About

Dr. Andrew J. Margenot is a Professor in the Department of Crop Sciences at the University of Illinois at Urbana-Champaign (UIUC). He serves as the Principal Investigator of the Soils Lab and holds several editorial roles including Editor in Chief of Geoderma, Section Editor for Plant and Soil, Technical Editor for the Soil Science Society of America Journal, and Associate Editor for the European Journal of Soil Science and Soil Use and Management. Dr. Margenot is also the Director of the Alma Mater Plots and the historic Morrow Plots, and he is an Associate Director and Founding Member of the Agroecosystem Sustainability Center at UIUC. Additionally, he holds affiliate faculty positions in the Program in Ecology, Evolution and Conservation Biology, the Center for Digital Agriculture, and the Center for African Studies at UIUC. His leadership roles and editorial contributions highlight his expertise and influence in soil science and agroecosystem sustainability.

Research topics

• Environmental science
• Computer Science
• Soil science
• Agronomy
• Biology
• Ecology
• Chemistry
• Geography
• Biochemistry
• Agroforestry
• Sociology
• Machine Learning
• Economics
• Mathematics
• Remote sensing
• Environmental resource management
• Environmental engineering
• Horticulture
• Animal science
• Chromatography
• Environmental planning
• Environmental economics
• Engineering
• Geology

Selected publications

• Alkalization solution affects selectivity of absorbance for colorimetric quantification of para-nitrophenol in soil enzyme activity assays

  Biology and Fertility of Soils · 2026-03-31

  articleOpen accessSenior author

  The alkalization step in soil enzyme activity assays can cause precipitation, potentially compromising colorimetric quantification of para-nitrophenol (pNP) product used to measure activity. We identified which soil enzyme activity assay matrices lead to the formation of a precipitate when alkalized using NaOH or tris(hydroxymethyl)aminomethane (Tris), characterized the precipitate, and quantified the extent to which the precipitate affected assayed soil enzyme activities. Precipitation occurred in matrices alkalized with 0.5 M NaOH (≈ 13 pH) but not in matrices alkalized with 0.1 M Tris (≈ 9 pH), and to a greater extent in matrices with modified universal (bufferuniversal) than acetate (bufferacetate) buffer. Thermodynamic modeling, mid-infrared Fourier transform infrared spectroscopy (FTIR), and elemental analysis indicated the precipitate was Ca(OH)2-based. Activities were higher for soil phosphomonoesterase assayed in bufferuniversal with NaOH than with Tris alkalization, but were similar for soil sulfatase assayed in bufferacetate. Alkalization with Tris avoids precipitates in soil enzyme activities and therefore stands to minimize inaccuracy of soil enzyme activity assays.

  PublisherOA PDFDOI

• First Metagenome-Assembled Genomes from the Historic Morrow Plots

  Zenodo (CERN European Organization for Nuclear Research) · 2026-03-19

  datasetOpen access

  This manuscript presents the first genome resolved metagenomic resource generated from the historic Morrow Plots, one of the longest running agricultural field experiments in the world. Using 33 shotgun metagenomes collected from soils under different crop rotation and fertilization treatments, the study reconstructed 230 metagenome assembled genomes, including both archaeal and bacterial lineages. The dataset highlights management associated patterns in soil microbial community structure, with a particular emphasis on archaeal ammonia oxidizers and other nitrogen cycling microorganisms. In addition to genome reconstruction, the study provides taxonomic assignments, genome quality statistics, and treatment resolved abundance profiles, creating a valuable reference for investigating how long term agricultural practices influence soil microbial ecology, nitrogen cycling, and soil health.

  PublisherDOI

• First Metagenome-Assembled Genomes from the Historic Morrow Plots Reveal Management-Associated Dominance of Archaeal Ammonia Oxidizers

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-25

  articleOpen access

  Abstract Soil microbial communities underpin both soil health and agricultural productivity, yet genome-resolved resources from long-term field experiments remain limited. Here, we present a genome-resolved metagenomic dataset from the historic Morrow Plots long-term experiment in central USA, comprising 33 shotgun metagenomes collected across diverse crop rotation and fertilization treatments in year 149 of the experiment. Using a co-assembly, multi-binner workflow, we recovered 230 metagenome-assembled genomes (MAGs), including 44 archaeal and 186 bacterial genomes spanning multiple soil-associated phyla. Among these, 59 MAGs were linked to nitrogen-cycling functions, including ammonia- and nitrite-oxidizing lineages. The dataset also includes genome quality metrics, taxonomic classification, and treatment-resolved abundance patterns across different management regimes. Importantly, these nitrogen guild MAGs enable comparative analyses of nitrifier ecology, genome diversity, and functional variation linked to management in agricultural soils. Together, these resources establish a unique benchmark for studying how agricultural practices shape soil microbial communities at genome level, with associated long-term crop yield and soil fertility changes since the experiment’s inception in 1876.

