Biology subjects

Pruess, B. M.

Publications and source records attributed to Pruess, B. M..

4 recordsLinked to original sources

bioRxiv2026

Azospirillum brasilense and cytidine as combination treatment to enhance drought resilience of peas

Aims: This study tested the efficacy of two combination treatments on drought resistance of peas; Azospirillum brasilense Sp7 together with either the chemoattractant seedling exudate compound cytidine or total pea seedling exudate. Methods and Results: Phenotypic characterization revealed that the treatment with cytidine (ACyt) was more efficient than that with seedling exudate (AEx). Drought tolerance of peas treated with ACyt was 68.9% higher than that of peas treated with the inoculant alone (A). Dry shoot weight of ACyt Drought plants was 30.7% higher than that of plants from the untreated control group NB Drought, drought recovery of ACyt plants was 21.6% better. 16S rDNA analysis revealed that increase in drought tolerance/recovery was accompanied by modulation of the rhizosphere. The abundance of the inoculant was 163% higher in ACyt plants when comparing drought treated to watered groups. Abundance of Azospirillum sp. was 954% higher in plants from the ACyt Drought group than those from NB Drought. The possibility arises that the ACyt treatment may contribute to protecting pea plants from drought by increasing the abundance of Azospirillum. Within the complete analysis of the 16S rDNA data set, both ACyt Drought and AEx Drought groups had similar increases in Shannon and Pielou alpha-diversity indices, relative to the NB Drought group. These two test groups also exhibited high abundances of Rhizobium and lower abundance of Massilia. Conclusion: The ACyt treatment enhanced drought tolerance and recovery. Both treatments enhanced alpha-diversity and modulated the rhizosphere.

microbiology↗

bioRxiv2025

Host-Specific Fluorescence Dynamics in Legume-Rhizobia Symbiosis During Nodulation

The legume-rhizobia symbiosis is a cornerstone of sustainable agriculture due to its ability to facilitate biological nitrogen fixation. Still, real-time visualization and quantification of this interaction remain technically challenging, especially across different host backgrounds. In this study, we systematically evaluate the efficacy of the nitrogenase system nifH promoter (PnifH) in driving expression of distinct fluorescent reporters; superfolder yellow fluorescent protein (sfYFP), superfolder cyan fluorescent protein (sfCFP), and various red fluorescent proteins (RFPs) within root nodules of determinate (Lotus japonicus-Mesorhizobium japonicum) and indeterminate (Pisum sativum-Rhizobium leguminosarum) systems. We show that PnifH-driven sfYFP and sfCFP yield strong, uniform, and reproducible fluorescence in nodules of both systems, facilitating reliable quantification of nodulation traits and strain occupancy. In contrast, RFPs including monomeric (mScarlet-I, mRFP1, mARs1) and multimeric (AzamiRed1.0) variants exhibited weak or inconsistent signals in pea. Notably, fluorescent labeling did not impair rhizobial competitiveness for root nodule occupancy, and PnifH-driven sfYFP and sfCFP reporters enabled robust multiplexed imaging in single-root and split-root assays. In the lotus, mScarlet-I worked robustly and facilitated a tripartite strain labeling system. Complementing our molecular toolkit, we established a deep learning-based analytical pipeline for high-throughput, automated quantification of nodulation traits, validated against standard ImageJ analysis. Altogether, our results identify PnifH-driven sfYFP and sfCFP as robust, broadly applicable reporters for legume-rhizobia symbiosis studies, while highlighting the need for optimized red fluorophores in some contexts. The integration of validated promoter-reporter constructs with state-of-the-art computational approaches provides a scalable framework for dissecting the spatial and competitive dynamics of plant-microbe mutualisms. IMPORTANCEThe legume-rhizobia symbiosis is central to sustainable agriculture through its capacity for biological nitrogen fixation, yet tools for real-time, quantitative visualization of this interaction remain limited. Here, we demonstrate that the nifH promoter (PnifH) effectively drives expression of superfolder yellow (sfYFP) and cyan (sfCFP) fluorescent proteins in both determinate (Lotus japonicus-Mesorhizobium japonicum) and indeterminate (Pisum sativum-Rhizobium leguminosarum) nodules. These reporters enable robust, reproducible fluorescence without impairing rhizobial competitiveness, supporting multiplexed imaging and quantitative nodulation analyses. By contrast, red fluorescent proteins exhibited host-dependent variability, underscoring the need for improved red fluorophores. Integration of validated promoter-reporter constructs with a deep learning-based image analysis pipeline establishes a scalable framework for high-throughput assessment of nodule occupancy and symbiotic dynamics. This work provides a practical molecular and computational toolkit for dissecting plant-microbe mutualisms across diverse host systems.

