Biology subjects

Kosina, S. M.

Publications and source records attributed to Kosina, S. M..

7 recordsLinked to original sources

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

Ultraviolet radiation and dehydration stress induce overlapping transcriptional and metabolic responses in Syntrichia mosses

O_LIProtection from excess solar radiation and access to sufficient water are important problems for terrestrial plants to solve. Desiccation tolerance (DT), defined as the ability to equilibrate to dry air and resume normal metabolic activity after rehydration, allows organisms to survive dry periods by limiting metabolic activity to periods of moisture availability. We compared separate and combined effects of chronic ultraviolet radiation (UVR) treatments (UV-A and UV-A/B) and a dehydration treatment (as a surrogate for desiccation) in the mosses Syntrichia ruralis and S. caninervis to uncover the nature of correlation between DT and UVR tolerance (UVRT). C_LIO_LIUsing a fully factorial experiment with combined transcriptomics and metabolomics, we tested for cross-talk (overlap in signaling pathways in response to different stressors but separate mechanisms of protection) in the genetic underpinnings of DT and UVRT and cross-tolerance (overlap in the mechanism of protection) these two stressors. C_LIO_LIShared transcriptomic response to the two stressors with no significant interaction between them suggested cross-talk between UVRT and DT for S. caninervis. Phenolic metabolites and transcripts were involved in the response to UVR and dehydration in both species. C_LIO_LISome candidate UVRT genes and metabolites were induced by UVR in S. ruralis, but not S. caninervis, supporting the hypothesis that S. ruralis has a more plastic, acclimatable UVR response than S. caninervis, and that these differences are predictable by their unique interaction with these stressors as poikilohydric organisms. C_LI

plant biology↗

bioRxiv2022

Extensive plant use of exometabolites

Root exudation has been extensively studied due to its importance in soil carbon cycling and in supporting growth of soil microbes. However, the extent and dynamics of plant uptake of exogenous metabolites is poorly understood. To gain new insights into these processes we used 13C-tracing to characterize plant uptake of exometabolites across a panel of diverse plant species (Arabidopsis thaliana, Brachypodium distachyon, Lotus japonicus, Panicum virgatum, and Kalanchoe fedtschenkoi) grown in sterile hydroponic cultures. The uptake of exometabolites accounted for 23% of the overall B. distachyon carbon budget, and we identified 33 metabolites that were taken up by plants. Counterintuitively, many metabolites had higher uptake rates during the day vs. night. Thirteen of the metabolites from root exudates were found to promote root growth in A. thaliana, including hydroxybenzoate, threonate, N-acetyl-glucosamine, and uracil. Together these results indicate that the root uptake of organics can account for a significant portion of the plant carbon budget and that exogenous small molecules used by plants alter root growth with implications for plant nutrition, organic farming, soil nutrient cycling, and rhizosphere community dynamics.

plant biology↗

bioRxiv2022

Dynamic Phaeodactylum tricornutum Exometabolites Shape Surrounding Bacterial Communities

The roles of exometabolites in mediating algal-bacterial interactions and regulating microbial community composition are not well understood. Here, we identified specific exometabolites from the model diatom Phaeodactylum tricornutum affecting abundance of specific bacterial taxa in isolation and in a community setting. We examined the response of a P. tricornutum-adapted enrichment community and found that both algal exudates and algal presence drove similar changes in community composition compared to controls. Using LC-MS/MS, we identified 50 metabolites produced by axenic P. tricornutum and found that different exometabolites accumulated during different algal growth phases. Profiling growth of 12 bacterial isolates representative of the enrichment community uncovered two algal exometabolites (out of 12 tested) which supported growth of a subset of isolates as a primary carbon source. We compared enrichment community response with and without the addition of two contrasting metabolites: 4-hydroxybenzoic acid, which supported isolate growth, and lumichrome, which did not. Exogenous metabolite additions did promote increased abundances of taxa that were able to utilize the metabolite in the isolate study, but also revealed the importance of factors relating to algal presence in regulating community composition. Collectively, this work demonstrates the influence of specific algal exometabolites in driving microbial community composition.

