About

Jenny Kao-Kniffin is a professor in the School of Integrative Plant Science, Horticulture Section. Her research centers on the belowground ecology of horticultural landscapes, with a focus on the ecology and management of invasive plants and weeds in horticultural landscapes, wetlands, and urban ecosystems. She studies how soil microorganisms impact plant populations, influencing plant growth, physiology, and fitness through beneficial interactions such as aiding in plant growth and fitness, as well as negative interactions like keeping populations in check. Her work applies microbial ecology concepts and techniques to uncover relationships between soil microbial communities and plant traits, including the development of microbial consortia, isolation of new microbial strains, and the purification of compounds that promote desirable plant populations while suppressing weeds.

Selected publications

• Assembly and Function of Fruit Microbiomes and Insights into Management

  Journal of the American Society for Horticultural Science · 2026-04-15

  articleOpen access

  The study of fruit microbiomes, defined as the microbial community in and on fruit, is a novel frontier that provides the potential for contextualizing pathogen infection and biocontrol in a more holistic and ecological approach. Differences in sample year tend to explain the greatest variation in fruit microbiome studies, with geography, preharvest management regime, and cold storage also resulting in pronounced shifts. However, effects of cultivar and fungicides can be more subtle, with some studies identifying minor or no shifts. This highlights that while agricultural management is important in shaping fruit microbiomes, environmental and spatiotemporal factors are also important to consider. Additionally, there is a need for more studies that delve deeper into the functional roles of the fruit microbiome, which require extension of ‘omics technologies such as shotgun metagenomics and metabolomics to move beyond taxonomic composition and begin to determine what important roles fruit microbial communities can play. Some studies are investigating the role of native microbiota in biocontrol and how native fruit microbiomes influence the fermentation process, and the field must build on these experiments to gain a more complete understanding of how the fruit microbiome is related to pathogen dynamics and modulation of fruit quality.

  PublisherDOI

• Rice Farming for Climate Change Adaptation in the Northeastern United States

  SSRN Electronic Journal · 2026-01-01

  preprintOpen access
  PublisherDOI

• Reduced Sorbitol Genotype Alters Postharvest Microbiomes of ‘Greensleeves’ Apples

  Journal of the American Society for Horticultural Science · 2025-09-01 · 2 citations

  articleOpen access

  Fruit microbiomes are capable of protecting their hosts from harmful pathogens and aiding in biocontrol; therefore, it is important to understand how differences in host genotype shape fruit microbial communities. The fruit species and even cultivars within a species can harbor different fruit microbiomes, but it has been difficult to establish how a single host gene can shape the microbiome structure. We investigated two genotypes of ‘Greensleeves’ apples with reduced sorbitol biosynthesis through antisense suppression of aldose 6-phosphate reductase with the wild type (WT) to assess how sugar composition of the fruit surface impacts microbial communities. We hypothesized that reduced sorbitol genotypes A4 and A10 would show an epiphytic microbiome different from that of the WT that corresponds to a difference in sugar composition on the fruit surface at harvest and during storage with and without postharvest treatment of fruit with 1-methycyclopropene (1-MCP), which is an inhibitor of ethylene perception. Throughout the sampling window (at harvest, 7 weeks storage, 13 weeks storage) across the 2 years of the study, the genotype, but not 1-MCP, was a significant predictor of microbiome composition. The A10 and A4 lines had an increased abundance of the pathogenic fungal genus Acremonium compared with that of the WT in one year. However, while A4 and A10 had different sugar compositions than that of WT in fruit flesh, no differences on the fruit surface were found. In addition, A4 and A10 showed microbiomes that were different from each other as well as different from that of the WT despite having the same reduced sorbitol phenotype, thus making it difficult to link microbiome differences to a specific physiological mechanism. This work represents an important step in showing the first example, to our knowledge, of how the cascading effects resulting from silencing a single gene can impact the assembly of postharvest fruit microbiomes.

  PublisherDOI

• Arbuscular mycorrhizal fungi enhance nitrogen acquisition from, but not carbon loss of, organic matter in soil

  New Phytologist · 2025-06-08 · 7 citations

  reviewOpen access

  Summary The effect of arbuscular mycorrhizal fungi (AMF) on decomposition can be regulated by their role in plant nitrogen acquisition due to their obligate biotrophic lifestyle. However, few studies have addressed the relationship between these two processes. We conducted an experiment using mycorrhizal‐defective mutants and wild‐types of two plant species with 13 C and 15 N dual‐labelled litter as tracers. A meta‐analysis of related studies was also performed to test the generality of the experimental results. Both our experiment and meta‐analysis found that AMF enhanced plant N acquisition from organic substrates, while substrate N and C remaining in the soil were not significantly reduced. We propose that AMF may reduce N loss from the system, which retains substrate N for plant uptake. Under N limitation, AMF may stimulate the deamination of organic substrates or selective mining of N‐rich soil organic matter. In addition, our meta‐analysis found significant influences of experimental designs on the observed outcomes. We conclude that AMF may facilitate the decoupling between plant N acquisition from, and C loss of, organic materials. However, more studies that simultaneously trace C and N allocation from organic substrates are needed to elucidate the underlying mechanisms.

