All living organisms require food for growth and survival. Heterotrophs depend on autotrophs such as green plants which can synthesize their own food unlike heterotrophic animals. Among heterotrophs, only humans and some insects have the remarkable ability to cultivate crops for food. While humans cultivate plants, three insect lineages—ants, termites, and beetles—cultivate fungi inside their nests in obligate mutualistic exo-symbioses. Interestingly, just like human agriculture, insect fungus farms are also threatened by weeds and pests, e.g. the farms of fungus-growing termites which cultivate Termitomyces fungi can be overgrown by weeds such as the parasitic fungus Pseudoxylaria. Studies on ant and beetle fungus-farming systems have uncovered the important role of chemicals and behaviour in helping these insects to protect their crops from parasitic fungi. On the other hand, studies on the termite system till now, have only revealed the presence of antifungal compounds and actinobacteria which are largely non-specific and inhibitory to the mutualistic crop fungi. Antifungal behavioural mechanisms, if present, are yet to be discovered. Therefore, this thesis focuses on different anti-Pseudoxylaria mechanisms employed by fungus-growing termites, viz. role of nest abiotic factors, mechanism of fungal recognition by termite hosts, behavioural response of termite to Pseudoxylaria presence and coupling of this behaviour to anti-Pseudoxylaria activity. The present thesis has been divided into six chapters. CHAPTER 1 gives a brief literature review on fungus-farming insects and the different mechanisms which insects employ in order to keep their fungal farms safe from growth of parasitic fungi with specific reference to fungus-growing termites. The obligate mutualistic interaction between termites and the Termitomyces fungus is 19–49 My-old and is, therefore, a very ancient agriculture system. The mutualistic fungus is cultivated on partially digested plant matter called fungus comb inside the nest and harvested by termites for nutrition. At the same time, the weedy fungal parasite Pseudoxylaria can compete with the mutualistic fungus for nutrition leading to negative effects on the fungal farms. Termite hosts are believed to use abiotic factors, antibiotics and hygienic behaviours to keep their fungal gardens free from parasitic fungi such as Pseudoxylaria. However, the actual mechanisms used by termites against parasitic fungi are unclear. Unravelling the proximate mechanisms used in fungal cultivar protection is central to understanding the evolutionary stability of these farming mutualisms. CHAPTER 2 examines the diversity and population genetic structure of Termitomyces and Pseudoxylaria strains associated with the fungus-growing termite Odontotermes obesus. Genetic diversity of cultivar and parasite could have important implications for the stability of the mutualistic interaction, e.g. genetic clonality arising from monoculture is generally thought to make populations more prone to infection by parasites. Using molecular phylogenetic tools, within-nest genetic homogeneity was found in Termitomyces species but not in Pseudoxylaria species. Lower OTU but higher genotypic diversity (within the most abundant OTU) was found in the genus Termitomyces compared to Pseudoxylaria. Additionally, population genetics methods suggested a sexual population structure for Termitomyces and clonal propagation for Pseudoxylaria species. This is the first study to investigate the population genetics of the symbiotic fungi associated with the termite genus Odontotermes or any other termite species from India. In CHAPTER 3, the effect of nest micro-environment alone on the growth of the parasitic fungus Pseudoxylaria was examined. For this, seasonal changes in nest xiii temperature and CO2 were recorded and in situ and ex situ growth experiments were performed on Pseudoxylaria. The monthly pattern of mound temperatures was found to be similar to the outside—cycling from highs in summer to lows in winter—but characterised by dampened variation compared to high daily fluctuations outside. Moreover, the mound CO2 levels were found to be orders of magnitude above atmospheric levels and, unlike the outside, were characterised by daily and monthly fluctuations. With in situ experiments during summer and winter, the effect of these dissimilar conditions—inside and outside mounds—was examined on Pseudoxylaria growth. The growth of the parasite was found to be greater inside than outside the mound. Following this, the growth of different parasite isolates under controlled ex situ conditions was examined—spanning the variation in environmental conditions that mounds exhibit daily and seasonally. High CO2 levels decreased parasitic fungal growth in general but temperature had an isolate-dependent effect. Taken together, these results suggested that the parasite is adapted to survive in the mound. However, mound environmental conditions still seemed to exert a negative effect on parasite growth, even if they cannot inhibit Pseudoxylaria completely. These results shed light on the possible new role of termite-engineered structures in impacting parasitic fungus ecology, independent of any direct role of termites in suppressing parasite growth. This is the first study to investigate the effect of abiotic factors on Pseudoxylaria growth. In CHAPTER 4, whether termites can differentiate between Termitomyces and Pseudoxylaria was investigated. In a novel, laboratory-based choice assay, termites displayed a differential response towards the two fungi by burying the Pseudoxylaria with agar. Also, termites were found to be able to differentiate between the fungi using olfactory cues, i.e. smell, alone, for this task. The mutualistic and parasitic