sclerotium rolfsii causing foot rot disease in Eleusine coracana (Ragi). The selection of potent rhizobacteria was based on plant-growth-promoting attributes using Venn set diagram and Bonitur scale. Bacillus pumilus MSTA8 and Bacillus amyloliquefaciens MSTD26 were selected because they were effective in root colonization, rhizosphere competence, and biofilm formation using root exudates of E. coracana L. rich with carbohydrates, proteins, and amino acids. The relative chemotaxis index of the isolates expressed the invasive behavior of the rhizosphere. During pot and field trials, the consortium of the rhizobacteria in a vermiculite carrier increased the grain yield by 37.87%, with a significant harvest index of 16.45. Soil analysis after the field trial revealed soil reclamation potentials to manage soil nutrition and fertility. Both indexes ensured crop protection and production in eco-safe ways and herald commercialization of Bacillus bio-inoculant for improvement in crop production and disease management of E. coracana.

La respiration anaérobie peut être un trait essentiel dans le mode de vie, la colonisation de l'environnement et la survie. Jusqu'à présent, la seule respiration anaérobie confirmée chez Agrobacterium spp. est la dénitrification. De façon intéressante, cette voie est inégalement répandue chez les agrobactéries. Ces observations m'ont amené à mon hypothèse, à savoir la respiration anaérobie et notamment la dénitrification pourraient expliquer la coexistence d'agrobactéries et leur distribution dans des niches spécifiques de la rhizosphère. Ma thèse visait à explorer les stratégies de respiration anaérobie d’Agrobacterium spp. et de les relier à l'adaptation de niche écologiques différentes. Les objectifs de ma thèse étaient (1) de caractériser tous les gènes impliqués dans la dénitrification chez A. fabrum C58 in vitro, (2) d'explorer les gènes de la dénitrification nécessaires à la colonisation des racines du maïs et (3) de découvrir de nouvelles respirations anaérobies pendant la colonisation racinaire du maïs (Figure 16). Réaliser des mutants et les tester dans des conditions particulières est le moyen classique de déterminer l'implication d'un gène dans une voie spécifique. Cependant, cette méthode implique une vision à priori et des connaissances solides sur les gènes cibles et ne peut pas être appliquée à toutes les situations. Nous avons alors dû développer une méthode plus adaptée pour identifier les gènes essentiels impliqués dans la croissance dans des conditions anaérobies spécifiques. - Gènes de dénitrification chez A. fabrum C58 in vitro. Pour compléter la voie de dénitrification chez A. fabrum C58 et identifier tous les gènes et régulateurs impliqués dans la dénitrification, nous avons adopté deux stratégies : Premièrement, une vision à priori pour (1) identifier la nitrate réductase impliquée dans la première étape de la dénitrification et (2) valider le rôle d'un ARN non codant dans le contrôle de la dénitrification. Pour ce faire, nous avons construit un mutant napA de A. fabrum C58 et un mutant de l'ARN non codant NopR et nous avons évalué leur croissance et leur capacité à produire du N2O dans des conditions anoxiques. Deuxièmement, pour identifier tous les gènes impliqués dans la dénitrification, nous avons construit une banque de transposons mutants de C58 et testé sa croissance dans des conditions de dénitrification in vitro en présence de nitrate ou de nitrite. - Rôle des gènes de la denitrification de A. fabrum C58 dans la colonisation racinaire du maïs. Il est bien connu que le séquençage de transposons (Tn-Seq) est une méthode très puissante pour déterminer les gènes nécessaires à la croissance bactérienne en présence de leur hôte. Pour déterminer les gènes de dénitrification impliqués dans la colonisation des racines en anoxie, nous avons utilisé la banque construite chez C58 et l’avons inoculée sur les plants de maï cultivées sur un sol fertile et cultivées dans des conditions inondées mimant des conditions anaérobies. Le séquençage des cellules d ‘A. fabrum C58 récupérées mettra en évidence les gènes impliqués dans la colonisation anaérobie de cette niche spécifique. - Découverte de nouvelles voies de respiration anaérobie chez A. fabrum C58. Pour découvrir de nouvelles voies de respiration anaérobie, nous avons mis en place des tests de croissance de C58 dans des conditions anoxiques en présence de sources de C et de N en tant qu'accepteurs terminaux d'électrons. De façon interéssante, en cultivant des souches WT et mutée dans le gène napA au contact de la racine de maïs dans des conditions anoxiques (chapitre 1), nous avons montré une croissance des deux souches. Ce résultats suggère que les exsudats de racine servent d'accepteurs d'électrons terminaux pour la croissance anaérobie de C58. Pour déterminer quels composés exsudés du maïs peuvent servir de TEA, les principaux métabolites ont été identifiés par HPLC et certains ont été testés en tant que TEA dans des conditions anoxiques
