About

Alonso Favela, Ph.D., is an incoming Assistant Professor in the School of Plant Sciences at the University of Arizona, starting in Spring 2024. An Arizona native with roots from Durango, Mexico, he earned his Bachelor of Science in Biology from the University of Arizona and completed his Ph.D. in Ecology, Evolution, and Conservation Biology at the University of Illinois at Urbana-Champaign. During his doctoral studies under Angela Kent, his research focused on understanding how genetic variation in plants shapes microbiome assembly and function, which sparked his passion for microbial ecology and plant biology. Following his Ph.D., he worked with Steve Allison at UC-Irvine, where his research centered on how diverse plant-microbiome interactions respond to long-term drought conditions. His work integrates plant biology and microbial ecology to explore the dynamics of plant-microbe relationships, particularly in the context of environmental stressors such as drought. Outside of his academic pursuits, Dr. Favela enjoys listening to podcasts, playing video games, hiking, and spending time with friends and family.

Research topics

• Ecology
• Biotechnology
• Biology
• Agronomy
• Environmental science
• Economics
• Genetics
• Agroforestry
• Natural resource economics

Selected publications

• Lost and found: Rediscovering microbiome-associated phenotypes that reshape agricultural sustainability

  Science Advances · 2026-01-01 · 2 citations

  articleOpen access1st authorCorresponding

  Modern agriculture faces an urgent need to improve nutrient use efficiency while reducing environmental impacts. Here, we show that ancestral traits controlling rhizosphere microbiome functions can be reintroduced into elite maize through targeted teosinte introgressions. Using near-isogenic lines, we mapped microbiome-associated phenotypes (MAPs) derived from teosinte that suppress nitrification and denitrification-key microbial processes contributing to nitrogen loss. These introgressions altered root exudate chemistry, resulting in distinct microbial assemblies and enhanced nitrogen retention. We identified candidate loci and exudate metabolites responsible for suppressive activity and demonstrated their functional effects in vitro. These findings reveal a genetic and biochemical basis for rewilding microbiome-mediated ecosystem services in crops, offering a scalable path toward sustainable nutrient management in global agriculture.

  PublisherDOI

• Author response for "The Impact of Microbial Interactions on Ecosystem Function Intensifies Under Stress"

  2024-07-28

  peer-review
  PublisherDOI

• Author response for "The Impact of Microbial Interactions on Ecosystem Function Intensifies Under Stress"

  2024-05-24

  peer-review
  PublisherDOI

• Sampling Root-Associated Microbiome Communities of Maize (<i>Zea mays</i>)

  Cold Spring Harbor Protocols · 2024-09-05 · 4 citations

  article1st authorCorresponding

  The soil microbiome of maize shapes its fitness, sustainability, and productivity. Accurately sampling maize's belowground microbial communities is important for identifying and characterizing these functions. Here, we describe a protocol to sample the maize rhizosphere (including the rhizoplane and endorhizosphere) and root zone (still influential but further from the root) in a form suitable for downstream analyses like culturing and DNA extractions. Although this protocol is written with Zea mays as the focus, these methods can generally be applied to any plant with similar fibrous root systems.

  PublisherDOI

• The Impact of Microbial Interactions on Ecosystem Function Intensifies Under Stress

  Ecology Letters · 2024-10-01 · 24 citations

  articleOpen access

  A major challenge in ecology is to understand how different species interact to determine ecosystem function, particularly in communities with large numbers of co-occurring species. We use a trait-based model of microbial litter decomposition to quantify how different taxa impact ecosystem function. Furthermore, we build a novel framework that highlights the interplay between taxon traits and environmental conditions, focusing on their combined influence on community interactions and ecosystem function. Our results suggest that the ecosystem impact of a taxon is driven by its resource acquisition traits and the community functional capacity, but that physiological stress amplifies the impact of both positive and negative interactions. Furthermore, net positive impacts on ecosystem function can arise even as microbes have negative pairwise interactions with other taxa. As communities shift in response to global climate change, our findings reveal the potential to predict the biogeochemical functioning of communities from taxon traits and interactions.

  PublisherOA PDFDOI

• The impact of microbial interactions on ecosystem function intensifies under stress

  2024-08-23

  preprintOpen access

  A major challenge in ecology is to understand how different species interact to determine ecosystem function, particularly in communities with large numbers of co-occurring species. We use a trait-based model of microbial litter decomposition to quantify how different taxa impact ecosystem function. Further, we build a novel framework that highlights the interplay between taxon traits and environmental conditions, focusing on their combined influence on community interactions and ecosystem function. Our results suggest that the impact of a taxon is driven by its resource acquisition traits and the community functional capacity, but that physiological stress amplifies the impact of both positive and negative interactions. Further, net positive impacts on ecosystem function can arise even as microbes have negative pairwise interactions with other taxa. As communities shift in response to global climate change, our findings reveal the potential to predict the biogeochemical functioning of communities from taxon traits and interactions.

