Biology subjects

Friedman, J.

Publications and source records attributed to Friedman, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Individual-specific recovery of the healthy human gut microbiota after antibiotics

Following disruption by broad-spectrum antibiotics, the human gut microbiome undergoes a prolonged recovery where coarse ecological features, such as species richness and diversity, are largely restored. However, as these features are shared by most healthy individuals, it remains unclear whether, even after strong perturbation, individuals preferentially return toward their own pre-treatment composition ('individual-specific recovery') or instead switch to alternative equally healthy states. Resolving this question is fundamental for evaluating the long-term impacts of antibiotics, because an individual's health is affected by their unique microbiome composition, affecting immune regulation and metabolic processing, so a state switch, even to a broadly healthy configuration, could carry unintended consequences. Here we compare each subject's post-antibiotic endpoint with their own baseline and with the baselines of every other subject, across four cohorts (n = 121) whose regimens ranged from a five-day fluoroquinolone course to a four-day three-drug combination given to deplete the gut community. The recovered community was significantly closer to the subject's own baseline than to the alternative healthy baselines in more than 90% of individuals under the mildest regimen and in two thirds of those under regimens that broadly target the gut anaerobes, remaining above chance in every cohort and the majority outcome even where most baseline taxa fell below detection during treatment. This specificity is not merely the persistence and fast regrowth of survivors: it persists among baseline taxa that remain undetected for weeks to months, and the same taxon re-establishes more readily in a host where it was previously detected than in one where it was not. Newly established taxa are consistently more functionally similar to the pre-treatment community than transient arrivals, and their identity correlates with the surviving community's composition in a substantial fraction of subjects. State switching, in contrast, was uncommon and occurred almost exclusively among subjects with the largest reduction in detected taxa during the treatment. Together, these observations reveal the individual-specific nature of the microbiome resilience to broad-spectrum antibiotics, whereas the compositional changes are not random but rather functionally and ecologically associated with the subject's baseline.

ecology↗

bioRxiv2026

Early bird dynamics reduce selection imposed by species interactions in boom-and-bust regimes

Interspecific interactions are a major force shaping evolution, yet the magnitude of their effect varies across ecosystems and interactions. What explains this variability remains underexplored. Here, we propose that the temporal dynamics of growth and resources are a key determinant. We study how the degree to which species interactions alter selection forces depends on a system's growth regime, ranging from steady chemostat-like growth to boom-and-bust cycles. Using consumer-resource simulations together with analytical approximations, we show that selection in boom-and-bust cycles is dominated by an early bird effect: because most generations elapse early in a growth cycle, when populations are small and resources are abundant, selection is concentrated in a period where species interactions are relatively weak. As a result, boom-and-bust dynamics diminish the degree to which growth rate reducing interactions alter selection. In contrast, interactions that act through mortality, such as the secretion of lethal toxins, operate regardless of growth phase and are therefore not reduced, and can even be amplified in boom-and-bust dynamics. These findings help contextualize estimates of the evolutionary effects of species interactions across experimental systems, and suggest that the growth regime is a coarse-grained, measurable feature that governs when biotic interactions leave a strong evolutionary mark.

evolutionary biology↗

bioRxiv2026

Cross-Resistance Limits the Ability of Antimicrobial Peptide Combinations to Delay Resistance Evolution

AimsAntimicrobial peptide (AMP) combinations have been proposed to delay resistance evolution, but it remains unclear what properties of a peptide pair determine whether a combination reduces resistance evolution relative to its component AMPs used alone. One suggested factor is mode of action, yet this has rarely been tested experimentally. In the current study we have asked whether mode of action or physicochemical similarity between peptides better predicts which combinations delay resistance. MethodsWe evolved Staphylococcus aureus with six AMPs with reported membrane-targeting and intracellular-targeting activity, individually and in all 15 pairwise combinations. We quantified resistance evolution, cross-resistance and fitness costs across the full AMP panel, and performed whole-genome sequencing on 126 evolved lineages. ResultsResistance varied across AMPs and correlated with peptide chain length, not mode of action. Cross-resistance was associated with physicochemical similarity, and similar peptides selected for overlapping mutations. Most combinations reduced resistance relative to single-AMP treatment, but those whose components shared cross-resistance were less effective, channeling evolution into convergent trajectories that resolve both selective pressures at once. Notably, mode of action did not predict combination outcome. ConclusionsCross-resistance, not mode of action, is a key factor in determining AMP combination efficacy. Physicochemical distance between peptides may serve as a practical predictor for cross-resistance, enabling selection of AMP combinations that are more likely to constrain resistance evolution.