Anaerobic respiration may be an essential trait in lifestyle, environment colonization and survival. Until now, the only confirmed anaerobic respiration in Agrobacterium spp. is denitrification. Interestingly, this pathway is unequally widespread among Agrobacteria. These observations led me to my hypothesis which is anaerobic respiration and notably denitrification could explain the coexistence of Agrobacteria and their distribution in specific niches in the rhizosphere. My thesis was undertaken to explore the anaerobic respiration strategies of Agrobacterium spp. and to relate them to niche adaptation. The objectives of my thesis were to (1) characterize all the genes involved in denitrification in A. fabrum C58 in vitro, (2) explore the genes of denitrification that are needed during maize root colonization and (3) discover new anaerobic respirations that occur during maize root colonization (Figure 16). Mutational analysis is the classic way to determine the involvement of a gene in specific pathway. However, this method implies an a priori view and solid knowledge on target genes and cannot be applied for every situation. We have to develop a more adapted method to identify essential genes involved in growth in specific anaerobic conditions. - Denitrification genes in A. fabrum C58 in vitro. To complete denitrification pathway in A. fabrum C58 and identify all the genes and regulators involved in the denitrification function, we adopted two strategies: Firstly, an a priori view to (1) identify the nitrate reductase involved in the first step of denitrification and (2) validate the role of a non-coding RNA in denitrification control. To do so, we constructed a mutant of napA of A. fabrum C58 and a mutant of the non-coding RNA NopR and we evaluated their growth and capacity to produce N2O under anoxic conditions. Secondly, to identify all the genes involved in denitrification, we constructed a mutant transposon library of C58 and tested its growth under denitrification conditions in vitro in the presence of either nitrate or nitrite. - Role of A. fabrum C58 denitrifying genes in the root colonization of maize. It is well known that Transposon-sequencing (Tn-Seq) is a very powerful method to determine genes required for bacterial growth in the presence of their host. To determine denitrifying genes involved in root colonization under anaerobic conditions, we used the library constructed in C58 and performed in planta assays. The mutant library was inoculated on maize plants grown on fertile-ground and cultured under flooded conditions miming anaerobic conditions. Sequencing the recovered A. fabrum C58 cells will evidence the genes involved in this anaerobically specific niche colonization. - Discovery of new anaerobic respiration pathways in A. fabrum C58. To discover new anaerobic respiration pathways, we set-up growth assays of C58 under anoxic conditions in the presence C and N sources as terminal electrons acceptors. Interestingly, by culturing WT and NapA-deficient strains in contact with maize root under anoxic conditions (Chapter 1), we showed growth of both strains, suggesting that root exudates serve as terminal electrons acceptors for anaerobic growth of C58. To determine which maize exuded compounds can serve as TEAs, primary metabolites were identified by HPLC and some were tested as TEAs under the set-up conditions

O uso de bactérias promotoras de crescimento vegetal ou agentes de biocontrole como inoculantes agrícolas é uma alternativa importante e ecologicamente correta, com grandes benefícios na agricultura para substituir, ou ao menos suplementar, a excessiva utilização de fertilizantes e pesticidas. Neste trabalho avaliamos a capacidade de biocontrole e de competência rizosférica de três bactérias com características de promoção de crescimento vegetal (Plant growth promoting - PGP): Bacillus mycoides B38V, Paenibacillus riograndensis SBR5 e Burkholderia sp. 89. As três bactérias avaliadas apresentaram grande versatilidade na utilização de substratos, o que poderia lhes garantir uma vantagem competitiva no ambiente rizosférico. Porém, inconsistências foram observadas nos ensaios em câmara de crescimento, ou seja, as características de PGP e de biocontrole observadas in vitro não se refletiram em benefícios para a planta. A linhagem 89 destacou-se pela produção de um metabólito estável com ampla atividade contra fungos fitopatogênicos. Através de abordagens genômicas e de análises multilocus, descrevemos Burkholderia sp. 89 como uma nova espécie membro do complexo Burkholderia cepacia, denominada de B. catarinensis 89T. O sequenciamento de seu genoma, seguido de uma análise pela ferramenta AntiSMASH, revelou a presença de um agrupamento gênico de peptídeo sintetases não ribossomais (NRPS) relacionadas com a biossíntese do sideróforo ornibactina e um agrupamento híbrido NRPS-policetídeo sintetase responsável pela biossíntese do glicolipopeptideo cíclico com atividade antifúngica burkholdina. Como estratégia de purificação de metabólitos secundários foi utilizada a metodologia da mineração de genoma combinada com fracionamento guiado por bioensaios seguida de análises em espectrômetro de massas. Desta forma, purificamos com sucesso duas variantes de ornibactina, D e F (761 e 789 Da, respectivamente), e detectamos a variante ornibactina B (m/z= 733) e as moléculas sinalizadoras homoserina lactonas C6-HSL, 3OH-C8-HSL e C8-HSL. Análises de espectrometria de massas demonstraram a presença de um grupo de metabólitos com massas de 1240, 1254, 1268, 1216, 1244 e 1272 Da, que, provavelmente, são novas variantes do antifúngico burkoldina. Sendo assim, B. catarinensis 89T possui potencial biotecnológico com possíveis aplicações farmacêuticas e agronômicas para o biocontrole de fungos fitopatogênicos.
