■ From clouds to our environment: proteomic study of microorganisms contained in clouds

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Description of the PhD project

Biologicals particles including bacteria, pollen and fungi can all be found in airborne particles, known as bioareosols. Bioaerosols can spread disease to human, plants, animals on the scale to meters to continent, due to the potential for long-distance transport in the atmosphere (DeLeon-Rodriguez et al 2013). Bioaerosols may also play a role in climate change and ecological processes and may even be beneficial for human health and the environment (Barr et al., 2013). A large variety of bioorganisms can be spread by bioaerosols, as bioaerosols could be generated from water containing microbes but also from soils (Joung et al., 2017).
Clouds represent one of the most important bioaerosols. Within the atmospheric system, clouds are atmospheric interface with the ground: they physically connect high altitude with the surface by being to a large extent at the origin of wet deposition of aerosols, including microorganisms. Cloud water is a complex mixture of soluble gas and particles dissolved into millions of micron-sized water droplets, and forming very reactive and dynamic systems (Vaïtilingom et al., 2013, Vaïtilingom et al., 2010). As non-soluble biological particles, some microorganisms can physically impact clouds by acting as embryos for the formation of water droplets and ice crystals, with subsequent impacts on hydrological cycles (Besaury et al., 2017). Observations of microbiological features in fog and clouds raised the possibility that these also represent habitats for microorganisms, where they would actively take part in the chemical reactivity through metabolic activity and nutrient utilization (Amato et al., 2017).
Clouds droplets host living cells. A study on microbial communities in cloud water by high throughput sequencing from DNA and RNA extracts, allowed to identify active species among community members. Communities consisted of 103 −104 bacteria and archaea mL-1 and 102−103 eukaryote cells mL-1. They appeared extremely rich, with more than 28 000 distinct species detected in bacteria and 2 600 in eukaryotes. Proteobacteria and Bacteroidetes
largely dominated in bacteria, while eukaryotes were essentially distributed among Fungi, Stramenopiles and Alveolata (Amato et al., 2017).
The present project aims at the development of a strategy for the study of microorganisms in clouds at the proteomic level. In the last years, proteomic has proved its complementary to genomic and transcriptomic, leading to a new field of sciences called proteogenomic. On the present project, proteomic analysis should allow a better annotation of genomic data leading to a better comprehension of metabolism state of living bacteria and ecosystems present in the cloud.


Proteomics, analytical chemistry, microfluidic, clouds, bacteriology, environment

Research unit

USR3149 Biological Mass Spectrometry & Proteomics

Description of the research Unit/subunit

Our laboratory has an expertise in proteomic and mass spectrometry, as proved by its appartenance in IPGG and Memolife Labex, FR FT-ICR network, IBISA label, that should allow completing this project. The latest generation of high resolution mass spectrometers will be available for this project. Microfluidics tools will be built at the IPGG Institute.

Name of the supervisor
Yann Verdier (yann.verdier (arobase) espci.fr)

Name of the co supervisor
Joëlle Vinh (joelle.vinh (arobase) espci.fr)

3i Aspects of the proposal

This innovative project can have applications in different areas. On the one hand, allowing the characterization of unknown organisms, it opens the door to discoveries of proteins with particular properties (Vaitaington et al 2013). On the other hand, different microorganisms have been described as being able to participate in the nucleation inducing the formation of clouds (Besaury et al., 2017). Another point is the study of dissemination of microorganisms and allergens. Finally, original markers could be identified, allowing the tracking of clouds and correlation with human activities. The benefits of this project could therefore interest industrial partners from different fields of interest, such as biotechnology, climatology, or environment. To reach this goal, our project will cross the frontiers between microfluidic, analytical chemistry and biology. The first aim of this project is the development of a strategy for the study of bacteria at the proteomic level. Samples will be prepared on a microfluidic devise, in order to reduce material lost. Then, mass spectrometers of latest generation will allow the analysis of complex mixtures with a high sensitivity. Their high resolution is an essential advantage for this kind of samples, containing a large number of organisms whom genome is not known. After analysis, protein identification is usually performed by comparison with proteic or genomic databases, or by de novo sequencing. Last, we plan to intersect our data with genomic data for better exploiting of proteomic data and a draft of genomic annotation. One of the potential benefits of this project is to identify markers that should allow to track cloud flows, and to correlate them with human activities. It will therefore be essential to develop international collaborations for the collection of samples. Depending on the progress of the project, we will establish contacts with all the necessary partners. The dissemination of the results (publication, congress) will be at the international level.

Expected Profile of the candidate

Master M2 with a dominant in analytical chemistry, or analytical instrumentation. A (theoretical) knowledge in mass spectrometry and miniaturized separation techniques is expected. The candidates should be interested in analytical chemistry applied to biology since this doctoral project is at the interface of the two domains. He/she should have validated a full M2 master degree, or engineering degree.

Important dates

Call for applications : from July 16th to September 17th 2018
Eligibility check results : Late September
3i Committee evaluation results : Late October
Interviews from the shortlisted candidates with the Selection Committee : Mid-December (week of December 10th)
Final results : Late December

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