fungi were found to emit unique volatile bouquets which could help termites to distinguish between them. This is important because, whether termites use antifungal compounds or hygienic behaviours, it is crucial that they are able to differentiate between the parasitic and mutualistic fungi so that they can selectively use antifungal mechanisms—whether chemical or behavioural—against Pseudoxylaria. This is of special significance because, many actinobacteria and anti-Pseudoxylaria compounds isolated from this system till now, lack specificity and inhibit the mutualistic Termitomyces as well. Also, fungal grooming and weeding behaviours as displayed by fungus-growing ants have not yet been reported in termites. This is the first study to show that termites have the behavioural capacity to differentiate between the mutualistic and parasitic fungi in an ecologically relevant setting. In CHAPTER 5, whether the burying of Pseudoxylaria could affect its growth was investigated. It was found that termites can utilise agar, glass beads and soil for deposition over the offered fungal plugs but the use of agar and glass beads did not inhibit Pseudoxylaria growth effectively. On the other hand, soil deposition was found to decrease growth of both Pseudoxylaria and Termitomyces fungi post-burial. However, Pseudoxylaria was found to be affected more strongly than Termitomyces. Further, hypoxia acting alone seemed to decrease only Pseudoxylaria survival without any apparent effect on Termitomyces. Therefore, hypoxia induced by soil deposition may be the reason behind the decrease in Pseudoxylaria survival. However, presence of antifungal compounds can not be ruled out and they may be selectively applied in larger quantities on Pseudoxylaria with soil deposition. This study demonstrates an anti-Pseudoxylaria activity of this insect behaviour, unique to termites among fungus-farming insects, to the presence of the parasitic fungus. CHAPTER 6 concludes the findings of this thesis and suggests a working model for the mechanism of growth suppression of Pseudoxylaria inside a termite nest. In particular, focus is on the important role of abiotic factors when combined with termite behaviour in the apparent absence of Pseudoxylaria from termite nests. These results not only shed new light on how the ecology of these fungi is affected by their termite host but also reveal the mechanistic bases that may contribute fundamentally to the evolutionary stability of this ancient mutualism.

La diversité fongique des meules de plusieurs espèces de Macrotermitinae a été analysée au niveau taxinomique, fonctionnel et génétique à l’aide d’une approche polyphasique associant plusieurs techniques complémentaires. L’objectif étant d’évaluer la spécificité des taxons fongiques associés aux meules ainsi que les relations qu’ils entretiennent avec les termites champignonnistes. Une grande variété de phylotypes cultivables appartenant majoritairement au phylum des Ascomycètes a été obtenue par isolement et séquençage des ITS fongiques, et peu de séquences se sont révélées être spécifiques à un genre de Macrotermitinae particulier. Les profils physiologiques obtenus ont mis en évidence la nature saprophytique de la majorité des phylotypes et confirmé l’absence de taxons spécifiques. Par PCR-DGGE de l’ADN total de meules, 100% des phylotypes ITS et 28S fongiques identifiés étaient affiliés au genre Termitomyces. La technique Suicide Polymerase Endonuclease Restriction (SuPER) a été adaptée à la mycoflore des meules pour limiter l’impact de l’ADN majoritaire du Termitomyces symbiotique. Celle-ci a permis la détection de plusieurs autres populations fongiques. Les analyses phylogénétiques ont montré d’une part la spécificité des Xylaria associés aux meules de Macrotermitinae bien qu’aucune co-évolution n’ait été observée avec les termites hôtes et d’autre part leur affiliation dans un sous-genre spécifique. Une analyse préliminaire des facteurs d’inhibition a également révélé l’implication des termites dans la régulation des communautés fongiques des meules. Dans leur ensemble, nos résultats illustrent clairement l’influence des Macrotermitinae sur les communautés fongiques telluriques pendant leurs différentes activités. / Fungal diversity of several Macrotermitinae fungus combs was analyzed at taxonomic, functional and genetic levels using a polyphasic approach. The aim of this thesis was to evaluate the specificity of fungal strains from combs and to elucidate their relationship with fungus-growing termites. A large variety of culturable phylotypes mainly belonging to Ascomycota phylum was retrieved using conventional isolation techniques followed by sequencing of ITS1-5.8S-ITS2 region. Based on the obtained results, there is evidence for any speciesspecificity between these taxa and a given genus of Macrotermitinae. This finding was supported by the physiological profile of some representative phylotypes which revealed the saprophytic nature of most of the isolates. By PCR-DGGE analysis of fungal ITS and LSU, all of the sequences were belonged to Termitomyces genus. The Suicide Polymerase Endonuclease Restriction method was adapted to the analysis of comb mycoflora for restricting the impact of the dominant Termitomyces DNA. As expected, this latter technique revealed non-Termitomyces fungal populations. Phylogenetic analysis also showed the specificity of termiteassociated Xylaria although they do not evolved with termite hosts, and also their affiliation to a new genus or at least a specific sub-genus. Preliminary investigation revealed the implication of termite workers in fungal regulation in fungus combs. All in one, our results clearly underline the great impact of fungus-growing termite species on soil fungal community during their activities.