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.

Crop rotation may be used to prevent the continuous selection of particular weed species adapted to one crop type. This might be useful for weed management, economy in herbicide applications and promoting biodiversity. Common simple crop sequences might be diversified by introducing perennial forage crops. Impacts of such perennial crops on weeds were studied with four approaches : 1) Large-scale weed surveys in 632 fields in western France showed that weed species composition differed most strongly between perennial alfalfa crops and annual crops. Comparisons of fields before, during and after perennial alfalfa suggested that community composition varies in a cyclic way during such crop rotations. Several weed species problematic in annual crops were suppressed during and after perennial crops, but the appearance of other species led to equal or even higher plant diversities. 2) A 3-year field experiment with contrasting crop management options allowed an investigation of the underlying mechanisms for this: The absence of soil tillage reduced weed emergence but increased the survival of established plants. The permanent vegetation cover and frequent hay cuttings reduced weed growth, plant survival and seed production. 3) Greenhouse experiments testing the regrowth ability of individual plants after cutting showed strong differences between species and functional groups. An two-factorial experiment suggested that the negative impacts of cutting and competition on weed growth were mainly additive. 4) Special measurements of weed seed predation in the field experiment showed positive correlations with vegetation cover, indicating that this ecosystem service may be particularly fostered by perennial crops. Consistent preferences of seed predators for certain weed species indicates that seed predation may be another cause of the observed weed community shifts.

La rotation de cultures peut être utilisée pour empêcher la sélection continue d’espèces adventices adaptées à un type de culture. Elle pourrait favoriser la gestion des adventices, l’économie d’herbicides et la biodiversité. Les successions de cultures simples d’aujourd’hui pourraient être diversifiées par des cultures fourragères pérennes. Les impacts des ces cultures sur les adventices ont été étudié utilisant quatre approches : 1) Des relevés d’adventices sur 632 champs dans l’ouest de la France ont montré que la composition spécifique varie le plus entre des cultures fourragères pérennes et des cultures annuelles. Une comparaison des champs avant, pendant, et après des cultures fourragères pérennes a suggéré que la composition des communautés varie d’une manière cyclique pendant ces rotations. Plusieurs espèces problématiques dans des cultures annuelles ont été supprimées pendant et après les cultures pérennes, mais l’apparition d’autres espèces a produit une diversité de plantes comparable, voire supérieure. 2) Une expérimentation au champ de trois ans avec des modes de gestion contrastés a permis d’étudier les mécanismes sous-jacents: L’absence de travail du sol a réduit la levée des adventices, mais a augmenté la survie des plantes adultes. Le couvert végétal permanent et les fauches fréquentes ont réduit la croissance, la survie des plantes et la production de graines. 3) Des expérimentations sous serre analysant la croissance poste fauche de plantes individuelles ont montré des différences importantes entre espèces et groupes fonctionnels. Une expérimentation à deux facteurs a suggéré que les impacts négatifs de la fauche et de la compétition sur la croissance des adventices ont été additifs. 4) Des mesures spéciales de prédation de graines d’adventices sur l’expérimentation au champ ont montré des corrélations positives avec le couvert végétal et la prédation, indiquant une importance particulière de ce service écosystémique dans des cultures pérennes. La préférence des graines de certaines espèces montre que la prédation de graines peut être une autre cause des changements de communautés d’adventices. / Crop rotation may be used to prevent the continuous selection of particular weed species adapted to one crop type. This might be useful for weed management, economy in herbicide applications and promoting biodiversity. Common simple crop sequences might be diversified by introducing perennial forage crops. Impacts of such perennial crops on weeds were studied with four approaches : 1) Large-scale weed surveys in 632 fields in western France showed that weed species composition differed most strongly between perennial alfalfa crops and annual crops. Comparisons of fields before, during and after perennial alfalfa suggested that community composition varies in a cyclic way during such crop rotations. Several weed species problematic in annual crops were suppressed during and after perennial crops, but the appearance of other species led to equal or even higher plant diversities. 2) A 3-year field experiment with contrasting crop management options allowed an investigation of the underlying mechanisms for this: The absence of soil tillage reduced weed emergence but increased the survival of established plants. The permanent vegetation cover and frequent hay cuttings reduced weed growth, plant survival and seed production. 3) Greenhouse experiments testing the regrowth ability of individual plants after cutting showed strong differences between species and functional groups. An two-factorial experiment suggested that the negative impacts of cutting and competition on weed growth were mainly additive. 4) Special measurements of weed seed predation in the field experiment showed positive correlations with vegetation cover, indicating that this ecosystem service may be particularly fostered by perennial crops. Consistent preferences of seed predators for certain weed species indicates that seed predation may be another cause of the observed weed community shifts. / Fruchtfolgen können dazu dienen, die kontinuierliche Selektion von Unkrautarten zu verhindern, die an eine bestimmte Kultur angepasst sind. Dies könnte dem Unkrautmanagement, der Einsparung von Herbiziden, und der Biodiversität dienen. Heutige, sehr einfache Furchtfolgen könnten durch mehrjährige Futterkulturen diversifiziert werden. Die Einflüsse solcher mehrjähriger Kulturen auf Unkräuter wurden in vier Ansätzen untersucht : 1) Vegetationsaufnahmen auf 632 Feldern in Westfrankreich zeigten, dass die Unkrautzusammensetzung zwischen mehrjährigen Futterkulturen und einjährigen Kulturen stark variiert. Der Vergleich von Feldern vor, während und nach mehrjährigen Futterkulturen legte nahe, dass die Pflanzengemeinschaft während solcher Fruchtfolgen zyklisch variiert. Mehrere problematische Unkrautarten wurden während und nach den mehrjährigen Kulturen zurückgedrängt. Das Auftauchen anderer Arten führte jedoch zu einer gleichbleibenden oder leicht erhöhten Pflanzenvielfalt. 2) Ein dreijähriger Feldversuch mit verschiedenen Bearbeitungsoptionen ermöglichte es, die zugrunde liegenden Mechanismen zu untersuchen: Die fehlende Bodenbearbeitung hat das Auflaufen der Unkräuter reduziert und das Überleben der adulten Pflanzen erhöht. Die permanente Vegetationsbedeckung und die häufigen Heuschnitte haben das Wachstum, das Überleben und die Samenproduktion vermindert. 3) Gewächshausexperimente zum Nachwachsen von Unkrautpflanzen nach Heuschnitten zeigten große Unterschiede zwischen verschiedenen Arten und funktionellen Gruppen. Ein Experiment mit zwei Faktoren lässt vermuten, dass die negativen Effekte der Schnitte und der Konkurrenz auf das Unkrautwachstum sich addieren. 4) Spezielle Messungen der Prädation von Unkrautsamen auf den untersuchten Feldern zeigten positive Korrelationen mit der Vegetationsbedeckung, was auf eine besondere Wichtigkeit dieser Ökosystemdienstleistung in ausdauernden Kulturen hindeutet. Die Präferenz von bestimmten Samenarten deutet darauf hin, dass Samenprädation ein weiterer Grund für die beobachteten Änderungen der Unkrautgemeinschaften sein kann.