About

Katy Denise Heath is a Professor and Head of Plant Biology at the University of Illinois, with an affiliate appointment in Microbiology and a professorship at the Carl R. Woese Institute for Genomic Biology. She earned her B.S. from the University of Illinois in 2000, her Ph.D. from the University of Minnesota in 2007, and completed a postdoctoral fellowship at the University of Toronto from 2007 to 2009. Her research centers on the evolution of mutualisms, which are species interactions that increase the fitness of all partners involved. These interactions, including mitochondria, mycorrhizae, and gut endosymbionts, are widespread in nature but can exhibit temporal and spatial heterogeneity, cheating, and evolutionary instability. Heath employs a multidisciplinary approach, utilizing quantitative genetics, population genetics, molecular biology, and ecology to investigate the conditions under which mutualisms evolve, remain stable, or break down, as well as the phenotypic and genetic variation within these interactions and the genes involved in coevolution. Her primary research focus is on plant-microbe interactions, particularly the symbiotic relationships between legumes and nitrogen-fixing bacteria known as rhizobia. She extensively studies the Medicago-Sinorhizobium mutualism, a genetic model with ecological significance, and also investigates other systems such as the soybean-Bradyrhizobium interaction, invasive clover-rhizobium and Medicago lupulina-Sinorhizobium interactions, and the native prairie legume Chamaecrista fasciculata with its associated rhizobia. Heath's work advances understanding of the evolutionary and ecological genetics underlying these mutualisms, contributing to knowledge about how mutualistic partnerships are maintained or disrupted in natural and agricultural contexts.

Research topics

• Ecology
• Biology
• Genetics
• Botany
• Evolutionary biology
• Horticulture

Selected publications

• Less cooperative belowground plant mutualists negatively affect aboveground herbivore growth and survival

  Research Square · 2026-03-02

  preprintOpen access
  PublisherOA PDFDOI

• Negative frequency-dependent selection maintains partner quality variation in a keystone nutritional mutualism

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-18

  articleOpen accessSenior author

  Abstract Mutualisms, interactions that benefit both partners, are critical for promoting biodiversity and ecosystem resiliency, yet are considered evolutionarily unstable and vulnerable to global change. Understanding how genetic variation in mutualisms is maintained is key to predicting their future persistence and explaining their long evolutionary history. While theory addresses factors maintaining variation in partner quality (the fitness benefits partners provide), few studies have experimentally tested these mechanisms. Here, we experimentally evolved multiple replicate populations of rhizobia, nitrogen-fixing mutualists of legumes, varying in partner quality under contrasting environments: nitrogen (N)-supplemented or N-free conditions, with or without host plants. After one year of rhizobial evolution, we quantified selection on partner quality across environments and evaluated resulting changes in mutualism traits and population-level genetic diversity. Strikingly, selection on partner quality was population-dependent: high-quality strains were favoured when initially rare but disfavoured when common, revealing negative-frequency dependent dynamics that can maintain variation. Although neither nitrogen-supplementation nor host presence directly imposed selection, both were critical for preserving genetic diversity in rhizobia populations – fuel for ongoing evolution. By demonstrating negative-frequency dependent selection in the legume-rhizobium mutualism, our study reveals a dynamic more akin to antagonistic interactions than traditionally assumed. This overlooked mechanism may be the key to explaining the ecological and evolutionary persistence of mutualisms under changing environments. Significance Statement Mutualisms are central to biodiversity, yet their stability is puzzling because the mechanisms thought to stabilize them tend to eliminate the genetic variation needed for continued adaptation, even though partners in nature show striking variation in quality. In an experimental evolution study of a keystone plant-microbe mutualism (legume–rhizobium symbiosis), we found that negative frequency-dependent selection allows high- and low-quality symbionts to coexist: high-quality strains are favoured only when rare. Environmental factors such as nitrogen addition or host presence did not alter which partners were selected, but they helped maintain genetic diversity needed for future adaptation. Our findings reveal an overlooked mechanism that stabilizes mutualisms and explain how these interactions can remain resilient under changing environmental conditions.