The use of plant growth promotion bacteria or biocontrol agents as agricultural inoculants is an important eco-friendly alternative to substitute, or at least supplement, the excessive use of fertilizers and pesticides. In this work, we evaluated the biocontrol potential and rhizosphere competence of three bacteria that had shown plant growth promotion (PGP) abilities: Bacillus mycoides B38V, Paenibacillus riograndensis SBR5 and Burkholderia sp. 89. All three bacteria presented great versatility in their substrate utilization, which could enable them to survive in a competitive rhizosphere environment. However, inconsistencies were observed in the greenhouse experiments, whereas their interesting abilities observed in vitro did not result in benefits to the plants. Strain 89 produces a stable metabolite with a wide range of antifungal activity. Genomic comparisons and multilocus sequence analysis revealed Burkholderia sp. 89 as a new species of the Burkholderia cepacia complex and we described it as B. catarinensis 89T. We sequenced its genome and analyzed it with the AntiSMASH tool. This in silico prediction revealed the presence of a nonribosomal peptide synthetase (NRPS) cluster, which is related to the production of the siderophore ornibactin. Moreover, a hybrid NRPS- polyketide synthetase cluster for the production of the antifungal cyclic glicolipopeptide burkholdin was also found. A genome mining combined with a bioassay-guided fractionation with further mass spectrometry analysis was applied for the purification of these compounds. This approach enabled us to purify and characterize two variants of the siderophore ornibactin, D and F (761 and 789 Da, respectively). Also, we could detect the variant ornibactin B (m/z= 733) and the quorum sensing molecules homoserine lactones C6-HSL, 3OH-C8-HSL and C8-HSL in the supernatant of B. catarinensis 89T. Mass spectrometry analysis showed the presence of a group of metabolites with the masses 1240, 1254, 1268, 1216, 1244 and 1272 Da, which are probably new variants of the antifungal metabolite burkoldin. Therefore, B. catarinensis 89T has a great biotechnological potential for the production of metabolites with pharmaceutical and agricultural applications for the biocontrol of phytopathogenic fungi.

The overall aim of this research was to improve the understanding of the ecology and diversity of Trichoderma species within the soil and rhizosphere of onion (Allium cepa L.) and potato (Solanum tuberosum L.) under intensive management in New Zealand. The indigenous Trichoderma population was measured in a field trial at Pukekohe over a three year period under six different crop rotation treatments. The treatments included two continuous onion and potato rotations (intensive), two onion/potato mixed rotation (conventional), and two green manure rotations (sustainable). Results showed that Trichoderma populations were stable in both the rhizosphere and bulk soil (1.5 x 10² to 8.5 x 10³ CFU g⁻¹ ODS). The planting and incorporation of an oat (Avena sativa L.) green manure in the sustainable rotations positively increased Trichoderma colony forming unit (CFU) numbers in the rhizosphere soil from 3.4 x 10² to 2.5 x 10³ g⁻¹ ODS. A Trichoderma species identification method was developed based on colony morphology. Representative isolates were verified using restriction fragment length polymorphism (RFLP) and DNA sequencing. The method allowed for rapid and reliable identification of isolated Trichoderma species. Five species were identified in the Pukekohe soil: T. asperellum, T. atroviride, T. hamatum, T. harzianum and T. koningii. Results showed identical species diversity between the rhizosphere, rhizoplane and bulk soil. The species did not strongly compete between each other for the rhizosphere ecological niche and differences in species proportions seemed to be caused by environmental factors rather than the rotation treatments. The incorporation of oat green manure in pots did not significantly promote the indigenous Trichoderma population size and diversity in the rhizosphere of onion plants up to 4 months old. The identified species were the same as in the field trial. The incorporation of onion scale residues was shown to result in low Trichoderma and high Penicillium CFU numbers and a reduction in plant size. Additionally, the presence of high levels (6.0 x 10⁵ CFU g⁻¹ ODS) of Penicillium CFU was negatively correlated with the presence of Trichoderma CFU. The effect of oat incorporation on Trichoderma saprophytic growth was also investigated in a soil sandwich assay and revealed no significant differences. A series of experiments indicated that onion extract obtained from dry onion scale residues had no antifungal activity against either Trichoderma or Penicillium and instead tended to promote their hyphal growth and sporulation. It also showed that competition between Penicillium and Trichoderma isolates was limited despite the ability of Penicillium to produce a wide range of inhibitory substances. Four indigenous Trichoderma species (T. atroviride, T. hamatum, T. harzianum and T. koningii) were shown to be rhizosphere competent in a split tube experiment over a 6 week period. The results of this experiment revealed that, the Trichoderma species clearly displayed differences in their ability to colonise the rhizosphere of young onion seedlings. Species such as T. koningii had the greatest rhizosphere colonising ability regardless of soil depth while T. harzianum displayed the weakest ability. Results also indicated that when inoculated as a mixture the four species competed with one another to colonise the rhizosphere. Overall, this research indicated that the studied crop rotation treatments and the use of oat as a green manure did not strongly promote indigenous Trichoderma populations. Species diversity was constant throughout the research with T. hamatum and T. koningii being the most frequently isolated species.