microbiology↗

bioRxiv2026

Basal BNIP3/NIX mitophagy is controlled by selective protection of sentinel receptors

Mitochondrial homeostasis is maintained by multiple quality control pathways, including mitophagy, which targets dysfunctional mitochondria for degradation. During receptor-mediated mitophagy, the outer membrane proteins BNIP3 and NIX directly recruit autophagy machinery to the mitochondrial surface, though their precise regulation is still unclear. In recent years, new BNIP3- and NIX-interacting proteins have been identified that influence mitophagic flux. PPTC7 and FBXL4 target BNIP3 and NIX for proteasomal turnover to keep levels of the receptors low, whereas TMEM11 is proposed to spatially control mitophagy by interacting with receptors at active mitophagy sites. However, it is unclear how each of these interactions is controlled and how they interplay with each other. Here, we identify a repressor of mitophagy, ARMC1, which forms a complex with TMEM11, BNIP3, and NIX. During mitophagy activation, ARMC1 dissociates from the complex, freeing the receptors to initiate mitophagy. We find that TMEM11 then acts in an antagonistic relationship with PPTC7, protecting the receptors from proteasomal degradation. Our data are consistent with a two-stage model. At steady state, a population of sentinel receptors is repressed and primed to respond to mitochondrial dysfunction. Once mitophagy is activated, TMEM11 protects BNIP3 and NIX, ensuring a sustained mitophagic response. Our findings provide a framework for understanding how two key regulatory pathways intersect to modulate receptor-mediated mitophagy.

Cell Biology↗

bioRxiv2026

Nutrient environments shape amino acid auxotrophy and cross-feeding

Auxotrophy, the absence of biosynthetic capacity for essential metabolites, is widespread in microbes and is thought to shape interactions within communities. Auxotrophies are often treated as fixed properties of organisms; however, evidence indicates that auxotrophic phenotypes can depend on environmental context, thereby affecting community assembly by cross-feeding. Here, we systematically quantify how nutrient environments shape both auxotrophy and cross-feeding. Using matched sets of six amino acid auxotrophs in Escherichia coli and Bacillus subtilis, we measured monoculture and pairwise coculture growth across 40 carbon and nitrogen environments. We find that auxotrophy itself is highly environment dependent, with strains growing in a substantial fraction of amino acid-free conditions despite lacking key biosynthetic enzymes. Cross-feeding likewise varies widely across species, environments, and auxotroph pairs. Despite this variability, cross-feeding outcomes exhibit consistent patterns within and across species. In particular, B. subtilis cross-feeds better overall and cross-feeding growth is better predicted by auxotroph type (i.e., which amino acids the strain cannot produce) than by environmental context. A machine-learning model recapitulates this pattern, identifying auxotroph type as the strongest predictor of cross-feeding growth, similar to species identity, exceeding the contributions of nutrient environment and prototroph growth. Together, these results show that environmental context reshapes both metabolic need and exchange, yet cross-feeding follows emergent patterns linked to the species and auxotrophy type, with implications for predicting community assemblies and the evolution of gene loss.

ecology↗

bioRxiv2026

Deciphering temporal antifungal dynamics of a rare actinomycete via integrated omics