  PublisherOA PDFDOI

• First Metagenome-Assembled Genomes from the Historic Morrow Plots

  Zenodo (CERN European Organization for Nuclear Research) · 2026-03-19

  datasetOpen access

  This manuscript presents the first genome resolved metagenomic resource generated from the historic Morrow Plots, one of the longest running agricultural field experiments in the world. Using 33 shotgun metagenomes collected from soils under different crop rotation and fertilization treatments, the study reconstructed 230 metagenome assembled genomes, including both archaeal and bacterial lineages. The dataset highlights management associated patterns in soil microbial community structure, with a particular emphasis on archaeal ammonia oxidizers and other nitrogen cycling microorganisms. In addition to genome reconstruction, the study provides taxonomic assignments, genome quality statistics, and treatment resolved abundance profiles, creating a valuable reference for investigating how long term agricultural practices influence soil microbial ecology, nitrogen cycling, and soil health.

  PublisherDOI

• Soil organic matter and F1 hybrid cultivar influence <i>Coffea arabica</i> yields in south‐central Guatemala

  Agronomy Journal · 2026-03-01

  articleOpen accessSenior authorCorresponding

  Abstract Smallholders produce 60% of global coffee ( Coffea arabica ) supply but lack recommendations on nutrient management. We tested hypothesized N‐ and K‐driven yield gaps using on‐farm omission trials established across 21 fields in Guatemala. The effects of a single and combined application of N (285 kg ha −1 ) and K (350 kg ha −1 ) were evaluated for coffee cherry yield; N and K concentrations of soil; leaf and coffee cherries; and yield‐based export of N, P, and K. Despite low soil‐extractable N and K, yields were similar among fertilization treatments, consistent with similar N and K concentrations in leaves and soil‐extractable pools over three intraseasonal timepoints. Yields were twofold greater in fields with high (4.1%–5.0%) versus low (2.5%–3.0%) soil organic matter (SOM), and 1.8‐fold greater for the F1 hybrid than traditional American varieties. Relatively constant cherry N, P, and K concentrations entailed scaling of macronutrient removal with yield. Because yields and N and K harvest export were unaffected by fertilization, nitrogen use efficiency and potassium use efficiency values were near‐zero or negative. Our results indicate that a single, high‐rate application of N and K fertilizers in smallholder coffee production on coarse‐textured soils in this region is neither agronomically nor economically sensible. Coffee smallholders may be able to increase yields by building SOM and employing hybrid varieties. While our multisite evaluation provided insight into coffee yield relationships with SOM and by coffee cultivar, intra‐seasonal variability may limit the applicability and reproducibility of coffee yield response to N and K fertilization due to single season evaluation.

  PublisherDOI

• Net mineralizable soil phosphorus cannot be measured by non‐isotopic approaches

  Agricultural & Environmental Letters · 2026-04-13

  articleOpen accessSenior authorCorresponding

  Abstract While radioisotopic pool dilution is widely regarded as the most reliable method for estimating soil phosphorus mineralization (P min ), high costs, low throughput, and safety requirements limit its use. We evaluated the potential of non‐radioisotopic approaches to estimating net P min by difference before and after aerobic incubation, analogous to potentially mineralizable nitrogen (N), using five common extractions (water, resin, Olsen, Bray‐1, and Mehlich‐3). Non‐radioisotopic methods generally failed to produce positive net P min rates (extractable P pre‐incubation &gt; post‐incubation), ranging from 18% (resin) to 0% (Mehlich‐3) in the detection of positive net P min . When detected, positive net P min values measured as post‐incubation difference in extractable P were underestimated by a factor of 3 to 274 relative to net P min measured by the radioisotopic approach. These findings demonstrate that net P min cannot be estimated by difference in extractable P after incubation, and point to the necessity of radioisotopic approaches for accurate measurements of soil P min .

  PublisherDOI

• Estimating soil phosphorus mineralization and immobilization: a comparison of isotope pool dilution vs and isotopic exchange kinetics frameworks

