About

Dr. Jean-Michel Ané is a professor in the Department of Plant and Agroecosystem Sciences and in the Department of Bacteriology at the University of Wisconsin-Madison. He received his Ph.D. in plant cellular and molecular biology from the University of Toulouse in France. He leads the Ané Lab, which studies beneficial associations between microbes and plants, with a focus on improving the benefits of microbes to crops, particularly biological nitrogen fixation in non-leguminous plants used in agriculture. His research aims to understand how symbiotic associations between plants and microbes develop, including the microbial signals and signaling pathways that control the establishment of plant-microbe symbioses and stimulate plant growth. The lab transfers knowledge gained from model plants such as Medicago truncatula and Brachypodium distachyon to crops like soybean, alfalfa, rice, and maize, to enhance agricultural productivity and sustainability. Dr. Ané's work emphasizes maintaining soil quality, protecting the environment, and reducing costs for food, feed, and biofuel production through plant biotechnology, molecular biology, genetics, and symbiosis research.

Research topics

• Biology
• Botany
• Cell biology
• Chemistry
• Biochemistry
• Agronomy
• Genetics
• Ecology
• Food science
• Environmental science

Selected publications

• A microfluidic spore chamber for long-term imaging of single-spore hyphal development.

  Fungal Genetics and Biology · 2026-04-27

  articleOpen access

  Understanding the life cycle of fungal spores is essential for elucidating their roles in pathogenesis, dispersal, and survival. However, studying spore development under controlled, spatially defined conditions remains challenging. Here, we present the Spore Chamber, a custom-built microfluidic platform engineered for parallel trapping and long-term imaging of individual spores under defined media conditions, enabling real-time visualization of hyphal development. Using Aspergillus fumigatus as a model organism, we demonstrate that sparse trapping of individual spores within size-matched trap geometries enables long-term time-lapse imaging of key developmental stages, including germination, polarized hyphal elongation, branching, and conidiophore formation. To assess the device's capacity to resolve morphogenetic responses to exogenous signals, we introduced lipochitooligosaccharides (LCOs) and short-chain chitooligosaccharides (COs). Rhizobium-derived, non-sulfated LCO (nsLCO) mixtures induced enhanced secondary branching (hyperbranching), a response not previously reported in A. fumigatus under these signal conditions, to our knowledge, whereas sulfated LCOs and CO4 did not significantly alter branching patterns. In addition, long-term confinement and imaging revealed rare developmental morphologies previously described primarily in mutant strains, including split conidiophore formation, elongated phialides, microcyclic conidiation, and chlamydospore development. Together, these results establish the Spore Chamber as a targeted microfluidic platform for single-spore phenotyping and long-term developmental analysis, with applications in fungal biology, chemical signaling studies, and host–microbe interaction research. • Developed a microfluidic Spore Chamber for sparse trapping and long-term imaging of individual fungal spores. • Enabled real-time visualization of Aspergillus fumigatus development from germination through conidiogenesis under controlled confinement. • Showed that rhizobium-derived non-sulfated lipochitooligosaccharides (nsLCOs) enhance secondary hyphal branching. • Captured rare developmental phenotypes in wild-type A. fumigatus , including split conidiophores and chlamydospore formation. • Documented microcyclic conidiation under microfluidic confinement conditions. • Provides a structured, adaptable platform for single-spore phenotyping and chemical signaling studies.

  PublisherDOI

• A network-based model of <i>Aspergillus fumigatus</i> elucidates regulators of development and defensive natural products of an opportunistic pathogen