  PublisherOA PDFDOI

• Elevated CO ₂ induces phyllosphere community changes in soybean

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-11

  article

  Abstract Plant-associated microbiomes play significant roles in determining their hosts’ responses to stress, which is increasingly common in a rapidly changing world. For example, foliar endophytes can increase tolerance to drought and decrease herbivory. Global atmospheric changes, such as increased atmospheric carbon dioxide concentration ([CO 2 ]), have the potential to directly and indirectly alter microbiome community structure in ways that affect host plants underscoring our need to understand how microbial communities in planta will change under global change. Here, we used a metabarcoding approach to assess community composition and network structure of bacterial and fungal phyllosphere microbiomes within soybean ( Glycine max ) exposed to ambient and elevated [CO 2 ] in the field. We found that fungal community composition differed between soybean grown in elevated and ambient [CO 2 ], while bacterial communities did not. Additionally, co-occurrence networks for both fungi and bacteria in elevated [CO 2 ] exhibited marked changes compared to the ambient networks including the composition of hub taxa. Overall, our findings suggest that anthropogenic change, such as elevated [CO 2 ], can cause profound shifts in community assembly of microbes within their plant hosts. Our findings may aid those developing agro-ecological strategies using microbes to improve crop traits, which necessitates understanding the drivers of microbiome community structure. Highlight Leaf-associated microbes benefit plants, but how climate change affects these communities remains unclear. We found that elevated CO 2 shifted fungal and bacterial community composition and network structure within soybean leaves.

  PublisherDOI

• Dominant foliar endophytes influence soybean yield and transcriptome

  FEMS Microbiology Ecology · 2025-05-13 · 2 citations

  articleOpen accessSenior author

  Microorganisms associated with plants can affect nutrient and water acquisition, plant defenses, and ecological interactions, with effects on plant growth that range from beneficial to antagonistic. In Glycine max (soybean), many studies have examined the soil microbiome and the legume-rhizobium relationship, but little is known about foliar endophytes, their effects on plant biomass and fitness, and how plants respond to their presence. To address these questions, we inoculated Glycine max with field-collected isolates of previously isolated, dominant strains of Methylobacterium and Colletotrichum in either sterile or non-sterile soil. We then used RNAseq to compare the transcriptomic responses of plants to single- and co-inoculation of endophytes. We found that all endophyte treatments increased soybean growth compared to control, but only in sterile soil. These results suggest context-dependency, with endophytes serving as facultative mutualists under stress or nutrient deprivation. Similarly, transcriptomic analyses revealed that soybean defense and stress responses depended on the interaction of endophytes; Methylobacterium elicited the strongest response but was modulated by the presence of Colletotrichum. Our findings highlight the environmentally dependent effects of co-existing endophytes within soybean leaves.

  PublisherOA PDFDOI

• Mobile gene clusters and coexpressed plant–rhizobium pathways drive partner quality variation in symbiosis

  Proceedings of the National Academy of Sciences · 2025-07-29 · 10 citations

  articleOpen accessSenior authorCorresponding

  Plant–microbe symbioses such as the legume–rhizobium mutualism are vital in the web of ecological relationships within both natural and managed ecosystems, influencing primary productivity, crop yield, and ecosystem services. The outcome of these interactions for plant hosts varies quantitatively and can range from highly beneficial to even detrimental depending on natural genetic variation in microbial symbionts. Here, we take a systems genetics approach, harnessing the genetic diversity present in wild rhizobial populations to predict genes and molecular pathways crucial in determining partner quality, i.e., the benefits of symbiosis for legume hosts. We combine traits, dual-RNAseq of both partners from active nodules, pangenomics/pantranscriptomics, and Weighted Gene Co-expression Network Analysis (WGCNA) for a panel of 20 Sinorhizobium meliloti strains that vary in symbiotic partner quality. We find that genetic variation in the nodule transcriptome predicts host plant biomass, and WGCNA reveals networks of genes in plants and rhizobia that are coexpressed and associated with high-quality symbiosis. Presence–absence variation of gene clusters on the symbiosis plasmid (pSymA), validated in planta, is associated with high or low-quality symbiosis and is found within important coexpression modules. Functionally our results point to management of oxidative stress, amino acid and carbohydrate transport, and NCR peptide signaling mechanisms in driving symbiotic outcomes. Our integrative approach highlights the complex genetic architecture of microbial partner quality and raises hypotheses about the genetic mechanisms and evolutionary dynamics of symbiosis.

