Management and rhizosphere microbial associations modulate genetic-driven nitrogen fate

Mitra Ghotbi^1,2*, Marjan Ghotbi³, Yakov Kuzyakov^4,5, William R. Horwath⁶

Affiliations:

Mitra Ghotbi

• ¹ Department of Natural Resources & Environmental Sciences, University of Illinois at Urbana-Champaign, IL, USA
• ² Department of Biology, Middle Tennessee State University at Murfreesboro, TN, USA

Marjan Ghotbi

• ³ GEOMAR Helmholtz Centre for Ocean Research at Kiel, Germany

Yakov Kuzyakov

• ⁴ Department of Soil Science of Temperate Ecosystems and Department of Agricultural Soil Science, Georg-August-University of Göttingen at Göttingen, Germany
• ⁵ Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia

William R. Horwath

• ⁶ Plant and Environmental Sciences Building, Department of Land, Air & Water Resources, University of California Davis, at Davis, CA, USA

Corresponding Author:

Mitra Ghotbi, PhD.

• Department of Biology, Middle Tennessee State University at Murfreesboro, TN, USA
• Email: [email protected]
• ORCID ID: 0000-0001-9185-9993

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The R codes relevant to each figure have been published here to assist readers in navigating and reproducing them easily.

Prerequisites: Ensure that the required packages are installed and loaded.

reqpkg <- c("phyloseq", "vegan", "microbiome", "DESeq2", 
            "plyr", "reshape2", "grid", "scales", "cluster", "ape", "dplyr","ggrepel",
            "igraph", "ggnet", "microbiomeutilities", "network", "SpiecEasi",
            "data.table", "decontam", "ggtext","microbiomeMarker", "devtools", "dada2", "ggplot2", "ggpubr",
            "agridat", "lme4", "rstatix", "emmeans", "lmerTest")

# Check against installed packages:
inpkg <- installed.packages()[, "Package"]
neededpkg <- reqpkg[!reqpkg %in% inpkg]

if (length(neededpkg) > 0) {
  cat("The following package(s) need to be installed:", paste(neededpkg, collapse = ", "), "\n")
  cat("Installing package(s)...\n")
  install.packages(neededpkg)
  cat("Package(s) installed successfully.\n")
} else {
  cat("All required packages are already installed.\n")
}

# Load required packages:
cat("Loading required packages...\n")
invisible(lapply(reqpkg, library, character.only = TRUE))
cat("All required packages loaded successfully.\n")

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Rhizosphere-nitrogen-fate by Mitra Ghotbi is licensed under Attribution-ShareAlike 4.0 International

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