  Nucleic Acids Research · 2026-01-05 · 2 citations

  articleOpen access

  Aspergillus fumigatus is a notorious pathogenic fungus responsible for various harmful, sometimes lethal, diseases known as aspergilloses. Understanding the gene regulatory networks that specify the expression programs underlying this fungus' diverse phenotypes can shed mechanistic insight into its growth, development, and determinants of pathogenicity. We used eighteen publicly available RNA-seq datasets of Aspergillus fumigatus to construct a comprehensive gene regulatory network resource. Our resource, named GRAsp (Gene Regulation of Aspergillus fumigatus), was able to recapitulate known regulatory pathways such as response to hypoxia, iron and zinc homeostasis, and secondary metabolite synthesis. Further, GRAsp was experimentally validated in two cases: one in which GRAsp accurately identified an uncharacterized transcription factor negatively regulating the production of the virulence factor gliotoxin and another where GRAsp revealed the bZip protein, AtfA, as required for fungal responses to microbial signals known as lipo-chitooligosaccharides. Our work showcases the strength of using network-based approaches to generate new hypotheses about regulatory relationships in Aspergillus fumigatus. We also unveil an online, user-friendly version of GRAsp available to the Aspergillus research community.

  PublisherDOI

• Genetic determinants of aerial root traits that support biological nitrogen fixation in maize

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-02 · 1 citations

  preprintOpen access

  Abstract Modern agriculture depends on chemically synthesized nitrogen fertilizer, which ensures high yields but also can carry significant environmental and economic costs. Biological nitrogen fixation (BNF) already supplies nitrogen to legume crops and several avenues of research are underway to extend it to non-legume crops. In maize ( Zea mays ), aerial roots have been shown to contribute to BNF in some varieties, and both having many aerial roots and large aerial roots contributes to the fixation trait. However, much of the genetics controlling aerial root number and size is still unknown. Here we validate and quantify BNF in maize varieties from Southern Mexico under controlled conditions and evaluate a population of double haploids derived from the elite inbred PHZ51 crossed with these varieties. We find that most aerial root traits (root number, nodes with roots, root size) are reasonably heritable (h 2 0.5-0.75) and generally uncorrelated with each other. QTL mapping identifies 5 QTL each affecting nodes with aerial roots and aerial root number per node; in both cases all but 1 QTL show an increase from the landrace allele. We also identify 11 QTL for aerial root diameter, with most positive QTL coming from PHZ51. Between the two populations, only a few QTL overlap, indicating a presumably high diversity of genes affecting aerial root morphology in landrace populations. Combining the best QTL into elite material may provide a path toward meaningful levels of BNF for maize, and additional work is needed to determine how viable this approach will be in field settings.

  PublisherOA PDFDOI

• EPP1 is an ancestral component of the plant Common Symbiosis Pathway

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-02 · 2 citations

  preprintOpen access

  Abstract The success of plants on land has been enabled by mutualistic intracellular associations with microbes for 450 million years (Delaux and Schornack 2021). Because of their intracellular nature, the establishment of these interactions requires tight regulation by the host plants. In particular, three genes – SYMRK, CCaMK and CYCLOPS – form the core of an ancestral common symbiosis pathway (CSP) for intracellular symbioses, and are conserved since the most recent common ancestor of land plants (Radhakrishnan et al. 2020; Delaux et al. 2015; Wang et al. 2010; Parniske 2008). Here, we describe EPP1 as a fourth gene committed to the CSP. Among land plants, EPP1 is conserved only in species able to associate with at least one type of intracellular symbiont. We found that loss-of-function epp1 mutants or EPP1 knock-down lines in four clades of land plants – legumes, Solanaceae, monocots and bryophytes – are all impaired in their ability to associate with arbuscular mycorrhizal fungi. We discovered that the plasma membrane-localized receptor-like SYMRK phosphorylates EPP1 on a conserved serine residue and that this phosphorylation is essential for symbiosis. Using a gain-of-function approach, we demonstrate that EPP1 is upstream of the nuclear kinase CCaMK. We propose that EPP1 is an ancestral component of the essential pathway that has regulated plant symbiosis for half a billion years.

