Microbial ecology · Soil biogeochemistry
I study how plants, microorganisms and soil chemistry interact—and how these relationships shape nutrient cycling and recovery from environmental stress.
01 / Research
My research connects rhizosphere biology, soil carbon and nitrogen cycling, and host-associated microbiomes. I combine controlled experiments and process measurements with molecular data and quantitative analysis to understand how biological interactions respond to changing environments.
Plant genotype, microbial partners and environmental stress shape rhizosphere processes, nitrogen cycling and plant performance. My work includes biological nitrification inhibition, microbial inoculation, flooding and herbivory.
I investigate how hydrological disturbance reorganizes soil–plant–microbiome function, with a focus on electron-transfer processes, elemental coupling and recovery after flooding and drought.
I integrate amplicon sequencing, metagenomics and reproducible computation to connect microbial community patterns with biological function, including absolute-abundance analysis using spike-in controls.
Developing independent research directions
Holobiont redox resilience across the maize domestication gradient, and HYDROREDOX: testing whether event-accessible electron-transfer architecture helps predict recovery after flood–drought cycles.
02 / Publications
Research across agricultural soils, plant-associated communities and host microbiomes. The downloadable CV includes additional publications and outputs.
Agriculture, Ecosystems & Environment
03 / Software
I develop R tools and workflows that connect biological questions to transparent, reproducible analysis.
R / Bioconductor
Estimate absolute abundance from microbial spike-in controls, supporting quantitative interpretation of microbiome data.
Explore the package ↗Code / Methods
Explore my open-source projects and analysis workflows, including tools for microbial ecology and redox resilience.
Visit my GitHub ↗04 / Research resources
Laboratory protocols and computational pipelines for soil, plant and microbiome research.
From sample collection to measurement.
Practical methods for work at the bench and in the field.
Protocols will be linked here as they become available.
Experimental procedures · Materials · Method notes
From raw data to interpretation.
Computational workflows for reproducible analysis.
Code and workflow documentation will be linked here as they become available.
Source code · Dependencies · Usage notes
05 / Curriculum vitae
Training and research across plant science, soil biogeochemistry, microbial ecology and computational biology.
Download academic CV ↗Kiel University, Germany
Plant Nutrition and Soil Science; Botanical Institute. Soil–plant–microbiome redox ecology and predictive-framework development.
Middle Tennessee State University, USA
Host-associated microbiomes, metagenomics, synthetic communities and fungal–bacterial interactions.
University of Illinois Urbana-Champaign, USA
Rhizosphere nitrogen cycling, biological nitrification inhibition and plant–microbe interactions.
ZEF, University of Bonn, Germany
Climate-change effects on plant performance, soil organic matter and greenhouse-gas emissions.
University of Bonn & University of California, Davis
Joint doctoral programme in soil microbial ecology and biogeochemistry. Advisors: Claudia Knief and William R. Horwath.
Shahed University, Iran
Biology and efficacy of Fusarium oxysporum isolates for biocontrol of Orobanche aegyptiaca.
IAU, East Azerbaijan, Iran
Thesis: tissue culture of carrot cells.
Greenhouse, mesocosm and field experiments; rhizosphere processes; microbial inoculation and synthetic communities; plant, root, soil and gas measurements; stable isotopes; DNA/RNA workflows; 16S/ITS profiling; metagenomics and transcriptomic analysis.
R, Bioconductor and Linux; mixed models, multivariate analysis and ecological networks; genome-resolved workflows; reproducible pipelines and R package development. Additional tools include TASSEL, Cytoscape, Gephi, SigmaPlot and GenGIS.
06 / Teaching & mentoring
I teach microbial ecology, bioinformatics and statistics by connecting mechanisms, experiments, measurements and interpretation. Reproducible code is part of the scientific argument.
My mentoring spans undergraduate, graduate and early-career researchers at UIUC, MTSU and Kiel. I emphasize clear expectations, constructive feedback and growing independence, with multiple entry points for students from different disciplinary backgrounds.
07 / Contact
For research collaborations, academic opportunities and conversations about soil–plant–microbe interactions.
mitra.ghotbi@gmail.com ↗