  PublisherOA PDFDOI

• Recycled Phosphorus Bioamendments from Wastewater Impact Rhizomicrobiome and Benefit Crop Growth: Sustainability Implications at Water-Food Nexus

  Environmental Science & Technology · 2025-01-22 · 15 citations

  article

  Phosphorus recovery through enhanced biological phosphorus removal (EBPR) processes from agricultural wastes holds promise in mitigating the impending global P shortage. However, the complex nutrient forms and the microbial augments, expected to exert a profound impact on crop rhizomicrobiome and thus crop health, remained unexplored. In this study, we investigated the impacts of EBPR biosolids on crops growth and rhizomicrobiome in comparison to chemical fertilizer and Vermont manure compost. Our findings revealed that EBPR biosolid augmentation promoted the best maize shoot growth traits with the least nutrient deficiency, evidencing its agricultural benefits. Biosolid augmentation significantly impacted the rhizomicrobiome with decreased biodiversity but higher activities with enriched taxa capable of utilizing various carbon sources. The novel single-cell Raman spectroscopy phenotyping technique uncovered the surprisingly high abundance (up to 30%) of polyphosphate-accumulating organisms (PAOs) in the rhizosphere and their distinctive variations in different biosolid amendments. Furthermore, the interactions between EBPR-derived PAOs such as Candidatus Accumulibacter phosphatis and soil native plant growth promoting rhizobacteria highlighted the previously overlooked status and yet-to-be-characterized functions of PAOs in P cycling. This study provides a novel perspective leveraging EBPR biosolids to facilitate plant growth with agronomic benefits, thereby contributing to more sustainable and ecologically responsible agricultural practices.

  PublisherDOI

• Common soil invertebrate (Collembola: Isotomiella minor) reduces weed biomass and alters weed communities

  Applied Soil Ecology · 2025-05-19

  articleOpen access

  Soil microarthropods affect soil ecosystems in a manner that may contribute to balancing the goals of building soil health and controlling weeds in organic agricultural systems. While soil microarthropod feeding behavior can affect plant growth, their impacts on plant communities in agricultural systems are largely unknown. A greenhouse experiment was conducted to investigate the impacts of microarthropods on weed communities. A model weed seed bank was used in each mesocosm, which included yellow foxtail ( Setaria pumila (Poir.) Roem&Schult.), giant foxtail ( Setaria faberi Herrm.), Powell amaranth ( Amaranthus powellii S. Watson ), waterhemp ( Amaranthus tuberculatus (Moq.) Sauer), common lambsquarters ( Chenopodium album L.), and velvetleaf ( Abutilon theophrasti Medik.). The study included three treatments: Collembola ( Isotomiella minor , Schaffer 1896) abundance (none, low, high), soil microbial community (sterilized/non-sterilized), and fertilizer (presence/absence of compost). A lab experiment examining individual weed species interactions with I. minor was conducted to elucidate the mechanisms driving the greenhouse experiment findings. Twenty seeds of each weed species were placed on moistened germination paper in containers with varying I. minor abundance levels (none, low, high, very high). Seed germination was recorded after five and seven days. In the greenhouse, the presence of I. minor increased total weed emergence during the first two weeks, but this effect diminished after three weeks. Increasing I. minor abundances generally decreased weed biomass, though this effect was greater in the non-sterilized soil. In the non-sterilized soil, I. minor presence decreased total aboveground weed biomass production by up to 23 %. The Amaranthus species, Powell amaranth and waterhemp, drove this effect with a 55 % and 32 % reduction in biomass, respectively. In tandem, the Amaranthus species had reduced abundances in the presence of I. minor . I. minor increased yellow foxtail germination in the lab, while not affecting the other weed species. This suggests that their effects on the Amaranthus weeds in the greenhouse were likely not caused by direct effects on germination, but instead through nutrient cycling or root herbivory. The proposed mechanism underlying these interactions is that I. minor can initially stimulate germination by feeding on seed coats, but when the seed coats are minimal can damage the seedling. Our findings indicate I. minor could impact weed growth in a manner that affects management decisions and outcomes. • Isotomiella minor decreased total aboveground weed biomass production by up to 23 %. • Powell amaranth (55 %) and waterhemp (32 %) biomass were most decreased by I. minor . • I. minor directly increased yellow foxtail germination in lab study. • Seed coat composition may influence the outcomes of seed-Collembola interactions.

