Biology subjects

Novak, V.

Publications and source records attributed to Novak, V..

9 recordsLinked to original sources

bioRxiv2026

Microbial exometabolite responses to root exudates from tallgrass prairie plants

Root exudates influence soil microbial community assembly and function, yet plant species-specific effects on microbially-driven metabolic transformations remain insufficiently characterized under controlled conditions. Here, we present a multi-omic dataset of exudate-microbe interactions across six plant species, including tallgrass prairie species (Helianthus pauciflorus, Carex brevior, Eragrostis spectabilis, Astragalus canadensis, and Panicum virgatum) and a model grass (Brachypodium distachyon), generated using an in vitro incubation experiment. Sterile root exudates were used to amend a soil-mimicking medium inoculated with a native tall-grass prairie soil microbiome. The dataset includes full-length 16S rRNA gene sequencing for microbial community profiling, untargeted LC-MS/MS metabolomics for exometabolomic profiling, and optical density measurements of microbial growth. We describe the axenic plant growth protocols, experimental design, data acquisition, processing workflows, and technical validation. This dataset provides a resource for investigating microbially mediated exometabolite transformations across diverse plant species to help understand rhizosphere processes, microbiome assembly, and ecosystem function.

microbiology↗

bioRxiv2026

What microbes want: exploring microbial substrate preferences with the Web of Microbes Agent

Understanding and predicting bacterial substrate preferences has broad utility from microbial interactions to selecting prebiotics. Isolate exometabolite profiling directly measures which compounds a given microbe utilizes from an array of metabolites in the environment. However, modeling, mining, and integrating these data are challenging. Here, we introduce a Bayesian Personalized Ranking (BPR) model applied to substrate preferences which we find learns to rank compounds by a given microbes preference. It was found to outperform the other ranking models (AUC = 0.93), proved robust to ablation, showed strong within-genus isolate pairs correlation (Spearman rank = 0.78) and predictive ability for new data. BPR was then used to create the Web of Microbes (WoM) Agent by integrating it with the Phydon growth model and Large Language Model (LLM) for autonomous orchestration tool calling and analysis. The WoM Agent accurately predicted substrate consumption by existing strain grown on a novel medium and correctly identified bacteria enriched in soil metabolite spike-in experiments. Additionally, the WoM Agent can use autonomous reasoning including to predict substrates that will selectively promote the growth of one clade of bacteria over another including helping interpret results and suggest new hypotheses and experiments. We anticipate broad applications in microbial cultivation, microbiome engineering, and environmental microbiology, with the agents capabilities further extensible through the integration of additional tools and use of rapidly improving LLMs.

systems biology↗

bioRxiv2025

Dopamine biosynthesis in plants

Dopamine, an essential human neurotransmitter, also plays important roles in plant-microbe interactions and abiotic stress tolerance. While dopamine biosynthesis is well-characterized in mammals, it remains largely unclear in plants. Through metabolite-based genome-wide association studies, we identified two putative polyphenol oxidase genes for dopamine biosynthesis in Brachypodium distachyon, located in the same chromosomal region as two tyrosine decarboxylase genes. Biochemical and knockout mutant analyses demonstrated that dopamine biosynthesis proceeds primarily via tyramine as an intermediate and contributes to plant tissue browning. Homology searches and functional assays indicate that this dopamine biosynthetic pathway is conserved across diverse plant species. This discovery provides valuable insights into plant dopamine biosynthesis with potential applications in reducing food browning, improving stress resilience, and bioengineering valuable compounds.

plant biology↗

bioRxiv2024

Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

microbiology↗

bioRxiv2024

Insights into the role of dopamine in rhizosphere microbiome assembly

Dopamine plays a critical role in animal physiology and interactions with gut microbes. In plants, dopamine is known to function in plant defense and abiotic stress tolerance; however, its role in mediating plant-microbiome interactions remains unexplored. In this study, we observed that dopamine is one of the most abundant exometabolites with natural variation in root exudates across diverse Brachypodium distachyon lines, suggesting a potential role in rhizosphere microbial assembly. To further investigate this, we colonized ten natural B. distachyon lines with a 16-member bacterial synthetic community (SynCom), collected paired metabolomic and 16S rRNA sequencing data, and performed an association analysis. Our results revealed that dopamine levels in root exudates were significantly associated with the abundance of six SynCom members in a hydroponic system. In vitro growth studies demonstrated that dopamine had a significant effect on the growth of the same six bacterial isolates. Additionally, treating soil directly with dopamine enriched Actinobacteria, consistent with both the SynCom-dopamine correlations and the isolate growth results. Collectively, our study underscores the selective influence of dopamine on rhizosphere microbial communities, with implications for precision microbiome management.

