Biology subjects

Molina-Santiago, C.

Publications and source records attributed to Molina-Santiago, C..

11 recordsLinked to original sources

bioRxiv2026

Cooperative siderophore use stabilizes a protective leaf microbiome

Plant-associated microbial communities provide crucial protection against pathogens. Specialized metabolites play key roles in plant-microbe and microbe-microbe interactions and, ultimately, in plant health; however, the molecular mechanisms underlying their plant-protecting properties remain largely unknown. Nutrient deficiency (e.g., iron) on leaf surfaces creates intense competition among microbes, driving both antagonism and cooperation. Using a gnotobiotic Arabidopsis thaliana model and a synthetic leaf microbial community, we show that community stability and plant protection depend on cooperative siderophore exchange between the basidiomycete yeast Rhodotorula kratochvilovae and commensal Pseudomonas species. Removal of Pseudomonas caused a strong shift in the community metabolome and accumulation of the yeast siderophore rhodotorulic acid (RA). RA selectively promoted the growth of commensal Pseudomonas via TonB-dependent transporters, which are absent in pathogenic Pseudomonas strains. Inactivation of these transporter genes abolished RA uptake, destabilized the synthetic community, and eliminated protection against Pseudomonas syringae infection. RA and Rhodotorula also induced host iron-deficiency and jasmonate-related defense metabolites, linking microbial cooperation to plant stress responses. These findings reveal that microbial siderophore exchange acts as a key mechanism that maintains stability in the phyllosphere microbiome. Rather than solely promoting competition, iron-binding compounds can serve as cooperative currencies that align microbial fitness with host protection.

microbiology↗

bioRxiv2025

Early seed priming with closely related Bacillus strains induces divergent physiological and defense responses in melon

Early microbial seed priming is a promising strategy to improve crop resilience, yet it remains unclear whether plants can discriminate among closely related beneficial strains and integrate dose-dependent microbial cues. We primed melon (Cucumis melo) seeds with two phylogenetically similar Bacillus strains (B. subtilis NCIB3610 and B. velezensis FZB42) and combined transcriptomic, metabolomic and physiological analyses across development. Despite comparable colonization, the strains provoked contrasting host programs and distinct dose responses. B. subtilis promoted radicle elongation, chloroplastic starch storage and drought tolerance irrespective of inoculum level, together with L-tryptophan and palatinose accumulation. By contrast, B. velezensis displayed a clear dose effect: low inoculum sustained normal radicle growth, whereas high inoculum transiently repressed it, coinciding with retrotransposon activation, suppression of AOS and proteasome genes, and enrichment of flavonoids and glutathione in leaves. Chemical assays showed that radicle inhibition requires the combination of surfactin, produced by both strains, with bacillomycin D, an iturin-type lipopeptide unique to FZB42; neither molecule alone reproduced the effect. This synergy links the strain-specific lipopeptide repertoire to the dose-dependent growth response. Although their early trajectories diverged, both primings converged on improved above-ground performance. 3610-primed plants restricted Botrytis cinerea via caffeic- and rosmarinic-acid accumulation, whereas FZB42-primed plants curtailed jasmonate-sensitive Tetranychus urticae mites through early JA-pathway activation. Our results demonstrate that melon perceives inoculum dose and microbial identity, translating them into distinct metabolic and defense programs that converge on stress resilience. These mechanistic insights-linking lipopeptide fingerprints, sentinel metabolites and defense transcripts-provide a framework for precision seed treatments in horticultural crops.

plant biology↗

bioRxiv2025

The offensive role of the Bacillus extracellular matrix in driving metabolite-mediated dialogue and adaptive strategies with pathogenic fungi

Bacterial{square}fungal interactions have traditionally been attributed to secondary metabolites, but the role of the bacterial extracellular matrix (ECM) in shaping these relationships has remained unclear. Here, we demonstrate that the ECM protein TasA is a key mediator in the antagonistic interaction between Bacillus subtilis and Botrytis cinerea. TasA enables Bacillus to tightly adhere to fungal hyphae, disrupts the {beta}-glucan layer, and compromises fungal cytoskeletal integrity synergistically with fengycin, which causes cytological damage. Additionally, TasA acts as a carrier for bacillaene, amplifying its fungistatic activity. In response, B. cinerea mounts a multifaceted defense, enzymatically degrading fengycin, producing antibacterial oxylipins, and activating adaptive programs such as hyphal branching and chlamydospore formation. Our findings reveal the previously unrecognized role of ECM components in fungal suppression and the modulation of fungal adaptive responses. This study reveals the complex interplay between microbial aggression and defense, providing new insights into the ecological dynamics of microbial competition and coexistence.

microbiology↗

bioRxiv2022

A non-invasive method for time-lapse imaging of microbial interactions and biofilm dynamics