  PublisherDOI

• A continuum of ecology and evolution contributes to mutualism breakdown between legumes and rhizobia

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-02

  articleOpen accessSenior author

  Abstract Ecological and evolutionary processes jointly shape community responses to environmental perturbations, yet are often examined separately – even in microorganisms, where they occur on similar timescales and are linked by mobile genetic elements like plasmids. Mutualism breakdown is a pressing challenge to examine this intersection, as shifts in diverse microbial communities might coincide with evolutionary changes in mutualistic traits within a key species. Here we study the legume-rhizobium mutualism after 33 years of nitrogen fertilization. Pairing manipulative inoculation studies with long-read amplicon sequencing provides unprecedented resolution across biological scales: whole bacterial community, genus Rhizobium, individual Rhizobium ASVs, and symbiosis plasmids. Clover host plants in N-fertilized plots encounter microbial communities depauperate in their preferred symbiont but enriched in other Rhizobium taxa; moreover, their symbiotic nodules house low-quality symbiosis plasmids. Thus, concurrent ecological and evolutionary shifts make mutualists both rarer and inferior and feed back to decrease the benefits hosts receive from mutualism.

  PublisherDOI

• Aboveground‐belowground microbial interactions in plants: A call to recognize the complexity within multispecies microbial communities

  American Journal of Botany · 2025-09-01

  articleOpen access

  Understanding and predicting plant responses to biotic and abiotic environments necessitates grappling with thousands of microbial interactions occurring within aboveground and belowground plant tissues. These distinct microbial communities are indirectly connected through their plant hosts, and aboveground-belowground (AGBG) microbial interactions could play large roles in plant health and drive plant community and ecosystem-level responses. In this review and synthesis, we first discuss mechanisms through which focal microbes directly and indirectly affect other microbes in distal plant compartments. We then add in a layer of complexity: How might microbial community interactions within aboveground plant organs affect root-associated microbiomes, and vice versa? We point to gaps in our knowledge that should drive future research agendas on how "discrete" microbial communities within plants influence one another-a key feature currently missing in plant microbiome research. We also discuss the utility of applying existing ecological theory to enhance the predictive power of plant microbiome research, particularly regarding the outcomes of AGBG microbial interactions across diverse environmental and ecological contexts. These efforts will be especially important within fields such as sustainable agriculture that seek to harness plant-microbiome interactions within a changed and ever-changing world.

  PublisherOA PDFDOI

• Plasmid transmission dynamics and evolution of partner quality in a natural population of <i>Rhizobium leguminosarum</i>

  mBio · 2025-11-10 · 2 citations

  articleOpen accessSenior author

  ABSTRACT Many bacterial traits important to host–microbe symbiosis are determined by genes carried on extrachromosomal replicons, such as plasmids, chromids, and integrative and conjugative elements. Multiple such replicons often coexist within a single cell and, due to horizontal mobility, have patterns of variation and evolutionary histories that are distinct from each other and from the bacterial chromosome. In nitrogen-fixing Rhizobium , genes carried on multiple plasmids make up a third of the genome, are necessary for the formation of symbiosis, and underlie bacterial traits, including host plant benefits. Thus, the genomics and transmission of plasmids in Rhizobium underlie the ecology and evolution of this important model symbiont. Here, we leverage a natural population of clover-associated Rhizobium in which partner quality has declined in response to long-term nitrogen fertilization. We use 62 novel, reference-quality genomes to characterize 256 replicons in the plasmidome and study their genomics and transmission patterns. We find that, of the four most frequent plasmid types, two (types II and III) have more stable size, larger core genomes, and track the chromosomal phylogeny (display more vertical transmission), while others (type I and type IV, or symbiosis plasmid, pSym) vary substantially in size and shared gene content and have phylogenies consistent with frequent horizontal transmission. We also find differentiation in pSym subtypes driven by long-term nitrogen fertilization. Our results highlight the variation in plasmid transmission dynamics within a single symbiont and implicate plasmid horizontal transmission in the rapid evolution of partner quality. IMPORTANCE Understanding how bacterial genes move through natural populations is critical for understanding how bacterial traits evolve. Nitrogen-fixing bacteria Rhizobium leguminosarum live in symbiosis with plants and are a model for studying plasmid transmission and how mobile genetic elements impact the evolution of bacteria and plants. Here, we characterize the genomes of a natural bacterial population, then use novel approaches to show that mechanisms of gene transmission vary across multiple plasmid types that coexist within R. leguminosarum cells. We find that changes in the frequency of specific pSym types are associated with the decline of symbiotic partner quality in strains isolated from environments undergoing long-term fertilization. These results underscore the importance of plasmid transmission and evolution in shaping ecosystem processes like nitrogen cycling via bacterial-plant symbiosis. Our study provides a framework for probing plasmid dynamics within natural bacterial populations and how plasmid transmission affects genetic diversity and ecological interactions in bacteria.