plant biology↗

bioRxiv2024

Insights into the role of root exudates in bacteriophage infection dynamics

Bacteriophages impact soil bacteria through lysis, altering the availability of organic carbon and plant nutrients. However, the magnitude of nutrient uptake by plants from lysed bacteria remains unknown, partly because this process is challenging to investigate in the field. In this study, we extend ecosystem fabrication (EcoFAB 2.0) approaches to study plant-bacteria-phage interactions by comparing the impact of phage-lysed and uninfected 15N-labeled bacterial necromass on plant nitrogen acquisition and rhizosphere exometabolites composition. We show that grass Brachypodium distachyon derives some nitrogen from amino acids in uninfected Pseudomonas putida necromass but not from virocell necromass. Additionally, the bacterial necromass elicits the formation of rhizosphere exometabolites, some of which (guanosine), alongside tested aromatic acids (p-coumaric and benzoic acid), show distinct effects on bacteriophage-induced lysis when tested in vitro. The study highlights the dynamic feedback between bacterial necromass and plants and suggests that root exudate metabolites can impact bacteriophage infection dynamics.

plant biology↗

bioRxiv2023

Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing galls

Many insects have evolved the ability to manipulate plant growth to generate extraordinary structures called galls in which insect larva can develop while being sheltered within and feeding on the plant. In particular, Cynipid (Hymenoptera: Cynipidae) wasps have evolved to form some of the most morphologically complex galls known and generate an astonishing array of gall shapes, colors, and sizes. However, the biochemical basis underlying these remarkable cellular and developmental transformations remains poorly understood. A key determinant in plant cellular development is the deposition of the cell wall to dictate the physical form and physiological function of newly developing cells, tissues, and organs. However, it is unclear to what degree cell walls are restructured to initiate and support the formation of new gall tissue. Here, we characterize the molecular alterations underlying gall development using a combination of metabolomic, histological, and biochemical techniques to elucidate how leaf cells are reprogrammed to form galls. Strikingly, gall development involves an exceptionally coordinated spatial deposition of lignin and xylan to form de novo gall vasculature. Our results highlight how Cynipid wasps can radically change the metabolite profile and restructure the cell wall to enable the formation of galls, providing new insights into the mechanism of gall induction and the extent to which plants can be entirely reprogrammed to form novel structures and organs.

plant biology↗

bioRxiv2023

Reproducible growth of Brachypodium distachyon in fabricated ecosystems (EcoFAB 2.0) reveals that nitrogen form and starvation modulate root exudation

Understanding plant-microbe interactions requires examination of root exudation under nutrient stress using standardized and reproducible experimental systems. We grew Brachypodium distachyon hydroponically in novel fabricated ecosystem devices (EcoFAB 2.0) under three inorganic nitrogen forms (NO3-, NH4+, NH4NO3), followed by nitrogen starvation. Analyses of exudates with LC-MS/MS, biomass, medium pH, and nitrogen uptake showed EcoFAB 2.0s low intra-treatment data variability. Furthermore, the three inorganic nitrogen forms caused differential exudation, generalized by abundant amino acids/peptides and alkaloids. Comparatively, N-deficiency decreased N-containing compounds but increased shikimates/phenylpropanoids. Subsequent bioassays with two shikimates/phenylpropanoids (shikimic and p-coumaric acids) on the rhizobacterium Pseudomonas putida or Brachypodium seedlings revealed that shikimic acid promoted bacterial and root growth, while p-coumaric acid stunted seedlings. Our results suggest: (i) Brachypodium alters exudation in response to nitrogen status, which can affect rhizobacterial growth; and (ii) EcoFAB 2.0 is a valuable standardized plant research tool. TeaserEcoFAB 2.0, a novel fabricated ecosystem device, has low data variability in studies of plant traits.

plant biology↗

bioRxiv2022

Heterotopic ossification in intact rat Achilles tendons is characterized by unique mineralized collagen fiber structures

Heterotopic ossification (HO) entails pathological mineral formation inside soft tissues. In human Achilles tendons, HO is often associated with tendinopathies, tendon weakness and pain. One hypothesis is that HO occurs in response to inflammation and by either intramembranous ossification, endochondral ossification, or a combination of both. However, refined details regarding HO deposition and microstructure are still unknown. In this study, we characterize HO in intact rat Achilles tendons through high-resolution phase contrast enhanced synchrotron X-ray tomographic imaging. Furthermore, we test the potential of using a procedure to induce local tissue injury by needling to study the relation between microdamage and formation of HO. The results show that HO occurs in all intact rat tendons occupying up to 1% of the total volume at 16 weeks of age. The HOs are characterized by an elongated ellipsoidal shape and by a distinctive fiber-like internal structure which suggests that some collagen fibers have become mineralized. The data indicates that the deposition along the fibers initiates in the pericellular area, and propagates into the intercellular area. The results also show that multiple HO deposits may merge into bigger structures with time by accession along unmineralized fibers. Furthermore, the presence of unmineralized regions within the deposits may indicate that HOs are not only growing, but mineral resorption can also occur. Additionally, phase contrast enhanced synchrotron X-ray tomography allowed to distinguish microdamage at the fiber level due to needling and it could in the future enable to elucidate the relation between local inflammation, microdamage, and HO deposition.

physiology↗