Past research @ LSTM, Montpellier

Genomics approaches to study plants - microorganisms symbiosis (2016-2022)

Stefano Colella's Present Interests and Activities

From October 2016 to August 2022 I worked at the “Laboratoire des Symbioses Tropicales et Méditerranéennes” (LSTM) in Montpellier where I develop genomics approaches (taking advantage of Next-Generation Sequencing technologies) to study plants - microorganisms symbiosis.

Team CAIRS « Cultures Associées, Interactions Rhizosphériques et Symbiotiques » (2021 - 2022)

In the context of the new five years LSTM project that started in 2021, with other colleagues, we founded a new team “Cultures Associées, Interactions Rhizosphériques et Symbiotiques” (CAIRS). In the CAIRS team, I shared my skills in genomics and bioinformatics in our research to characterize the interactions between rhizobia and bacterial components of the rhizosphere microbiota, established during compatible and efficient cereal/legume associations.

The closing of the LSTM laboratory planned for the end of 2023 forced me to find a novel team and laboratory to continue my research activity at INRAE.

Team MASCE « Mécanisme d’Adaptation de la Symbiose au Contrainte de l’Environnement » (2016-2020)

Working in the MASCE team, I developed genomics approaches (taking advantage of Next-Generation Sequencing technologies) to identify symbiotic traits involved in the adaptation of nodulating plants to environmental constraints. In the context of the ARN project PSYCHE, I worked on identifying gene expression networks induced by systemic signalling in response to abiotic and biotic stresses in the legume model Medicago truncatula [2,5]. In this project context, I contributed in close collaboration with the Genomic Network team at the Institute of Plant Science (IPS2, Paris - Saclay) to the development of DiCoExpress, a tool to process multifactorial RNAseq experiments [3]. Working in the team, I shared by genomics and data analysis expertise in other projects being developed [1,4]. Increasing basic knowledge about symbiotic legumes adaption to soil heterogeneity and response to different stresses will help select better legumes varieties.

Publications

Peer-reviewed papers

Boivin S, Ait Lahmidi N, Sherlock D, Bonhomme M, Dijon D, Heulin-Gotty K, Le-Queré A, Pervent M, Tauzin M, Carlsson G, Jensen E, Journet EP, Lopez-Bellido R, Seidenglanz M, Marinkovic J, Colella S, Brunel B, Young P, Lepetit M. Host-specific competitiveness to form nodules in Rhizobium leguminosarum symbiovar viciae. New Phytol. Dec 24. doi: 10.1111/nph.16392, 2019. [PubMed][New Phytol-Open Access]
Lambert I, Pervent M, Le-Queré A, Clement G, Tuzin M, Severac D, Benezech C, Tillard P, Martin Magniette ML, Colella S, Lepetit M. Responses of Mature Symbiotic Nodules to the Whole Plant Systemic Nitrogen Signaling. J Exp Bot. May 9. doi: 10.1093/jxb/eraa221, 2020. [PubMed][J Exp Bot - Open Access]
Lambert I, Paysant-Le Roux C, Colella S, Martin Magniette ML. DiCoExpress: a tool to process multifactorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models. Plant Methods vol.16, 68. https://doi.org/10.1186/s13007-020-00611-7 , 2020. [PubMed] [Plant Methods - Opens Access]
Duong B, Nguyen HX, Phan HV, Colella S, Trinh PQ, Hoang GT, Nguyen TT, Marraccini P, Lebrun M, Duponnois R. Identification and characterization of Vietnamese coffee bacterial endophytes displaying in vitro antifungal and nematicidal activities. Microbiol Res. Sept 27 doi: 10.1016/j.micres.2020.126613, 2020 [PubMed] [Microbiol Res.]
Pervent M, Lambert I, Tuzin M, Karouani A, Severac D, Nigg M, Jardinaud M-F, Colella S, Martin Magniette ML, Lepetit M. Systemic control of nodule formation by plant nitrogen demand requires autoregulation-dependent and independent mechanisms. J Exp Bot. Dec 4;72(22):7942-7956. doi: 10.1093/jxb/erab374, 2021. [PubMed][J Exp Bot]
Baudry K, Paysant-Le Roux C, Colella S, Castandet B , Martin Magniette ML. Analyzing Multifactorial RNA-Seq Experiments with DicoExpress. J Vis Exp. Jul 29;(185), 2022. doi: 10.3791/62566. [PubMed] [JoVE]
Martin ML, Pervent M, Lambert I, Colella S, Tancelin M, Severac D, Clement G, Tillard P, Lepetit M. Localized osmotic stress activates systemic responses to N limitation in Medicago truncatula-Sinorhizobium symbiotic plants. Front Plant Sci Nov 20: 14: 1288070, 2023. doi: 10.3389/fpls.2023.1288070. [PubMed][Front Plant Sci]

In the bioRxiv archive for life sciences

Pervent M, Lambert I, Tuzin M, Karouani A, Severac D, Nigg M, Jardinaud M-F, Colella S, Martin Magniette ML, Lepetit M. Autoregulation dependent and independent mechanisms are responsible for the systemic control of nodule formation by the plant N demand. bioRxiv 2021.02.03.429583 , February 03, 2021. doi: https://doi.org/10.1101/2021.02.03.429583 [bioRXiv - open acces]. Now published in J Exp Bot doi: 10.1093/jxb/erab374

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