  PublisherDOI

• Co-inoculation with novel nodule-inhabiting bacteria reduces the benefits of legume–rhizobium symbiosis

  Canadian Journal of Microbiology · 2024-03-20 · 7 citations

  articleOpen accessSenior author

  The ecologically and economically vital symbiosis between nitrogen-fixing rhizobia and leguminous plants is often thought of as a bi-partite interaction, yet studies increasingly show the prevalence of non-rhizobial endophytes (NREs) that occupy nodules alongside rhizobia. Yet, what impact these NREs have on plant or rhizobium fitness remains unclear. Here, we investigated four NRE strains found to naturally co-occupy nodules of the legume Medicago truncatula alongside Sinorhizobium meliloti in native soils. Our objectives were to (1) examine the direct and indirect effects of NREs on M. truncatula and S. meliloti fitness, and (2) determine whether NREs can re-colonize root and nodule tissues upon reinoculation. We identified one NRE strain (522) as a novel Paenibacillus species, another strain (717A) as a novel Bacillus species, and the other two (702A and 733B) as novel Pseudomonas species. Additionally, we found that two NREs (Bacillus 717A and Pseudomonas 733B) reduced the fitness benefits obtained from symbiosis for both partners, while the other two (522, 702A) had little effect. Lastly, we found that NREs were able to co-infect host tissues alongside S. meliloti. This study demonstrates that variation of NREs present in natural populations must be considered to better understand legume–rhizobium dynamics in soil communities.

  PublisherDOI

• Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-10-22 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Many bacterial traits important to host-microbe symbiosis are determined by genes carried on extrachromosomal replicons such as plasmids, chromids, and integrative and conjugative elements. Multiple such replicons often coexist within a single cell and, due to horizontal mobility, have patterns of variation and evolutionary histories that are distinct from each other and from the bacterial chromosome. In nitrogen-fixing Rhizobium, genes carried on multiple plasmids make up almost 50% of the genome, are necessary for the formation of symbiosis, and underlie bacterial traits including host plant benefits. Thus the genomics and transmission of plasmids in Rhizobium underlie the ecology and evolution of this important model symbiont. Here we leverage a natural population of clover-associated Rhizobium in which partner quality has declined in response to long-term nitrogen fertilization. We use 62 novel, reference-quality genomes to characterize 257 replicons in the plasmidome and study their genomics and transmission patterns. We find that, of the four most frequent plasmid types, two (types II &amp; III) have more stable size, larger core genomes, and track the chromosomal phylogeny (display more vertical transmission), while others (types I &amp; IV – the symbiosis plasmid, or pSym) vary substantially in size, shared gene content, and have phylogenies consistent with frequent horizontal transmission. We also find differentiation in pSym subtypes driven by long-term nitrogen fertilization. Our results highlight the variation in plasmid transmission dynamics within a single symbiont and implicate plasmid horizontal transmission in the evolution of partner quality.

  PublisherOA PDFDOI

Recent grants

• BII-Implementation: GEMS: Genomics and eco-evolution of multi-scale symbioses

  NSF · $12.4M · 2020–2026

• Collaborative Research: Evolution in LTER Experiments: Ecological and Evolutionary Consequences of Long-Term Nitrogen Addition for the Legume-Rhizobium Mutualism

  NSF · $145k · 2013–2017

• Collaborative Research: How Mountains Maintain Biodiversity: A Multidisciplinary Characterization of a Pleistocene Refugium in the Interior Pacific Northwest

  NSF · $251k · 2012–2016

Frequent coauthors

• Michael A. Grillo

  University of Illinois Urbana-Champaign

  25 shared

• Peter Tiffin

  University of Minnesota

  16 shared

• Shawn P. Brown

  University of Memphis

  14 shared

• John R. Stinchcombe

  University of Toronto

  11 shared

• James W. Dalling

  11 shared

• Justin C. Podowski

  Argonne National Laboratory

  11 shared

• Jennifer A. Lau

  Indiana University Bloomington

  9 shared

• Rebecca T. Batstone

  University of Illinois Urbana-Champaign

  8 shared

Labs

• Heath LabPI