Fungal phytopathogens pose a persistent threat to global crop production, and widespread use of chemical fungicides has driven resistance development and environmental concerns, necessitating sustainable alternatives. Actinomycetes produce diverse bioactive metabolites, yet natural product discovery has disproportionately focused on Streptomyces, leaving rare actinomycete taxa underexplored. Saccharomonospora xinjiangensis XJ-54 is a rare actinomycete exhibiting strong antifungal activity against Fusarium phytopathogens, including Fusarium oxysporum f. sp. cucumerinum (FORC), and harbors numerous biosynthetic gene clusters (BGCs) of unknown function. However, as in many rare actinomycetes, BGCs may be transcriptionally silent under standard laboratory conditions, and their expression dynamics remain poorly understood. To elucidate the molecular basis of antifungal activity in S. xinjiangensis XJ-54, we integrated genomic, transcriptomic, and metabolomic analyses. Cell-free supernatants inhibited FORC after 5 days of fermentation, with activity increasing by day 7. Time-resolved RNA sequencing demonstrated that all genomically-identified BGCs were transcriptionally active but exhibited distinct growth-phase-dependent expression patterns, with approximately half upregulated during exponential growth, and the remainder following transition to stationary phase. We observed temporal variations in transcriptional coupling between cluster-specific regulators and biosynthetic genes. LC-MS-based metabolomics showed growth-phase-dependent metabolite shifts, including stationary phase accumulation of secoiridoid-like monoterpenoids, N-acyl amines, and alkaloids (imidazoles, pyridines, indoles), correlating with the observed antifungal phenotype. Bioactivity-guided fractionation subsequently yielded an active fraction containing a predicted halogenated alkaloid that induced hyphal damage in FORC. These findings indicate that antifungal activity in S. xinjiangensis XJ-54 arises from temporally coordinated biosynthetic programs, providing a framework for optimizing growth conditions and prioritizing BGCs for functional characterization. ImportanceThe discovery of new antifungal compounds is critical for sustainable agriculture and medicine, yet most natural product research has focused on screening a narrow range of well-studied microorganisms. Rare actinomycetes represent an untapped reservoir of chemical diversity, but their biosynthetic potential is predominantly unknown. By integrating time-resolved transcriptomics with metabolomics, we show that the rare actinomycete Saccharomonospora xinjiangensis XJ-54 produces antifungal metabolites through temporally coordinated biosynthetic programs. Contrary to the prevailing assumption that the majority of biosynthetic gene clusters (BGCs) are silent, all BGCs in this strain were transcriptionally active under standard cultivation conditions, with expression patterns that were strongly growth-phase dependent. This work provides a roadmap for unlocking the biosynthetic potential of rare actinomycetes and accelerating the discovery of antifungal natural products that can be applied in agriculture and human health.

microbiology↗

bioRxiv2026

Biosynthetic diversity and antifungal potential of soil-derived Saccharomonospora strains

Soilborne fungal pathogens pose persistent challenges to sustainable agriculture, driving demand for biological alternatives to synthetic fungicides. While actinomycetes, particularly Streptomyces have yielded numerous antifungal compounds, less-explored genera, such as Saccharomonospora represent untapped sources of novel bioactive metabolites for plant protection. Our previous work identified Saccharomonospora as strongly associated with plant disease suppression in organically-amended soils and harbored numerous uncharacterized biosynthetic gene clusters (BGCs). Here, we investigated the biosynthetic capacity and antifungal potential of Saccharomonospora using comparative genomics, untargeted metabolomics, and in vitro bioassays. Cell-free supernatants from six strains (five soil-derived type strains and one novel isolate) were evaluated against three Fusarium phytopathogens. All strains inhibited at least one pathogen, with S. xinjiangensis and S. viridis R81 exhibiting the highest and broad-spectrum activity. Metabolomic profiling of the two most bioactive strains and one moderately active strain (S. cyanea) revealed that [~]40% of detected metabolites were shared across the three strains although their relative abundances varied. S. xinjiangensis and S. viridis R81 displayed higher abundances of shared metabolite classes than S. cyanea, including alkaloids, polyketides, and peptide derivatives. Comparative genomics across the genus revealed that most BGCs, particularly those encoding non-ribosomal peptides synthetases and polyketides synthases, were strain-specific and had low sequence similarity to characterized BGCs. In contrast, BGCs encoding, indole, ectoine, arylpolyene, and terpene were ubiquitous across the genus. Collectively, these findings demonstrate that Saccharomonospora produce antifungal metabolites and harbor diverse, uncharacterized BGCs, positioning this "less-explored" actinomycete genus as a promising source of bioactive compounds for managing soilborne fungal pathogens. ImportanceActinomycetes have historically been rich sources of antifungal metabolites for agriculture and pharmaceuticals, but discovery efforts have focused largely on Streptomyces, leaving other genera underexplored. This study demonstrates that Saccharomonospora, a rare actinomycete genus, produces antifungal metabolites active against major Fusarium pathogens and harbors largely uncharacterized biosynthetic gene clusters, indicating a reservoir of novel chemistry. These findings establish Saccharomonospora as a promising yet underutilized resource for discovering new antifungal agents, expanding the toolkit for sustainable plant disease management beyond traditional actinomycete sources.

microbiology↗

bioRxiv2025

Seasonal life-history trade-offs differ between plants derived from seed versus rhizomes in Saponaria officinalis