  PublisherOA PDFDOI

• Sampling and Analysis of the Maize Microbiome

  Cold Spring Harbor Protocols · 2024-09-05 · 6 citations

  articleOpen access

  Maize is an important plant for both global food security and genetics research. As the importance of microorganisms to plant health is becoming clearer, there is a growing interest in understanding the relationship between maize and its associated microbiome; i.e., the collection of microorganisms living on, around, and inside the plant. The ultimate goal of this research is to use these microbial communities to support more robust and sustainable maize production. Here, we provide an overview of recent progress in the field of maize microbiome research. We discuss the major microbiome compartments (rhizosphere, phyllosphere, and endosphere) and known functions of the microbiome. We also review the methods currently available to study the maize microbiome and its functions, and discuss how to carry out maize microbiome experiments, including both a general workflow (suitable for most microbiome analyses) and maize-specific experimental considerations.

  PublisherOA PDFDOI

• Manipulating the Maize (<i>Zea mays</i>) Microbiome

  Cold Spring Harbor Protocols · 2024-09-05 · 1 citations

  article

  ) is a multifaceted cereal grass used globally for nutrition, animal feed, food processing, and biofuels, and a model system in genetics research. Studying the maize microbiome sometimes requires its manipulation to identify the contributions of specific taxa and ecological traits (i.e., diversity, richness, network structure) to maize growth and physiology. Due to regulatory constraints on applying engineered microorganisms in field settings, greenhouse-based experimentation is often the first step for understanding the contribution of root-associated microbiota-whether natural or engineered-to plant phenotypes. In this protocol, we describe methods to inoculate maize with a specific microbiome as a tool for understanding the microbiota's influence on its host plant. The protocol involves removal of the native seed microbiome followed by inoculation of new microorganisms; separate protocols are provided for inoculations from pure culture, from soil slurry, or by mixing in live soil. These protocols cover the most common methods for manipulating the maize microbiome in soil-grown plants in the greenhouse. The methods outlined will ultimately result in rhizosphere microbial assemblages with varying degrees of microbial diversity, ranging from low diversity (individual strain and synthetic community [SynCom] inoculation) to high diversity (percent live inoculation), with the slurry inoculation method representing an "intermediate diversity" treatment.

  PublisherDOI

• Author response for "The Impact of Microbial Interactions on Ecosystem Function Intensifies Under Stress"

  2024-09-04

  peer-review
  PublisherDOI

• Genetic variation in Zea mays influences microbial nitrification and denitrification in conventional agroecosystems

  Plant and Soil · 2024-05-18 · 12 citations

  articleOpen access1st authorCorresponding

  Abstract Background and Aims Nitrogenous fertilizers provide a short-lived benefit to crops in agroecosystems, but stimulate nitrification and denitrification, processes that result in nitrate pollution, N 2 O production, and reduced soil fertility. Recent advances in plant microbiome science suggest that genetic variation in plants can modulate the composition and activity of rhizosphere N-cycling microorganisms. Here we attempted to determine whether genetic variation exists in Zea mays for the ability to influence the rhizosphere nitrifier and denitrifier microbiome under “real-world” conventional agricultural conditions. Methods To capture an extensive amount of genetic diversity within maize we grew and sampled the rhizosphere microbiome of a diversity panel of germplasm that included ex-PVP inbreds ( Z. mays ssp. mays ), ex-PVP hybrids ( Z. mays ssp. mays ), and teosinte ( Z. mays ssp . mexicana and Z. mays ssp. parviglumis ). From these samples, we characterized the microbiome, a suite of microbial genes involved in nitrification and denitrification and carried out N-cycling potential assays. Results Here we are showing that populations/genotypes of a single species can vary in their ecological interaction with denitrifers and nitrifers. Some hybrid and teosinte genotypes supported microbial communities with lower potential nitrification and potential denitrification activity in the rhizosphere, while inbred genotypes stimulated/did not inhibit these N-cycling activities. These potential differences translated to functional differences in N 2 O fluxes, with teosinte plots producing less GHG than maize plots. Conclusion Taken together, these results suggest that Zea genetic variation can lead to changes in N-cycling processes that result in N leaching and N 2 O production, and thereby are selectable targets for crop improvement. Understanding the underlying genetic variation contributing to belowground microbiome N-cycling into our conventional agricultural system could be useful for sustainability.

  PublisherOA PDFDOI

Frequent coauthors

• Angela D. Kent

  University of Illinois Urbana-Champaign

  23 shared

• Martin Bohn

  Synopsys (Germany)

  9 shared

• Sierra S. Raglin

  University of Illinois Urbana-Champaign

  7 shared

• Henrik Vibe Scheller

  University of California, Berkeley

  6 shared

• Trent R. Northen

  Joint BioEnergy Institute

  6 shared

• Gregory Bonito

  Michigan State University

  4 shared

• Jonathan H. Diab

  Joint BioEnergy Institute

  4 shared

• Lorenzo J. Washington

  University of California, Berkeley

  4 shared

Labs

• Favela LabPI