  PublisherDOI

• Geno-pheno characterization of crop rhizospheres: an integrated Raman spectroscopy and microbiome approach in conventional and organic agriculture

  Frontiers in Microbiology · 2025-11-28

  articleOpen accessSenior authorCorresponding

  Introduction Agricultural management practices strongly influence soil microbiomes, with broad implications for ecosystem function. Yet, the combined phenotypic and compositional dynamics of rhizosphere microbial communities across conventional and organic farming systems remain poorly characterized, underscoring the need for integrated approaches to understand how management decisions drive microbial assembly and function. Methods We investigated microbial communities associated with conventionally and organically cultivated horticultural crops across multiple farms in New York State. To capture both taxonomic and functional dimensions, community composition was characterized using 16S rRNA gene sequencing, and phenotypic traits were assessed with a newly developed single-cell Raman microspectroscopy (SCRS) approach. This dual strategy allowed us to link microbial identity with metabolic potential and adaptive traits. Results Farming practice significantly shaped microbiome clustering, independent of site or plant species. SCRS-based phenotyping revealed distinct biochemical profiles: organic systems favored lipid-accumulating phenotypes linked to energy storage and stress resilience, whereas conventional systems promoted carbon-rich phenotypes associated with rapid assimilation and biomass production. Network analysis identified Pseudomonas and nitrogen-fixing taxa as ecological hubs in conventional systems, while organic soils were enriched in Bacilli class plant growth-promoting rhizobacteria (e.g., Tumebacillus, Bacillus, Paenibacillus, Brevibacillus ) and contained microorganisms bearing antibiotic resistance genes. Discussion Our findings highlighted that management regimes drive distinct microbial functional traits and community structures. By integrating genotypic and phenotypic analyses, particularly microbial phenotyping via SCRS, we uncovered adaptive traits that differentiate conventional and organic systems, offering new insight into how plant production practices shape microbial assembly and ecological function.

  PublisherOA PDFDOI

• Synergistic enhancement of Sorghum bicolor nutrient uptake and growth by EBPR microbiomes and AM fungi

  Research Square · 2025-08-22

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• Climate warming enhances biodiversity and stability of grassland soil phosphorus-cycling microbial communities

  The ISME Journal · 2025-01-01 · 8 citations

  articleOpen access

  Climate warming poses significant challenges to global phosphorus sustainability, an essential component of Earth biogeochemistry cycling and water-food-energy nexus. Despite the crucial role of polyphosphate-accumulating organism as key functional microbial agents in phosphorus cycling, the impacts of global climate warming on polyphosphate accumulating organism communities remain largely enigmatic. This study investigates the effects of climate warming on the taxonomic, network, and functional profiles of soil bacterial polyphosphate-accumulating organisms, leveraging fluorescence-activated cell sorting and single-cell Raman spectroscopy. Climate warming enhances both taxonomic and functional biodiversity of polyphosphate-accumulating organisms via biotic interactions and environmental filtering, with observed functionality-biodiversity relationships supporting the functional redundancy theory. Furthermore, polyphosphate-accumulating organism network complexity and stability rise under warming with strengthened positive relationships, supporting stress gradient hypothesis and the belief that complexity begets stability. Finally, polyphosphate-accumulating organisms are significantly correlated to key ecosystem functioning in carbon and phosphorus cycling under warming. Our study suggests that preserving polyphosphate-accumulating organism communities is crucial for maintaining soil ecosystem functioning and sustainable phosphorus management in a warming world and opens avenues for predicting the responses of other functional microbial groups to climate change, beneficially or maliciously.

  PublisherOA PDFDOI

• Packing Line Processes Reshape Apple Microbiomes: Differential Effects of Chlorine and Waxing on Bacterial and Fungal Communities

  HortScience · 2025-08-05 · 1 citations

  articleOpen access

  Modern postharvest apple processing facilities include steps to ensure the safety and storage of fresh-market fruit. Packing lines typically include a chlorine sterilization process before fruit waxing to maximize postharvest fruit quality. We investigated the role of chlorine dump tank sanitation and waxing in shaping microbiome community assembly on apples, which is relevant for postharvest pathogen colonization and infection. We hypothesized that each step of postharvest processing would indicate further shifts in fruit microbiome composition, notable at the prechlorine and postchlorine dump tank stages, followed by the fruit-waxing step. We found that the packing line process affected bacterial composition, but there were minimal effects on fungal composition and only at specific sampling times. In addition, adding wax to fruit increased bacterial diversity, but there was no effect with chlorine sanitation. Bacterial shifts were strongest after the waxing step, with more than half of all genera increasing in relative abundance. Using PICRUSt2, we predicted metagenomic profiles and observed that taxonomic shifts corresponded with a variety of metabolic pathways increasing in abundance, including an unexpected increase in pathways associated with methanogenesis. Although PICRUSt2 predictions on their own are prone to false positives, this finding coincides with the presence of known methanogens of the class Methanobacteria in waxed samples. The results suggest that commercial packing line processes shape the apple microbiome, uncovering potentially novel functions such as methane regulation in postharvest waxed fruit, with implications for fruit preservation and quality.

  PublisherDOI