  Soil Biology and Biochemistry · 2026-03-17 · 1 citations

  articleSenior authorCorresponding
  PublisherDOI

• Optimal soil storage methods for enzyme activity assays: a meta-analysis

  Soil Biology and Biochemistry · 2026-01-30

  articleOpen accessSenior authorCorresponding

  The lack of standardized soil storage methods for enzyme assays has restricted cross-comparison of soil enzyme activities in the literature, and reported effects of soil sample storage on enzyme activities are often study-specific and conflicting. We conducted a systematic literature review and a meta-analysis to (1) identify data gaps in evaluations of storage effects on soil enzyme activities and (2) quantify enzyme activity responses to soil sample storage method and duration. Evaluated storage methods were (i) cold (field moist soils at 2 to 7°C), (ii) freeze (field moist soils at -5 to -35°C) or (iii) air-dry (air-drying and storing at room temperature, assumed to be ≈24°C) relative to activities assayed ≤ 24 h of soil sampling (field fresh) and/or in soils under cold storage. Twenty-two research articles (1917-2025) evaluated 106 soils for effects of three soil storage methods on activities of β-glucosidase (BG), phosphomonoesterase (PME, assayed at pH 4.0-6.5), N -acetyl-β-glucosaminidase (NAG), and urease (URE). Most soils were acidic (86%), and were Oxisols (34%) or Mollisols (19%). Soil storage decreased BG (9-55%) and PME (7-53%) activities relative to activities in field fresh soils, with the least decreases with cold storage, and NAG activities (33-68%), with the least decreases with cold and freeze storage. Greatest decreases occurred with air-drying for BG, PME and NAG relative to activities in field fresh soils or under cold storage. Only cold storage (8%) decreased URE activity. Enzyme activities were independent of storage duration except for BG activity under cold storage. The decreases in activities due to storage were mostly inconsistent across soil pH, clay, OC, and orders, and varied by assay methods. Based on least decreases in activities that were consistent across soil properties and types, the most appropriate soil storage methods appeared to be cold storage ≤ 3 d for chromogenically assayed BG activity and freeze storage for fluorogenically assayed BG and PME activities. • Soil refrigeration, freezing, and air-drying decreased BG, PME, and NAG activities • Urease activity decreased with refrigeration, unaffected by freezing and air-drying • Storage effects unrelated to pH, clay, and organic C, but varied by assay method • ≤ 3 d of soil refrigeration most suitable for chromogenic assays of BG activities • Soil freezing most suitable for fluorogenic assays of BG and PME activities

  PublisherDOI

• Long-term nitrogen fertilization does not necessarily suppress soil nitrogen mineralization via enzymatic pathways

  Applied Soil Ecology · 2026-04-23

  articleOpen accessSenior authorCorresponding

  Nitrogen (N) fertilization supports high yields of cereal crops, but the extent to which such exogenous N inputs may impact soil N provisioning through enzyme-catalyzed depolymerization and mineralization is contested. We tested the hypothesis that exogenous N inputs suppress soil N mineralization by leveraging a long-term field experiment in an Argiudoll representative of the U.S. Midwest. We quantified: (1) total organic carbon (TOC) and N, (2) potentially mineralizable N (PMN) as a proxy for soil N provisioning capacity, (3) microbial biomass C (MBC) and N (MBN), and (4) activities of 12 N-hydrolytic enzymes as proxies for N depolymerization-mineralization potential rates across a 42 y urea-based fertilization gradient of 0, 67, 135, 202, and 269 kg N ha −1 . Soil PMN, MBN, TN and N-hydrolytic enzyme activities, except for two aminopeptidase and urease activities, as well as MBC, TOC and C: N were unaffected by N fertilization (i.e., 0 vs 69–269 kg ha −1 ). Under N fertilization, we found weak evidence for suppression of N mineralization: relative to the lowest N fertilization rate (67 kg ha −1 ), PMN was 23% lower ( p = 0.104) at 269 kg ha −1 and four of eight aminopeptidase activities, either on soil mass or TOC basis, were 24–284% lower ( p = 0.031–0.091) at 202 kg ha −1 than the lowest N fertilization rate (67 kg ha −1 ), suggesting partial suppression of an intermediate step of multistep N depolymerization. Despite fertilization with urea, urease activity was 78–84% lower ( p = 0.019) at 202 kg N ha −1 than 0 and 67 kg N ha −1 . Overall, we do not find evidence that N fertilization across a wide range of rates suppresses soil N depolymerization and mineralization enzyme activities, nor potentially mineralizable N, in the long-term in maize-based agroecosystems situated on Mollisols that dominate the US Midwest. Given the reliance of the over 40 million ha of maize-based production on exogenous N inputs in the U.S. Corn Belt, our results suggest limited negative impacts on soil N mineralization in the long-term. • Soil N cycling was evaluated in a 42 y N fertilization gradient (0–269 kg ha −1 ). • Fertilization (0 vs 67–269 kg ha −1 ) did not impact N pool sizes or process rates. • Potentially mineralizable N was unaffected by N fertilization ( p = 0.12). • Certain soil aminopeptidase activities were lower at 202 than at 67 kg N ha −1 . • Soil protease, deaminase and chitinase activities unaffected by N fertilization.

  PublisherDOI

• Accelerated phosphorus immobilization at high soil temperatures may decrease net mineralization

  Soil Biology and Biochemistry · 2026-01-19 · 4 citations

  articleSenior author
  PublisherDOI

Recent grants

• SCC-IRG Track 1: Co-Producing Community - An integrated approach to building smart and connected nutrient management communities in the US Corn Belt

  NSF · $2.0M · 2021–2026

Frequent coauthors

• Kaiyu Guan

  35 shared

• Jordon Wade

  Syngenta (Switzerland)

  22 shared

• Sanjai J. Parikh

  University of California, Davis

  18 shared

• Lowell E. Gentry

  University of Illinois Urbana-Champaign

  16 shared

• Sheng Wang

  Northeastern University

  14 shared

• Francisco J. Calderón

  Oregon State University

  14 shared

• Chongyang Li

  University of Illinois Urbana-Champaign

  14 shared

• Wendy H. Yang

  University of Illinois Urbana-Champaign

  12 shared

Labs

• Soils LabPI

Education

• PhD, Land, Air and Water Resources

  University of California Davis

  2016