Predoctoral Researcher in Plant Microbiome Ecology and Microbial Interactions

Autonomous University of Madrid (Universidad Autónoma de Madrid); España; On-site; EUR 21,000 - 27,000; Full time

Job summary

Autonomous University of Madrid (Universidad Autónoma de Madrid) in Spain seeks a PhD candidate for the RHIZOINTERACT project. The role combines computational biology with experimental microbiology to study wheat rhizosphere microbiomes and plant-beneficial inoculants.

The researcher will work on genome-scale metabolic models, flux balance analysis, and multi-omics data integration, with opportunities to present findings at meetings and in publications.

Qualifications

• Master’s degree in Microbiology, Biotechnology, Bioinformatics or related field and admission to the PhD Programme in Microbiology at Universidad Autónoma de Madrid.
• Experience combining experimental microbiology with bioinformatics and/or genome‑scale metabolic modelling; experience with GEM reconstruction and FBA using CarveMe/COBRApy/MICOM will be valuable.
• English proficiency at least B2 level is required.

Responsibilities

• Carry out a PhD within the RHIZOINTERACT project framework, focusing on bacterial interactions and wheat rhizosphere microbiome assembly.
• Perform genome analyses, multi-omics data analysis and modelling; curate and reconstruct GEMs, perform FBA and simulate metabolic interactions.
• Design and execute bacteria–bacteria interaction assays and plant–microbe experiments with wheat; contribute to publications and conferences.

Skills

Bioinformatics

Genome-scale modelling

Flux balance analysis

Experimental microbiology

English proficiency (B2)

Education

Master’s degree in Microbiology, Biotechnology, Bioinformatics or related field

Tools

CarveMe

COBRApy

MICOM

MATLAB

R

Python

Job description

Organisation/Company Autonomous University of Madrid (Universidad Autónoma de Madrid) Department Faculty of Sciences, Department of Biology Research Field Agricultural sciences Biological sciences » Biology Researcher Profile First Stage Researcher (R1) Positions PhD Positions Application Deadline 30 Nov 2026 - 23:59 (Europe/Madrid) Country Spain Type of Contract Temporary Job Status Full-time Hours Per Week 37,5 Offer Starting Date 1 Jan 2027 Is the job funded through the EU Research Framework Programme? Not funded by a EU programme Is the Job related to staff position within a Research Infrastructure? No

Offer Description

The successful candidate will carry out a PhD within the framework of the RHIZOINTERACT project (PID2025-169677OA-I00), focused on bacterial interactions and the ecological principles governing the assembly of the wheat rhizosphere microbiome and the integration of plant-beneficial inoculants.

A major component of the project will involve bioinformatics and metabolic modelling. The researcher will reconstruct, analyse and curate genome-scale metabolic models (GEMs), perform flux balance analysis (FBA), and model metabolic interactions among bacterial strains and microbial communities. The candidate will also analyse bacterial genomes and high-throughput sequencing datasets, including functional annotation, comparative genomics, amplicon sequencing, metagenomics, metatranscriptomics and related multi-omics data.

Experimental work will complement these computational approaches and will include the maintenance and phenotypic characterization of plant-associated bacterial collections, classical and molecular microbiology, bacterial genetics, and bacteriophage propagation and characterization.

The project will involve the design and execution of bacteria–bacteria interaction assays, including metabolic and non‑metabolic interactions, co‑cultures, synthetic microbial communities (SynComs), arrival‑order experiments, strain drop‑out/drop‑in experiments, and assays of inoculant integration. Computational predictions will be iteratively tested and refined using experimental data.

The researcher will also perform plant–microbe experiments using wheat microcosms and monitor bacterial community composition and dynamics. The candidate will analyse, integrate, interpret and present the resulting data, participate in national and international scientific meetings, contribute to scientific publications, outreach and knowledge‑transfer activities, and may participate in the co‑supervision of BSc and MSc research projects.

Practical experience in microbiology and bacterial culture techniques, including strain isolation and characterization, phenotyping, culture media preparation, and maintenance and management of bacterial collections.

Experience in experimental studies of bacteria–bacteria interactions, including carbon‑source utilization screening, bacterial co‑cultures, synthetic microbial communities (SynComs), plant–microbe assays and/or bacteriophage infection assays.

Experience in molecular biology, including DNA and RNA extraction and purification, PCR, electrophoresis and bacterial genetic manipulation.

Strong background in bioinformatics and biological data analysis, including experience with R and/or Python, genome assembly and annotation, comparative genomics, amplicon sequencing analysis, metagenomics, metatranscriptomics and/or metaproteomics. Experience with MATLAB will also be valued.

Experience in the reconstruction, analysis and curation of genome‑scale metabolic models (GEMs) and flux balance analysis (FBA) will be particularly valued. Experience with metabolic modelling tools such as CarveMe, COBRApy, MICOM or equivalent frameworks, as well as the experimental validation of metabolic predictions, will be considered especially relevant.

Prior research experience in microbiology, microbial ecology, plant‑ and seed‑associated bacteria, bioinformatics or metabolic modelling will be valued, including participation in scientific publications and conference communications.

Knowledge of additional languages will be considered an asset.

Specific Requirements

Candidates must hold a Master’s degree in Microbiology, Biotechnology, Bioinformatics or a related field and meet the requirements for admission to the PhD Programme in Microbiology at Universidad Autónoma de Madrid.

Previous research experience combining experimental microbiology with bioinformatics and/or genome‑scale metabolic modelling will be particularly valued. Experience with GEM reconstruction and curation, flux balance analysis, and tools such as CarveMe, COBRApy, MICOM or equivalent frameworks will be considered especially relevant.

English proficiency equivalent to B2 level or higher is required.

Languages ENGLISH Level Good

Languages SPANISH Level Basic

Additional Information

Full‑time predoctoral contract for a maximum duration of 4 years, with a gross salary in accordance with the conditions established for predoctoral contracts associated with the 2025 Knowledge Generation Projects call.

The fellowship includes funding for doctoral training and international research stays in accordance with the conditions of the call. The researcher will also have opportunities to participate in national and international conferences and specialized training activities.

Eligibility criteria

Candidates must hold a university degree and a Master’s degree, or equivalent qualifications granting access to doctoral studies in Spain, and meet the requirements for admission to the PhD Programme in Microbiology at Universidad Autónoma de Madrid.

Candidates holding a PhD degree are NOT eligible for this position.

Selection process

Applications will be evaluated by the appointed Selection Committee according to the criteria and subcriteria established in the UAM call. The evaluation will consider the candidates’ academic and research background, previous experience, and suitability for the scientific and technical profile of the position.