Complex interactions between microbial populations can greatly affect the overall properties of a microbial community, sometimes leading to cooperation and mutually beneficial coexistence, or to competition and the death or displacement of particular organisms or sub-populations. Interactions between different biofilm populations are highly relevant in diverse scientific areas, from antimicrobial resistance to microbial ecology. The utilization of modern microscopic techniques has provided new and interesting insight into how bacteria interact at the cellular level to form and maintain microbial biofilms. However, our ability to follow complex intra- and inter-species interactions in vivo at the microscopic level has remained somewhat limited. Here, we detail BacLive, a novel non-invasive method for tracking bacterial growth and biofilm dynamics using high resolution fluorescence microscopy and an associated ImageJ processing macro (https://github.com/BacLive) for easier data handling and image analysis. Finally, we provide examples of how BacLive can be used in the analysis of complex bacterial communities. ImportanceCommunication and interactions between single cells are continuously defining the structure and composition of microbial communities timely and spatially. Methods routinely used to the study of these communities at cellular level rely on sample manipulation what deprives from microscopic time lapse experiments on a given sample. BacLive is conceived as a method for the non-invasive study of the formation and development of bacterial communities, such as biofilms, and the dynamics of formation of specialized subpopulations in time-lapse experiments. In addition we prove that BacLive largely simplifies the analysis of the data generated.

microbiology↗

bioRxiv2022

Sporulation activated via σW protects Bacillus from a Tse1 peptidoglycan hydrolase T6SS effector

Bacterial communities constantly interact with various community members employing diverse offensive and defensive tools to reach coexistence. The extracellular matrix and sporulation are defensive mechanisms used by Bacillus cells when they interact with Pseudomonas strains expressing a type VI secretion system (T6SS). Here, we define Tse1 as the main toxin mobilized by the Pseudomonas T6SS that triggers sporulation in Bacillus. We characterize Tse1 as a peptidoglycan hydrolase that indirectly alters the dynamics and functionality of the Bacillus cell membrane. We also delineate the response of Bacillus cells to Tse1, which through the coordinated actions of the extracellular sigma factor {sigma}W and the cytoplasmic histidine kinases KinA and KinB, culminates in activation of the sporulation cascade. We propose that this cellular developmental response is conserved in Bacilli to defend against the toxicity of T6SS-mobilized Tse1 effector.

microbiology↗

bioRxiv2021

Mutualistic interactions between B. subtilis and seeds dictate plant development

A tightly coordinated developmental program controls precise genetic and metabolic reprogramming that dictates efficient transition of the seeds from dormancy to metabolically active seedlings. Beneficial microbes are known to stimulate the germination of the seeds or adaptation of the seedlings; however, investigations of exact mechanisms mediating these interactions and the resulting physiological responses of the plants are only beginning. Bacillus subtilis is commonly detected in the plant holobiont and belongs to the group of microbes that provide multifaceted contribution to the health of the plants. The present study demonstrated that B. subtilis triggered genetic and physiological responses in the seeds that determined subsequent metabolic and developmental status of adult plants. Chemically diverse extracellular matrix of Bacillus was demonstrated to structurally cooperate in bacterial colonization of the seed storage tissues. Additionally, an amyloid protein and fengycin, which are two components of the extracellular matrix, targeted the oil bodies of the seed endosperm, provoking changes in lipid metabolism or accumulation of glutathione-related molecules that stimulated two different plant growth programs: the development of seed radicles or overgrowth and immunization of adult plants. We propose this mutualistic interaction is conserved in Bacilli and plant seeds containing storage oil bodies.

microbiology↗

bioRxiv2021

GNPS Dashboard: Collaborative Analysis of Mass Spectrometry Data in the Web Browser

Access to web-based platforms has enabled scientists to perform research remotely. A critical aspect of mass spectrometry data analysis is the inspection, analysis, and visualization of the raw data to validate data quality and confirm statistical observations. We developed the GNPS Dashboard, a web-based data visualization tool, to facilitate synchronous collaborative inspection, visualization, and analysis of private and public mass spectrometry data remotely.

bioinformatics↗

bioRxiv2021

Chemical interplay and complementary adaptative strategies toggle bacterial antagonism and co-existence

Bacterial communities are in a continuous adaptive and evolutionary race for survival. A myriad of molecules that kill, defend, or mediate communication between bacterial cells of different lineages shape the final structure of the microbial community. In this work we expand our knowledge on the chemical interplay and specific mutations that modulate the transition from antagonism to co-existence between two plant-beneficial bacteria, Pseudomonas chlororaphis PCL1606 and Bacillus amyloliquefaciens FZB42. We reveal that the bacteriostatic activity of bacillaene produced by Bacillus relies on an interaction with the protein elongation factor FusA and how mutations in this protein lead to tolerance to bacillaene and other protein translation inhibitors. Additionally, we describe how the unspecific tolerance to antimicrobials associated with mutations in the glycerol kinase GlpK is provoked mainly by a decrease of Bacillus cell membrane permeability among other pleiotropic cellular responses. We conclude that nutrient specialization and mutations in basic biological functions are bacterial evolutive and adaptive strategies that lead to the coexistence of two primary competitive bacterial species rather than their mutual eradication.

