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.
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, nutrient cycling and plant performance. My work includes biological nitrification inhibition, microbial inoculation, flooding, herbivory and fungal pathogen stress.
I investigate how hydrological disturbance reorganizes soil–plant–microbiome function, with a focus on electron-transfer processes and elemental coupling, and on the recovery process that follows flooding and drought.
I integrate amplicon sequencing, metagenomics, metatranscriptomics and reproducible computation — including absolute-abundance analysis using spike-in controls — to connect microbial community patterns with biological function.
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.
Publications
Research across agricultural soils, plant-associated communities and host microbiomes. The downloadable CV includes additional publications and outputs.
Agriculture, Ecosystems & Environment
Software
I develop R tools and workflows that connect biological questions to transparent, reproducible analysis.
R / Bioconductor · Version 1.2.0
Estimating Absolute Abundance from Microbial Spike-in Controls
A modular workflow for absolute microbial quantification using single spike-in taxa or synthetic microbial communities. Supports spike-in validation, preprocessing, scaling-factor estimation, absolute-abundance conversion, bias correction and normalization, with phyloseq and TreeSummarizedExperiment compatibility.
BiocManager::install("DspikeIn")
Install BiocManager first with install.packages("BiocManager"), then run the command above.
MIT licence · Package DOI ↗
R / CRAN · Version 1.0.6
Diagnostics for Soil–Plant–Microbial Redox Recovery
Integrate longitudinal soil, plant and microbial observations to examine redox disturbance and recovery. Includes recovery signatures, fixed-reference domain scores, observation-coverage diagnostics, and conditional calculations of oxygen demand and accessible electron capacity.
install.packages("HRRI")
R ≥ 4.3.0 · MIT licence · Package DOI ↗
R / GitHub · Version 0.4.19
From fungal confrontation photographs to matched-control results.
FunMel measures the colour, shape and image-darkness profiles of approximately round Zymoseptoria tritici colonies around another fungus. It separates target colonies from central fungal tissue and connected hyphal growth, preserves image provenance and custom metadata, and compares treatments with their own set controls.
install.packages("remotes")
remotes::install_github("mghotbi/FunMel")Restart R before loading an updated package. R ≥ 4.1 and source-compilation tools are required: Xcode Command Line Tools on macOS, matching Rtools on Windows, or R development tools and ImageMagick development libraries on Linux. For installed tutorials, use build_vignettes=TRUE during installation.
All research software ↗Built with curiosity. Shared for reproducibility.
Research resources
A little open-science toolbox for soil, plant and microbiome research. Explore public protocols here, or visit GhotbiLab for available methods and code.
From sample collection to measurement.
Practical methods for work at the bench and in the field.
Public protocols are available below. Browse additional methods at GhotbiLab.
Public SOPs are linked below. Other resources become visible as they are released.
From raw data to interpretation.
Computational workflows for reproducible analysis.
Browse available scripts and workflow documentation at GhotbiLab.
Browse publicly available repositories for code, dependencies and usage notes.
Curriculum vitae
Training and research across plant science, soil biogeochemistry, microbial ecology and computational biology.
Download academic CV ↗Institute of Plant Nutrition and Soil Science and Botanical Institute, Kiel University
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 California, Davis and University of Bonn
Joint doctoral programme in soil microbial ecology and biogeochemistry. Advisors: William R. Horwath and Claudia Knief.
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.
Teaching and 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.
Contact
For research collaborations, academic opportunities and conversations about soil–plant–microbe interactions.
mitra.ghotbi@gmail.com ↗