Summary of the thesis project
Tropical forests are among the most biodiverse ecosystems on Earth and play a central role in global biogeochemical cycles, including carbon, water, and nitrogen regulation. Beyond the forest floor, the canopy forms a structurally complex habitat hosting a vast diversity of plants, animals, and microorganisms. Vascular and non‑vascular epiphytes create unique microhabitats colonized by bacteria, fungi, and protists that drive essential processes such as nutrient recycling and plant health maintenance. While most studies have focused on soil and root microbiota, the phyllosphere of tropical canopies remains poorly understood. These microbial communities are shaped by both stochastic (dispersal, neutral dynamics) and deterministic (environmental and host filtering) processes. In canopy environments, the scarcity of soil‑derived nitrogen enhances the ecological importance of diazotrophic microorganisms capable of atmospheric N₂ fixation, yet their diversity and functional roles are still largely unknown.
This PhD project aims to characterize the microbial communities inhabiting tropical forest canopies, identify the factors shaping their assembly, and assess their contribution to nitrogen cycling and ecosystem resilience. The study focuses on three main objectives: (1) describing the taxonomic and functional diversity of canopy microorganisms, particularly nitrogen‑fixing and denitrifying taxa; (2) quantifying the contribution of canopy components (epiphytes, leaves, bark, suspended soils) to nitrogen cycling; and (3) evaluating the responses of microbial communities and functions to environmental disturbances such as drought and deforestation.
Fieldwork will be conducted in French Guiana as part of an interdisciplinary research program. Microbial diversity will be assessed through DNA metabarcoding and analyzed using bioinformatics pipelines. Environmental variables and plant functional traits will serve as explanatory factors in multivariate analyses designed to disentangle host‑driven and environmental influences. Nitrogen fixation and denitrification rates will be measured to evaluate canopy‑level nutrient fluxes. In parallel, the aquatic microecosystems of tank bromeliads will be used as natural models to test microbial community responses to environmental changes. This integrative framework will link microbial diversity, food‑web structure, and ecosystem processes within the canopy.
By providing a novel understanding of canopy microbiota and their functional roles, this thesis will highlight the contribution of aboveground microbial processes to tropical forest stability and nutrient cycling. It will help integrate canopy microbiomes into global ecosystem models and improve our understanding of plant–microbe interactions as drivers of tropical forest resilience under global change.
Context
Tropical forests are among the most biodiverse terrestrial ecosystems on Earth. They harbour over half of all known plant and animal species, yet cover only about 12% of the planet’s land surface (Antonelli et al., 2018). Beyond biodiversity, these ecosystems also play a fundamental role in maintaining global ecosystem services, such as high primary productivity, regulation of global hydrological cycles, carbon and nitrogen cycling (Beer et al., 2010; Pan et al., 2011; Spracklen et al., 2012). This functionality is driven not only by the diversity of the forest floor but also by the complexity of the canopy. Tropical forest canopies form a complex matrix of leaves and branches whose structural complexity is further enhanced by the presence of vascular (e.g. orchids, bromeliads) and non-vascular (e.g. bryophytes, lichens) epiphytes. The canopy thus represents one of the largest surfaces of the phyllosphere colonised by a great diversity of metazoans and microorganisms, including bacteria, fungi, protists (Vacher et al., 2016). Together, these organisms constitute a dynamic food web that likely plays a major role in plant health and ecosystem functioning through nutrient cycling.
Understanding the factors that shape the diversity and composition of plant-associated microbiota has become a central research topic over the past decade (Simon et al., 2019; Kohl, 2020). However, most studies have focused on soil and root-associated microorganisms. In contrast, the microbial communities inhabiting the phyllosphere (i.e. the aboveground plant parts, and particularly the surface and internal tissues of leaves, Vorholt, 2012) remain comparatively underexplored, often restricted to a few model or crop species (Sohrabi et al., 2023). As in other microbial ecosystems, stochastic and deterministic processes jointly govern these communities, but in plant-associated microbiota, these dynamics are further influenced by host ecological traits, thus adding an additional layer of complexity. Determining the extend to which the plant host have deterministic effects and contribute to microbial community composition and assembly patterns is essential to disentangle host-driven selection from environmentally driven processes.
In tropical canopies, plants and their associated microbiota have limited access to soil-derived nitrogen and may depend on biological N₂ fixation to meet their nutritional requirements (proteins, nucleic acids). This process can substantially enhance the mineral nutrition of epiphytic plants (Hietz et al., 2002). Nevertheless, comprehensive knowledge about the identity, ecology, and functional roles of canopy microorganisms (including both diazotrophic and denitrifying taxa) remains scarce (Nakamura et al., 2017). Understanding these microbial communities is therefore essential to elucidate canopy-level contributions to nutrient cycles and their potential responses to environmental change.
Objectives
This thesis aims to characterise microbial communities within tropical forest canopies, to identify the deterministic and stochastic factors shaping these communities, and to assess their functional contribution to host plant health and ecosystem functioning in the context of global change.
This project will address three specific objectives:
(1) What are the diversity and community structure of canopy-associated microorganisms, including N₂-fixing and denitrifying taxa, present in tropical tree canopies?
(2) How do different canopy components and their associated microbiota contribute to nitrogen cycling?
(3) How do environmental perturbations affect microbial communities and their functional roles in ecosystem processes?
Beyond the taxonomic description of microorganisms, this thesis aims to integrate the functional dimension of canopy microbiota within an ecosystem perspective. It will provide key insights into how plant–microbe interactions shape biogeochemical cycles in tropical environments and contribute to the resilience of these ecosystems under global change. The expected results will offer a solid foundation for incorporating canopy processes into global models of nutrient and carbon fluxes—currently focused on soils—as well as a more integrated understanding of the role of epiphytic microbiota in sustaining the health and functional diversity of tropical forests.