microbiology↗

bioRxiv2021

Biofilm Interaction Mapping and Analysis (BIMA): A tool for deconstructing interspecific interactions in co-culture biofilms

Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of P. stutzeri biofilms, in combination with consortia based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition and invasion) between colony forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between P. stutzeri strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and thirteen other species of pseudomonas isolated from non-contaminated soil. The metabolites and genes associated with both active co-culture growth and inhibitory growth were investigated using mass spectrometry based metabolomics and mutant fitness profiling of a DNA-barcoded mutant library. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and metabolomics. IMPORTANCEThe Biofilm Interaction Mapping and Analysis (BIMA) methodology provides a way to rapidly screen for positive and negative interspecific interactions, followed by an analysis of the genes and metabolites that may be involved. Knowledge of these may offer opportunities for engineered strains with improved function in biotechnology systems. P. stutzeri, an organism with wide-spread utilization in consortia based biotechnologies, was used to demonstrate the utility of this approach. Where little is known about the factors influencing biofilm based interactions, elucidation of the genes and metabolites involved allows for better control of the system for improved function or yield.

microbiology↗

bioRxiv2021

A defined medium based on R2A for cultivation and exometabolite profiling of soil bacteria

Exometabolomics is an approach to assess how microorganisms alter their environments through the depletion and secretion of chemical compounds. Comparisons of inoculated with uninoculated media can be used to provide direct biochemical observations on depleted and secreted metabolites which can be used to predict resource competition, cross-feeding and secondary metabolite production in microbial isolates and communities. This approach is most powerful when used with defined media that enable tracking of all depleted metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through LC-MS/MS. Here, we describe the construction of a defined medium, the Northen Lab Defined Medium (NLDM), that not only supports the growth of diverse bacteria but is defined and therefore suited for exometabolomic experiments. Metabolites included in NLDM were selected based on their presence in R2A medium and soil, elemental stoichiometry requirements, as well as knowledge of metabolite usage by different bacteria. We found that NLDM supported the growth of 53 phylogenetically diverse soil bacterial isolates and all of its metabolites were trackable through LC-MS/MS analysis. These results demonstrate the viability and utility of the constructed NLDM medium for cultivating and characterizing diverse microbial isolates and communities. Originality-Significance StatementWe build a defined medium based on the metabolite composition of R2A medium and soil, elemental stoichiometry requirements, and knowledge of metabolite usage by different bacteria. The newly formulated defined medium was evaluated on its ability to support the growth of soil isolates and its application for metabolite utilization profiling. We found that of 53 phylogenetically diverse soil bacterial isolates grew on the defined medium and all of its metabolites were trackable through LC-MS/MS analysis. This demonstrates the viability and utility of the constructed defined medium for cultivating and characterizing diverse microbial isolates and communities.

microbiology↗

bioRxiv2021

Conservation of isolate substrate preferences in mixed communities revealed through ribosomal marker protein profiling

Assessment of structure-function relationships is a central theme in microbial ecology. However, the degree that isolate metabolic activities are conserved in communities remains unclear. This is because tracking population dynamics and substrate partitioning in microbial communities remains technically challenging. Here, we describe the application of a mass spectrometry-based ribosomal marker protein profiling with stable isotope probing approach that allows for concurrent monitoring of community structure dynamics and resource assimilation within a five-member synthetic soil bacterial community. Using this approach, we find that isolate substrate preferences for glutamine and phenylalanine are largely conserved in the community and can be predicted using a weighted-sum model. However, time-series monitoring revealed a significant delay in phenylalanine incorporation by two of the strains, as well as enhanced growth for Variovorax paradoxus presumably due to interspecies interactions. The unique utility of this approach to temporally probe resource incorporation and community structure enables deciphering the dynamic interactions occurring within the community. Extension of this approach to other communities under various environmental perturbations is needed to reveal the generality of microbial conservation of substrate preferences.

microbiology↗