microbiology↗

bioRxiv2019

Dual functionality of the TasA amyloid protein in Bacillus physiology and fitness on the phylloplane

Bacteria can form biofilms that consist of multicellular communities embedded in an extracellular matrix (ECM). Previous studies have demonstrated that genetic pathways involved in biofilm formation are activated under a variety of environmental conditions to enhance bacterial fitness; however, the functions of the individual ECM components are still poorly understood. In Bacillus subtilis, the main protein component of the ECM is the functional amyloid TasA. In this study, we demonstrate that beyond their well-known defect in biofilm formation,{Delta} tasA cells also exhibit a range of cytological symptoms indicative of excessive cellular stress, including DNA damage accumulation, changes in membrane potential, higher susceptibility to oxidative stress, and alterations in membrane dynamics. Collectively, these events can lead to increased programmed cell death in the colony. We show that these major physiological changes in{Delta} tasA cells are likely independent of the structural role of TasA during amyloid fiber formation in the ECM. The presence of TasA in cellular membranes, which would place it in proximity to functional membrane microdomains, and mislocalization of the flotillin-like protein FloT in{Delta} tasA cells, led us to propose a role for TasA in the stabilization of membrane dynamics as cells enter stationary phase. We found that these alterations caused by the absence of TasA impair the survival, colonization and competition of Bacillus cells on the phylloplane. Taken together, our results allow the separation of two complementary roles of this functional amyloid protein: i) structural functions during ECM assembly and interactions with plants, and ii) a physiological function in which TasA, via its localization to the cell membrane, stabilizes membrane dynamics and supports more effective cellular adaptation to environmental cues.

microbiology↗

bioRxiv2018

Extracellular matrix components are required to protect Bacillus subtilis colonies from T6SS-dependent Pseudomonas invasion and modulate co-colonization of plant

Bacteria adapt to environmental changes and interact with other microorganisms using a wide array of molecules, metabolic plasticity, secretion systems and the formation of biofilms. Some research has looked at changes in the expression of biofilm related genes during interactions between different bacterial species, however no studies have directly demonstrated the functional significance of biofilms in modulating such interactions. In this study, we have explored this fundamental question by studying the interaction between Bacillus subtilis 3610 and Pseudomonas chlororaphis PCL1606. We demonstrate the important role of the extracellular matrix in protecting B. subtilis colonies from infiltration by Pseudomonas. Surprisingly, we find that the Pseudomonas type VI secretion system (T6SS) is required in the cell-to-cell contact with matrix-impaired B. subtilis cells, revealing a novel role for T6SS against Gram-positive bacteria. In response to P. chlororaphis infiltration, we find that B. subtilis activates sporulation and expresses motility-related genes. Experiments using plant organs demonstrate the functional importance of these different bacterial strategies in their coexistence as stable bacterial communities. The findings described here further our understanding of the functional role played by biofilms in mediating bacterial social interactions.

microbiology↗

bioRxiv2018

Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages

A major aspect of our daily lives is the need to acquire, store and prepare our food. Storage and preparation can have drastic effects on the compositional chemistry of our foods, but we have a limited understanding of the temporal nature of processes such as storage, spoilage, fermentation and brewing on the chemistry of the foods we eat. Here, we performed a temporal analysis of the chemical changes in foods during common household preparations using untargeted mass spectrometry and novel data analysis approaches. Common treatments of foods such as home fermentation of yogurt, brewing of tea, spoilage of meats and ripening of tomatoes altered the chemical makeup through time, through both chemical and biological processes. For example, brewing tea altered its composition by increasing the diversity of molecules, but this change was halted after 4 min of brewing. The results indicate that this is largely due to differential extraction of the material from the tea and not modification of the molecules during the brewing process. This is in contrast to the preparation of yogurt from milk, spoilage of meat and the ripening of tomatoes where biological transformations directly altered the foods molecular composition. Comprehensive assessment of chemical changes using multivariate statistics showed the varied impacts of the different food treatments, while analysis of individual chemical changes show specific alterations of chemical families in the different food types. The methods developed here represent novel approaches to studying the changes in food chemistry that can reveal global alterations in chemical profiles and specific transformations at the chemical level.\n\nO_LSTHighlightsC_LSTO_LIWe created a reference data set for tomato, milk to yogurt, tea, coffee, turkey and beef.\nC_LIO_LIWe show that normal preparation and handling affects the molecular make-up.\nC_LIO_LITea preparation is largely driven by differential extraction.\nC_LIO_LIFormation of yogurt involves chemical transformations.\nC_LIO_LIThe majority of meat molecules are not altered in 5 days at room temperature.\nC_LI

biochemistry↗