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Thesis defences

PhD Oral Exam - Sachin Naik, Biology

Microbiomics of Populus

Monday, August 17, 2020 (all day)

This event is free


School of Graduate Studies


Daniela Ferrer



When studying for a doctoral degree (PhD), candidates submit a thesis that provides a critical review of the current state of knowledge of the thesis subject as well as the student’s own contributions to the subject. The distinguishing criterion of doctoral graduate research is a significant and original contribution to knowledge.

Once accepted, the candidate presents the thesis orally. This oral exam is open to the public.


Species of the genus Populus, commonly known as poplars, are one of the most widely used groups of forest trees in North America and Europe. Poplars play a significant ecological role as a pioneer species in the boreal forest, and as a dominant species in riparian forests where they serve as rich wildlife habitats. Numerous natural and artificial hybrids of poplars with superior qualities are widely used in commercial plantations. However, many hybrid poplars are susceptible to the leaf spot and stem canker causative pathogenic fungal species, Sphaerulina musiva which limits the utility of hybrid poplars as plantation trees. At present, there is no control measure to combat the disease caused by S. musiva. The plant microbiome—mainly endophytic microbes—are known to interact with pathogenic microbes and play a crucial role in the ecology and evolution of plants. Understanding the endophytic microbial associations in Poplars along with their interactions with S. musiva is invaluable for developing new methods for combating the stem cankers caused by this pathogen. In the present study, we found a number of endophytic microbes in Poplars that inhibit the fungal pathogen S. musiva and may serve as a potential source to develop biocontrol agents against S. musiva.

In the first study (Chapter 2), we characterized the endophytic fungal community in Populus species in the Gault Nature Reserve in Mont-Saint-Hilaire, Quebec. We investigated the dual culture interactions of endophytes against S. musiva. We isolated 367 endophytic fungal isolates grouped into 46 genera. Alternaria was the dominant and most common genus isolated. We found certain genera of endophytic fungi were unique to specific Populus species. Only a few endophytic fungi exhibited antagonistic activity against S. musiva and showed differential competitive ability. The endophytic fungus Fusarium sporotrichioides showed the strongest antagonistic activity against S. musiva and can be used as a potential source to develop a biocontrol microbe against S. musiva.

In the second study (Chapter 3), we investigated interactions between Bacillus velezensis EB14, an endophytic bacterial strain isolated from poplars, and S. musiva. We found significant inhibition of S. musiva by the endophytic bacterium, B. velezensis. We also discovered the production of anti-fungal Iturin compounds (iturin A1, subtulene A, iturin A2, iturin A9 and fengycin) along with four unknown compounds in Bacillus velezensis. In addition, we found that B. velezensis EB14 exhibited varying level of competitive ability against the endophytic fungal microbiome of Populus.

In the third study (Chapter 4), we elucidated the evolutionary relationships of the isolated Bacillus strain EB14, and performed a comparative genome analysis of the Bacillus velezensis EB14 strain with its closest relatives. We report the 4.07Mbp draft genome of Bacillus velezensis EB14. This genome encodes 13 secondary metabolite gene clusters which includes Surfactin, Rhizoactin, Bacillibactin, Fengycin, Bacillaene, Difficidin, Macrolactin, and Bacilysin. The presence of genes involved in plant bacterial interactions further validates the potential of using Bacillus velezensis EB14 strain to develop as a biocontrol microbe in forestry and agriculture. Furthermore, pan and core genome analysis revealed that Bacillus strains associated with plants possessed genes involved in cell wall degradation, polyketide synthesis, and environment sensors. Most of these genes were clade specific and found in B. amyloliquefaciens, B. siamensis, and the conspecific group of B. velezensis.

The last chapter (Chapter 5), examines one of the most perplexing questions in endophyte biology: How and why do endophytes produce metabolites similar to host plant derived secondary metabolites? Here, we review the endophyte literature on secondary metabolite production and show that detailed studies are required for conclusive demonstration of metabolite production, as well as to explain the adaptive significance of production of these metabolites by endophytic fungi.

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