Many perennial plants reproduce both sexually through seeds and asexually through vegetative clones, and these contrasting origins can shape subsequent life-history strategies. Because clonal propagules begin with greater parental resource provisioning, whereas seedlings establish independently, these alternative origins create natural variation in early resource availability and developmental trajectories. This variation provides an opportunity to test predictions from life-history theory: while investment in current reproduction is expected to trade off with future growth or survival, such costs are often difficult to detect unless reproductive effort varies substantially among individuals or is experimentally manipulated. In this study, we compared growth, reproduction, and survival of seed- and rhizome-origin individuals of the invasive perennial Saponaria officinalis across three years in a common garden. We also manipulated reproductive effort in a subset of plants through pollen supplementation and tracked seasonal changes in flowering and seed production. Seedlings initially grew faster and made more branches and flowers than rhizome-origin plants, but by the second year rhizomes were larger and had more flowers. Seedlings also exhibited far worse survival than rhizomes. Across the flowering season, seed number per capsule declined, consistent with both increasing competition among flowers and declining resource availability. Pollen-supplemented seedlings had the most seeds per capsule early in the season and were the only group to suffer overwinter mortality, indicating a survival cost of elevated early reproductive investment. Overall, our findings show that reproductive origin influences allocation to growth, reproduction, and survival, with consequences for the establishment and spread of this invasive weed.

ecology↗

bioRxiv2025

Life-history evolution under artificial selection in a clonal plant

The response of natural populations to selection and the role of genetic correlations in constraining or facilitating evolutionary change is fundamental to adaptation. We use artificial selection to investigate the evolutionary response of clonal reproduction in the common monkeyflower (Mimulus guttatus), a species with extensive life history variation. We first characterize the standing genetic variation in a single perennial population, and then conduct four generations of divergent artificial selection on stolon number--the mechanism of clonal reproduction in this species. To start, stolon number had moderate heritability (H{superscript 2}=0.25) and was negatively genetically correlated with reproductive traits. Artificial selection produced a clear but asymmetrical response. High selection lines made significantly more stolons, while low lines diverged less from controls. Analyses of G matrices revealed that selection not only changed trait means but also genetic correlations, with high lines diverging more in multivariate genetic architecture. Our results demonstrate that single populations harbor sufficient genetic variation to respond rapidly to selection on clonality, and the response is shaped by existing patterns of genetic covariation. The capacity for rapid evolution of clonal traits is particularly relevant as climate change alters selection and shifts the relative advantages of sexual versus clonal life-history strategies.

evolutionary biology↗

bioRxiv2025

Competitive pre-ordering during planning persists in kinematically fused sequential movements

Results in human and non-human primates have shown that elements of a movement sequence are pre-ordered in parallel competitively before execution, a process known as competitive queueing (CQ). However, it is unclear whether the preplanning of individual movements persists in continuous skilled actions that involve greater biomechanical integration and is associated with the formation of new motor primitives (neural fusion). We investigated how kinematics impact sequence planning in a handwriting-like task asking whether fusing velocity curves between adjacent movements affects movement preparation. Participants were trained and tested for two days to perform two sequences of four sequential centre-out-and-back movements from memory in a delayed sequence production task using a stylus on a Wacom tablet. To manipulate kinematic fusion between subsequent strokes, participants were assigned to one of three groups that were trained to perform the sequences either with acute, right or obtuse angles between sequential targets. Probe trials assessed the availability of constituent movement elements for fast and accurate execution towards each target during planning. Movement elements associated with later sequence positions were less available than earlier movements, regardless of kinematic fusion, in line with CQ findings for discrete typing sequences in humans. Importantly, a more pronounced CQ gradient was associated with higher fusion, faster initiation and greater accuracy of sequence production. These findings indicate that kinematically fused sequential actions do not result in the formation of new movement primitives (neural fusion) with a single movement plan. Instead, they continue to be planned separately and are associated with skilled performance. New & NoteworthyUsing a handwriting-like sequencing task, we manipulated kinematic fusion through target geometry and examined the relative availability of individual movements towards targets as a marker of competitive queuing (CQ) during planning. Contrary to the assumption that behavioural fusion reflects their neural fusion of movements into a new motor primitive, we show that even under high levels of fusion, the underlying sequence elements remain competitively pre-ordered by their sequence position benefitting performance.

neuroscience↗

bioRxiv2025

Optimal foraging for simple organisms, the single-input marginal valuetheorem

Most organisms devote a great deal of time and energy to locating and consuming food, making efficient foraging crucial for their evolutionary success. Consequently, Optimal Foraging has been widely studied, but mainly in relatively complex animals with strong sensory and cognitive abilities. However, most living organisms, from bacteria to lower invertebrates, lack these abilities and still must forage efficiently. Here we extend one of the main theorems in Optimal Foraging, the Marginal Value Theorem, to organisms with minimal sensory and cognitive abilities; in particular, we consider individuals whose only sensory input is their feeding rate. To do so, we reformulate a continuous version of the Marginal Value Theorem, finding that individuals should adapt their speed to achieve a marginal feeding rate equal to the average feeding rate for the environment whenever possible, where the marginal feeding rate is defined as the feeding rate they would have if they returned to an already-visited location. We also find that, when faced with uncertainty, moving intermittently is more efficient than moving at constant speed, because this speed variability enables more robust estimates of the marginal feeding rate. Our results generalize Optimal Foraging Theory to organisms with strong sensory constraints, and unify classical results derived for patchy environments to those applicable in arbitrary environments.