bioengineering↗

bioRxiv2025

Azospirillum brasilense Sp7 and tomato seedling exudate or cytidine reduced disease symptoms on yellow pear tomatoes caused by Pseudomonas syringae pv. tomato DC3000

Tomatoes are an important crop worldwide and phytopathogens can cause devastating losses. This study describes a treatment, consisting of Azospirillum brasilense Sp7 and either tomato seedling exudate or the exudate compound cytidine. The combination of A. brasilense Sp7 with cytidine showed a remarkable reduction of 83.4% in disease severity of tomatoes challenged with Pseudomonas syringae pv. tomato DC3000. Replacing cytidine with exudate was less effective at 71%, but the reduction in disease severity was still larger than by A. brasilense Sp7 alone at 55%. This reduction in disease severity was not paralleled by a decrease in P. syringae in leaf homogenates. Cytidine caused a 6.7 fold increase in A. brasilense Sp7 16S rDNA in root homogenates. In phyllosphere and rhizosphere, treatments modulated the microbial composition. In the phyllosphere, specific associations between treatment groups and bacterial orders could be computed. In the rhizosphere, principal component analysis revealed that variation along PC1 was dominated by the presence or absence of A. brasilense. Intriguingly, the inoculant caused an increase in the abundance of other Azospirillales species. Les tomates sont une culture dimportance mondiale, et les phytopathogenes peuvent entrainer des pertes devastatrices. Notre etude decrit un traitement compose dAzospirillum brasilense Sp7 et soit dun exsudat de plantules de tomate, soit de la cytidine, un compose particulier provenant des exsudats et suppose avoir un effet chimiotactique. Lassociation de A. brasilense Sp7 avec la cytidine a entraine une reduction remarquable de 83,4 % de la severite de la maladie parmi les plantes de tomate infectees par Pseudomonas syringae pv. tomato DC3000. Le remplacement de la cytidine par des exsudats etait moins efficace (71 %), bien que la reduction de la severite de la maladie ait demeure superieure a celle obtenue avec A. brasilense Sp7 seul (55 %). Cette diminution de la severite de la maladie na toutefois pas ete accompagnee dune reduction de la concentration de P. syringae dans les homogenats foliaires. La cytidine a provoque une augmentation de 6,7 fois de lADNr 16S de A. brasilense Sp7 dans les homogenats racinaires. Dans la phyllosphere et la rhizosphere, les traitements ont module la composition microbienne. Dans la phyllosphere, des associations specifiques entre les groupes du traitement et les ordres bacteriens ont pu etre calculees. Dans la rhizosphere, lanalyse en composantes principales a montre que la variation de laxe PC1 etait dominee par la presence ou labsence dA. brasilense. De maniere interessante, linoculum a entraine une augmentation de labondance dautres especes dAzospirillales.

microbiology↗

bioRxiv2021

Crowdsourcing biocuration: the Community Assessment of Community Annotation with Ontologies (CACAO)

Experimental data about known gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a ten-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills. Significance StatementThe primary scientific literature catalogs the results from publicly funded scientific research about gene function in human-readable format. Information captured from those studies in a widely adopted, machine-readable standard format comes in the form of Gene Ontology annotations about gene functions from all domains of life. Manual annotations based on inferences directly from the scientific literature, including the evidence used to make such inferences, represents the best return on investment by improving data accessibility across the biological sciences. To supplement professional curation, our CACAO project enabled annotation of the scientific literature by community annotators, in this case undergraduates, which resulted in contribution of thousands of validated entries to public resources. These annotations are now being used by scientists worldwide.

bioinformatics↗