  PublisherOA PDFDOI

• Mucilage produced by aerial roots hosts diazotrophs that provide nitrogen in Sorghum bicolor

  PLoS Biology · 2025-03-03 · 8 citations

  articleOpen accessSenior authorCorresponding

  Sorghum (Sorghum bicolor) is an important food, feed, and fodder crop worldwide and is gaining popularity as an energy crop due to its high potential for biomass production. Some sorghum accessions develop many aerial roots and produce an abundant carbohydrate-rich mucilage after rain. This aerial root mucilage is similar to that observed in landraces of maize (Zea mays) from southern Mexico, which have been previously shown to host diazotrophs. In this study, we characterized the aerial root development of several sorghum accessions and the impact of humidity on this trait. We conducted a microbiome study of the aerial root mucilage of maize and sorghum and isolated numerous diazotrophs from field sorghum mucilage. We observed that the prevailing phyla in the mucilage were Pseudomonadota, Bacteroidota, and Bacillota. However, bacterial abundances varied based on the genotype and the location. Using acetylene reduction, 15N2 gas feeding, and 15N isotope dilution assays, we confirmed that these sorghum accessions can acquire about 40% of their nitrogen from the atmosphere through these associations on aerial roots. Nitrogen fixation in sorghum aerial root mucilage offers a promising avenue to reduce reliance on synthetic fertilizers and promote sustainable agricultural practices for food, feed, fodder, and bioenergy production.

  PublisherOA PDFDOI

• Convergent evolution of <i>NFP</i> -facilitated root nodule symbiosis

  Proceedings of the National Academy of Sciences · 2025-09-09 · 2 citations

  articleOpen access

  The origin and phylogenetic distribution of symbiotic associations between nodulating angiosperms and nitrogen-fixing bacteria have long intrigued biologists. Recent comparative evolutionary analyses have yielded alternative hypotheses: a multistep pathway of independent gains and losses of root nodule symbiosis vs. a single gain followed by numerous losses. A detailed reconstruction of the history of genes involved in signaling between nitrogen-fixing bacteria and potential hosts, particularly lipo-chitooligosaccharide (LCO) signaling, is needed to distinguish between these hypotheses. LCO recognition by plants involves the Nod Factor Perception ( NFP ) gene family; in the legume model Medicago truncatula (Fabales), MtNFP is essential for establishing rhizobial symbiosis. Here, we document convergent evolution of NFP , indicating multiple origins of LCO-driven symbiosis. In contrast to previous models that explain the recruitment of NFP via a single duplication in the ancestor of the nitrogen-fixing clade, our phylogenomic and synteny results suggest this duplication does not span the entire clade. Tandem duplication in a common ancestor of Cucurbitales and Rosales resulted in the NFP1 and NFP2 groups. In contrast, the phylogenetically closest paralog of MtNFP is MtLYR1 , located on a different chromosome within a large syntenic block. All available data indicate that a large-scale duplication resulted in MtNFP and MtLYR1 , likely corresponding to a whole-genome duplication in an ancestor of subfamily Papilionoideae of Fabaceae. We show that MtNFP and the NFP2 -like group are not orthologous, indicating multiple independent gains of NFP -based LCO signaling. This molecular convergence provides a possible mechanism for multiple gains of root nodule symbiosis across the nitrogen-fixing clade.

  PublisherOA PDFDOI

• From glomalin to glomalose: unraveling the molecular identity of the <scp>MAb32B11</scp> antigen

  New Phytologist · 2025-06-06 · 6 citations

  articleOpen accessSenior authorCorresponding

  Glomalin, a substance produced by arbuscular mycorrhizal (AM) fungi, has well-documented benefits for plant and soil health, including water retention and soil aggregation. Glomalin quantification has been performed by enzyme-linked immunosorbent assay (ELISA) using a monoclonal antibody, MAb32B11, that has been described as targeting a heat shock protein 60 (RiHSP60). In this study, we re-examined the molecular nature of the antigen recognized by MAb32B11. MAb32B11 did not cross-react with the RiHSP60 polypeptide. Glomalin extracts of Rhizophagus irregularis showed strong and dose-dependent cross-reactivity with MAb32B11 even when protein levels were undetectable, raising doubts about the proteinaceous nature of the antigen. Protease treatments of glomalin extracts did not affect the ELISA signal. However, treatment with periodate, which degrades polysaccharides, significantly reduced the signal. A strong correlation between carbohydrate content and the ELISA signal was observed in glomalin extracts. These findings indicate that MAb32B11 recognizes a carbohydrate, likely originating from cell walls of AM fungi. Further analysis of glomalin extracts using size exclusion chromatography suggests that the epitope of MAb32B11 is a complex carbohydrate in the size range of 511-600 kDa. Understanding the true nature of glomalin will enhance our ability to quantify it accurately and leverage its agricultural benefits.