Methods
This PhD project is part of an interdisciplinary and collaborative program that aims to discover and characterize the microbial communities in tropical forests and to unravel the ecological underlying their assembly and functioning. Some datasets have already been obtained in ongoing projects, and additional data will be collected to further address the project’s objectives. Consequently, the PhD work carries minimal risk, as existing data can be exploited for scientific publications, while the PhD student will also have the opportunity to develop original questions and approaches within the scope of the PhD project.
All previous and forthcoming field campaigns are or will be conducted in French Guiana, a biodiversity hotspot offering exceptional opportunities for research in the tropical forest canopy. The PhD will focus on multiple canopy components, including vascular and non‑vascular epiphytic plants with contrasting morphological and physiological adaptations, canopy soil, tree bark, and leaves. Field and experimental approaches will be implemented to meet the scientific objectives and to link microbial diversity with ecosystem processes.
The PhD student will use DNA metabarcoding to characterize microbial communities with the different canopy components. Bioinformatics analyses will be mainly performed using the OBITools and the metabaR packages. Environmental variables (temperature, light, relative humidity) and plant traits (root and leaf characteristics) will be measured and considered as explanatory variables. Multivariate statistical analyses will be applied to infer the drivers and assembly processes of microbial communities and to identify key taxa and functions.
Nitrogen fixation and denitrification will be quantified across the different canopy components to clarify their relative contribution to nitrogen inputs and outputs in the forest ecosystem. To assess the impacts of perturbations such as deforestation and drought on microbial diversity and ecosystem functioning, the project will exploit a natural microecosystem: the microbial–faunal food web inhabiting the rainwater‑filled leaves of tank bromeliads. This integrative framework will provide a unique opportunity to link microbial community structure, environmental change, and biogeochemical cycles in tropical forest canopies.
Environment of the thesis
The PhD student will be affiliated with the CRBE and hosted at building 4R1 of Université de Toulouse. Field missions in French Guiana are also planned to complete the datasets. A collaboration with UMR ECOFOG in Kourou will ensure adequate material conditions.
This thesis will be supported by the LabEx CEBA (Centre d’Etude sur la Biodiversité Amazonienne) through the MicroEpiN and INTRACTIF projects. Additional support will be provided by the MICROBARK project funded by the FR AIB.
This thesis will rely on internal collaborations within the CRBE, as well as national partnerships (UMR LRSV Toulouse, UMR ECOFOG Kourou, UMR LMGE Clermont-Ferrand). The student will also collaborate with members of the Bromeliad Working Group, an international consortium of researchers studying bromeliad ecology and their associated macro- and microfauna.
Profile and skills required
This project is anchored in scientific disciplines relating to the fields of microbial ecology, molecular ecology and biogeochemistry. Through his or her academic career and internships, the candidate must show interest and experience in these main research areas. Ideally, the candidate should present skills in one or more of the following areas: DNA extraction, PCR, metabarcoding, bioinformatics, advanced biostatistics, and measurements of plant traits and fluxes. However, some of these skills can be acquired through project collaborators. Advanced technical skills in R are essential for conducting exploratory and statistical analyses. The candidate should also have strong analytical and writing abilities, capacity to work in multidisciplinary teams, and the ability to work independently.
Références bibliographiques*
Antonelli, Alexandre, Alexander Zizka, Fernanda Antunes Carvalho, et al., 2018. Amazonia is the primary source of Neotropical biodiversity. Proceedings of the National Academy of Sciences 115: 6034 6039.
Beer C, Reichstein M, Tomelleri E, Ciais P, Jung M, Carvalhais N, Rödenbeck C, Arain MA, Baldocchi D, Bonan GB, et al. 2010. Terrestrial gross carbon dioxide uptake: global distribution and covariation with climate. Science 329: 834–838.
Hietz P, Wanek W, Wania R, Nadkarni NM. 2002. Nitrogen-15 natural abundance in a montane cloud forest canopy as an indicator of nitrogen cycling and epiphyte nutrition. Oecologia 131: 350–355.
Kohl, K. D., 2020. Ecological and evolutionary mechanisms underlying patterns of phylosymbiosis in host-associated microbial communities. Philosophical Transactions of the Royal Society B, 375, 20190251
Nakamura A, Kitching RL, Cao M, Creedy TJ, Fayle TM, Freiberg M, Hewitt CN, Itioka T, Koh LP, Ma K, et al. 2017. Forests and their canopies: achievements and horizons in canopy science. Trends in Ecology & Evolution 32: 438–451.
Pan Y, Birdsey RA, Fang J, Houghton R, Kauppi PE, Kurz WA, Phillips OL, Shvidenko A, Lewis SL, Canadell JG, et al. 2011. A large and persistent carbon sink in the world’s forests. Science 333: 988–993.
Simon, J. C., Marchesi, J. R., Mougel, C., & Selosse, M. A., 2019. Host-microbiota interactions: from holobiont theory to analysis. Microbiome, 7, 1-5.
Sohrabi R., Paasch B. C., Liber J. A., He S. Y., 2023. Phyllosphere Microbiome. Annual Review of Plant Biology 74, 539-568.
Spracklen D, Arnold S, Taylor C. 2012. Observations of increased tropical rainfall preceded by air passage over forests. Nature 489: 282–5.
Vacher C, Hampe A, Porté AJ, Sauer U, Compant S, Morris CE. 2016. The phyllosphere: microbial jungle at the plant–climate interface. Annual Review of Ecology, Evolution, and Systematics 47: 1–24.
Vorholt J. A., 2012. Microbial life in the phyllosphere. Nature Reviews Microbiology 10, 828-840.
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