animal behavior and cognition↗

bioRxiv2024

Reversion to metabolic autonomy underpins evolutionary rescue of a bacterial obligate mutualism

Populations facing lethal environmental change can avoid extinction by undergoing rapid genetic adaptation, a phenomenon termed evolutionary rescue. While this phenomenon has been the focus of much theoretical and empirical research, our understanding of evolutionary rescue in communities consisting of interacting species is still limited, especially in mutualistic communities, where evolutionary rescue is expected to be constrained by the less adaptable partner. Here, we explored empirically the likelihood, population dynamics, and genetic mechanisms underpinning evolutionary rescue in an obligate mutualism in which auxotrophic Escherichia coli strains exchanged essential amino acids reciprocally. We observed that >80% of the communities avoided extinction when exposed to two different types of lethal and abrupt stresses. Of note, only one of the strains survived in all cases. Genetic and phenotypic analyses show that this strain reverted to autonomy by metabolically bypassing the auxotrophy, but we found little evidence of specific adaptation to the stressors. Crucially, we found that the mutualistic partners were substantially more sensitive to both stresses than prototrophs, so that reversion to autonomy was sufficient to alleviate stress below lethal levels. We observed that increased sensitivity was common across several other stresses, suggesting that this may be a general property of obligate mutualisms mediated by amino acid exchange. Our results reveal that evolutionary rescue may depend critically on the specific genetic and physiological details of the interacting partners, adding rich layers of complexity to the endeavor of predicting the fate of microbial communities facing intense environmental deterioration.

evolutionary biology↗

bioRxiv2024

Degradation of indole-3-acetic acid by plant-associated microbes

Plant-associated microbiota affect pant growth and development by regulating plant hormones homeostasis. Indole-3-acetic acid (IAA), a well-known plant hormone, can be produced by various plant-associated bacteria. However, the prevalence of microbes with the capacity to degrade IAA in the rhizosphere has not been systematically studied. In this study, we analyzed the IAA degradation capabilities of bacterial isolates from the roots of Arabidopsis and rice. Using genomics analysis and in vitro assays, we found that 21 out of 189 taxonomically diverse bacterial isolates possess the ability to degrade IAA. Through comparative genomics and transcriptomic assays, we identified iac-like or iad-like operon in the genomes of these IAA degraders. Additionally, the regulator of the operon was found to be highly conserved among these strains through protein structure similarity analysis. Some of the IAA degraders could utilize IAA as their sole carbon and energy source. In planta, most of the IAA degrading strains mitigated Arabidopsis seedling root growth inhibition (RGI) triggered by exogenous IAA. Importantly, we observed increased colonization preference of IAA degraders from soil to root according to the frequency of the biomarker genes in metagenome-assembled genomes (MAGs) collected from different habitats, suggesting that there is a close association between IAA degraders and IAA-producers. In summary, our findings further the understanding of the functional diversity and roles of plant-associated microbes.

microbiology↗

bioRxiv2023

Evolution in microbial microcosms is highly parallel regardless of the presence of interacting species

During laboratory evolution, replicate bacterial populations often follow similar trajectories, thus their evolution is potentially predictable. However, predicting the evolution of natural populations, which are commonly embedded in multispecies communities, would prove extremely difficult if adaptations are contingent on the identity of the interacting species. The extent to which adaptations typically depend on coevolving partners remains poorly understood, since coevolution is commonly studied using small-scale experiments involving few species, making it challenging to extract general trends. To address this knowledge gap, we study the adaptations that occurred in strains of each of 11 species that were either evolved in monoculture or in multiple pairwise co-cultures. While we detect slight but significant partner-specific effects we find that the majority of evolutionary changes that occur are robust across strains that evolved with different partners; species growth abilities increase by a similar factor regardless of partners identity, shifts in community compositions and interactions are similar between pairs of coevolved and separately evolved strains, and the majority of parallelly mutated genes were detected in multiple biotic conditions. We hypothesized that these results might arise from the fact that ancestral strains are maladapted to the abiotic environment, thus having a pool of adaptations that are beneficial regardless of the biotic partners. