Biology subjects

Zhalnina, K.

Publications and source records attributed to Zhalnina, K..

9 recordsLinked to original sources

bioRxiv2025

Bacterial fitness for plant colonization is influenced by plant growth substrate

O_LIBacteria colonize plants and contribute to their health. Despite advances in our understanding of bacterial plant colonization, the extent to which growth substrate influences the molecular mechanisms enabling bacteria to efficiently colonize plants remains poorly understood. C_LIO_LITo evaluate if genes important for plant colonization are influenced by substrate, we used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Paraburkholderia graminis OAS925, an efficient rhizosphere colonizer, and Brachypodium distachyon plants grown in six different substrates. C_LIO_LIOf the 382 rhizosphere colonization genes that we identified in strain OAS925, 348 genes (91.1%) are dependent on the growth substrate evaluated, and 34 genes (8.9%) are shared across all the substrates. To further characterize the plant colonization fitness genes, we compared our data to growth in 110 distinct in vitro conditions. To validate our results, we used individual mutants of selected genes and tested them in different growth substrates. We also show the influence of substrate on colonization by P. phytofirmans PsJN, Variovorax sp. OAS795 and Rhizobium sp. OAE497. C_LIO_LIOur data confirms that bacterial fitness for plant colonization is strongly influenced by plant growth substrate type, and highlights the importance of taking this parameter into consideration when engineering bacterial strains for improved host colonization. C_LI

microbiology↗

bioRxiv2023

Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem

Studying plant-microbe-soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacteria inoculation practices and plant harvesting time points affect the reproducibility of a microbial synthetic community (SynCom) in association with the model grass Brachypodium distachyon. We tested three microbial inoculation practices: seed inoculation, transplant inoculation, and seedling inoculation; and two harvesting points: early (14-day-old plants) and late (21 days post-inoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community only when harvesting at an early time point but not at the late stage. As the SynCom showed a persistent association with B. distachyon at 21 days post-inoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacteria inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB-B. distachyon-SynCom fabricated ecosystem and recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems.

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

Life history strategies and niches of soil bacteria emerge from interacting thermodynamic, biophysical, and metabolic traits

Efficient biochemical transformation of belowground carbon by microorganisms plays a critical role in determining the long-term fate of soil carbon. As plants assimilate carbon from the atmosphere, up to 50% is exuded into the area surrounding growing roots, where it may be transformed into microbial biomass and subsequently stabilized through mineral associations. However, due to a hierarchy of interacting microbial traits, it remains elusive how emergent life-history strategies of microorganisms influence the processing of root exudate carbon. Here, by combining theory-based predictions of substrate uptake kinetics for soil bacteria and a new genome-informed trait-based dynamic energy budget model, we predicted life history traits and trade-offs of a broad range of soil bacteria growing on 82 root exudate metabolites. The model captured resource-dependent trade-offs between growth rate (power) and growth efficiency (yield) that are fundamental to microbial fitness in communities. During early phases of plant development, growth rates of bacteria were largely constrained by maximum growth potential, highlighting the predictive power of genomic traits during nutrient-replete soil conditions. In contrast, selection for efficiency was important later in the plant growing season, where the model successfully predicted microbial substrate preferences for aromatic organic acids and plant hormones. The predicted carbon-use efficiencies for growth on organics acids were much higher than typical values observed in soil. These predictions provide mechanistic underpinning for the apparent efficiency of the microbial route to mineral stabilization in the rhizosphere and add an additional layer of complexity to rhizosphere microbial community assembly.

ecology↗

bioRxiv2022

Metabolic traits and the niche of bulk soil bacteria in a Mediterranean grassland

Soil microorganisms have adapted to compete and exploit different metabolic niches in their physically and chemically diverse environment via evolution and acquisition of distinct physiological and biochemical traits. As the interface for most carbon and nutrient exchange between plants and microorganisms, the rhizosphere has received substantial attention. By comparison, what is commonly termed bulk-soil (soil free of living roots) represents a far greater volume and surface area throughout the season, and substantially higher taxonomic and phylogenetic diversity; the traits and activity of its inhabitants may also have a significant impact on overall soil function. We used a combination of comparative genomics and exoproteomics to identify metabolic traits of bacteria adapted to life in bulk soil and compared these with traits of bacteria living in the rhizosphere of wild oat, Avena barbata. In bulk soil bacteria, we observed: (i) greater investment in extracellular polymer-degrading enzyme production; (ii) greater potential for secretion (presence of signal peptides) of polymer-degrading enzymes; (iii) production of accessory proteins (carbohydrate binding modules) fused with glycoside hydrolases that enhance substrate affinity, stabilize, and increase reaction rates of polymer degrading enzymes; and (iv) organization of polymer degradation machinery within gene clusters that facilitate co-transcription of enzymes, transcription factors and transporters for polymer depolymerization products. Together, these findings suggest that unlike rhizosphere-adapted bacteria--which specialize on small molecules released primarily as root exudates--bulk soil-adapted bacteria have evolved to exploit plant polymers. This biochemically costly strategy may be mitigated by protein-level adaptations that enhance the efficiency of extracellular enzyme-mediated substrate acquisition. IMPORTANCEPlant-soil-microbe interactions are dynamic and complex, with significant implications for ecosystem functioning. Microbial traits, such as nutrient acquisition and growth yield, combined with soil and climate parameters, impact major biogeochemical processes and can define the future fate of soil carbon. Diverse soil microorganisms occupy different physical habitats within soil and exploit distinct niches by expressing different metabolic traits. Identifying and quantifying traits that underlie their fitness and function is key for understanding and predicting how soil carbon transformation and stabilization will change in the future or can be managed through intervention.

microbiology↗

bioRxiv2022

Nutrient and moisture limitation reveal keystone metabolites that link switchgrass rhizosphere metabolome and microbiome dynamics

Plants exude large quantities of rhizosphere metabolites that can modulate composition and activity of microbial communities in response to environmental stress. While rhizodeposition dynamics have been associated with rhizosphere microbiome succession, and may be particularly impactful in stressful conditions, specific evidence of these connections has rarely been documented. Here, we grew the bioenergy crop switchgrass (Panicum virgatum) in a marginal soil, under nutrient limited, moisture limited, +nitrogen (N), and +phosphorus (P) conditions, to identify links between rhizosphere chemistry, microbiome dynamics, and abiotic stressors. To characterize links between rhizosphere microbial communities and metabolites, we used 16S rRNA amplicon sequencing and LC-MS/MS-based metabolomics. We measured significant changes in rhizosphere metabolite profiles in response to abiotic stress and linked them to changes in microbial communities using network analysis. N-limitation amplified the abundance of aromatic acids, pentoses, and their derivatives in the rhizosphere, and their enhanced availability was linked to the abundance of diverse bacterial lineages from Acidobacteria, Verrucomicrobia, Planctomycetes, and Alphaproteobacteria. Conversely, N-amended conditions enhanced the availability of N-rich rhizosphere compounds, which coincided with proliferation of Actinobacteria. Treatments with contrasting N availability differed greatly in the abundance of potential keystone metabolites; serotonin, ectoine, and acetylcholine were particularly abundant in N-replete soils, while chlorogenic, cinnamic, and glucuronic acids were found in N-limited soils. Serotonin, the keystone metabolite we identified with the largest number of links to microbial taxa, significantly affected root architecture and growth of rhizosphere microorganisms, highlighting its potential to shape microbial community and mediate rhizosphere plant-microbe interactions. SignificancePlants and microorganisms release metabolites that mediate rhizosphere host-microbe interactions and modulate plant adaptation to environmental stresses. However, the molecular mechanisms that underpin rhizosphere metabolite-microbiome dynamics, their functional relationships, and the biological role of plant- or microbial-produced soil metabolites remain largely unknown. Here, we found the abundances of specific classes of rhizosphere soil metabolites were responsive to abiotic stressors, and also connected to specific shifts in the rhizosphere microbial community and plant phenotypes. We propose a suite of understudied rhizosphere compounds as keystone metabolites that may structure the rhizosphere microbiome and influence plant metabolism in response to nutrient availability. These links between rhizosphere metabolites and microbial communities point to research avenues where we might leverage plant-microbe interactions to engineer enhanced rhizosphere microbiome function, plant and ecosystem health.

microbiology↗

bioRxiv2022

A reproducible and tunable synthetic soil microbial community provides new insights into microbial ecology

Microbial soil communities form commensal relationships with plants to promote the growth of both parties. Optimization of plant-microbe interactions to advance sustainable agriculture is an important field in agricultural research. However, investigation in this field is hindered by a lack of model microbial community systems and efficient approaches for building these communities. Two key challenges in developing standardized model communities are maintaining community diversity over time and storing/resuscitating these communities after cryopreservation, especially considering the different growth rates of organisms. Here, a model community of 17 soil microorganisms commonly found in the rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, has been developed and optimized for use with fabricated ecosystem devices (EcoFABs). EcoFABs allow reproducible research in model plant systems, with precise control of environmental conditions and easy measurement of plant-microbe metrics. The model soil community grows reproducibly in vitro between replicates and experiments, with high community -diversity achieved through growth in low-nutrient media and adjustment of starting composition ratios for the growth of individual organisms. The community additionally grows in EcoFAB devices and regrows with a similar composition to unfrozen communities following cryopreservation with glycerol, allowing for dissemination of the model community. Our results demonstrate the generation of a stable microbial community that can be used with EcoFAB devices and shared between research groups for maximum reproducibility. ImportanceMicrobes associate with plants in distinct soil communities, to the benefit of both the soil microbes and the plant. Interactions between plants and these microbes can improve plant growth and health and are therefore a field of study in sustainable agricultural research. In this study, a model community of 17 soil bacteria has been developed to further reproducible study of plant-soil microbe interactions. Preservation of the microbial community has been optimized for dissemination to other research settings. Overall, this work will advance soil microbe research through optimization of a robust, reproducible model community.

microbiology↗

bioRxiv2019

Root morphology and exudate availability is shaped by particle size and chemistry in Brachypodium distachyon

Root morphology and exudation define a plants sphere of influence in soils, and are in turn shaped by the physiochemical characteristics of soil. We explored how particle size and chemistry of growth substrates affect root morphology and exudation of the model grass Brachypodium distachyon. Root fresh weight and root lengths were correlated with particle size, whereas root number and shoot weight remained constant. Mass spectrometry imaging suggested that both, root length and number shape root exudation. Exudate metabolite profiles detected with liquid chromatography / mass spectrometry were comparable for plants growing in glass beads or sand with various particles sizes, but distinct for plants growing in clay. However, when exudates of clay-grown plants were collected by removing the plants from the substrate, their exudate profile was similar to sand- or glass beads-grown plants. Clay particles sorbed 20% of compounds exuded by clay-grown plants, and 70% of compounds of a defined exudate medium. The sorbed compounds belonged to a range of chemical classes, among them nucleosides/nucleotides, organic acids, sugars, and amino acids. Some of the sorbed compounds could be de-sorbed by a rhizobacterium (Pseudomonas fluorescens WCS415), supporting its growth. We show that root morphology is affected by substrate size, and that root exudation in contrast is not affected by substrate size or chemistry. The availability of exuded compounds, however, depends on the substrate present. These findings further support the critical importance of the physiochemical properties of soils are crucial to consider when investigating plant morphology, exudation, and plant-microbe interactions.

plant biology↗

bioRxiv2018

Multi-lab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

O_LIThere is a dynamic reciprocity between plants and their environment: On one hand, the physiochemical properties of soil influence plant morphology and metabolism, while on the other, root morphology and exudates shape the environment surrounding roots. Here, we investigate both of these aspects as well as the reproducibility of these responses across laboratories.\nC_LIO_LIThe model grass Brachypodium distachyon was grown in phosphate-sufficient and phosphate-deficient mineral media, as well as in sterile soil extract, within fabricated ecosystem (EcoFAB) devices across four laboratories.\nC_LIO_LITissue weight and phosphate content, total root length, root tissue and exudate metabolic profiles were found to be consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct in all laboratories, with root hairs four times longer compared to other growth conditions. Further, plants depleted half of the investigated metabolites from the soil extract.\nC_LIO_LITo interact with their environment, plants not only adapt morphology and release complex metabolite mixtures; they also selectively deplete a range of soil-derived metabolites. The EcoFABs utilized here generated high inter-laboratory reproducibility, demonstrating that their value in standardized investigations of plant traits.\nC_LI

plant biology↗