  PublisherOA PDFDOI

• EvoNet: A phylogenomic and systems biology approach to identify genes underlying plant survival in marginal, low‐N soils

  2025-07-02

  reportOpen access

  The DOE‐BER “EvoNet” project investigates the genetic and molecular basis of plant resilience in extreme environments. We do this by identifying key genes that enable “extreme survivor” species to thrive in the nitrogen-poor soils of Chile’s hyper-arid Atacama Desert. Our collections focus on 32 Atacama extremophile species, including seven grass species with potential biofuel applications. To identify genes-of-importance to survival we compared genomic and transcriptomic profiles of extremophile species that thrive in the Atacama to those of closely related “sister” species from nitrogen-rich arid and mesic regions of California. Deep RNA sequencing and de novo transcriptome assembly across these triplet species sets supported a phylogenomic framework for identifying positively selected genes associated with adaptive divergence. Our integrative analysis combined ecological and environmental data, metagenomics, evolutionary and systems biology, and metabolomics. This enabled us to create an unprecedented framework for systematically understanding how non-model plants have adapted to survive in extreme conditions. Our resulting database of positively selected ortholog groups in the extremophile plants offers promising targets for engineering crop and biofuel species with enhanced resilience to drought and extreme weather. Additionally, our newest dataset explores and exploits a complementary metabolomic approach. This new aspect provides innovative strategies to manipulate plant cell metabolism, further supporting efforts to improve agricultural productivity in the face of extreme climates. Importantly, our combined evolutionary- and metabolomic-based strategies focused on convergent patterns of adaptation, providing a genetic and metabolomic toolkit for improving crop and biofuel resilience across diverse plant species. Finally, our novel exploration of ecological and evolutionary dynamics delivered to the community a phylogenomic computational pipeline called “PhyloGeneious.” Our continued adaptations of this pipeline are publicly available to expedite evolutionary genomic research for future scientific discoveries. In total, our DOE-BER has provided genomic, metabolomic, and computational strategies to understand how extremophile plants provide evolutionary and physiological targets for improving agricultural and biofuel production.

  PublisherOA PDFDOI

• Response to Bennett et al. Comment

  Elementa Science of the Anthropocene · 2024-01-01

  articleOpen accessSenior author

  Reply to Bennett, A, Van Deynze, A, Shapiro, H-Y, Weimer, B. 2024. An informed response to Kloppenburg et al. (2024)—Nagoya Protocol. DOI: https://doi.org/10.1525/elementa.2024.00012.

  PublisherOA PDFDOI

• Author Correction: Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants

  Nature Communications · 2024-08-01 · 1 citations

  erratumOpen access

  Correction to: Nature Communications https://doi.org/10.1038/s41467-024-48036-3, published online 27 May 2024&#13;\nhttp://hdl.handle.net/10261/361232

  PublisherOA PDFDOI

Frequent coauthors

• Giles Oldroyd

  University of Cambridge

  88 shared

• Brendan K. Riely

  University of California, Davis

  79 shared

• Charles Rosenberg

  58 shared

• Frédéric Debellé

  Epicura

  58 shared

• Julien Lévy

  58 shared

• Jean Dénarié

  Interactions Arbres-Microorganismes

  55 shared

• Douglas R. Cook

  University of California, Davis

  53 shared

• R. Varma Penmetsa

  Plant (United States)

  53 shared

Labs

• Ané LabPI

  Not provided

Education

• Ph.D., Plant Pathology

  University of Wisconsin-Madison

  1993

• M.S., Plant Pathology

  University of Wisconsin-Madison

  1989

• B.S., Botany

  University of Wisconsin-Madison

  1985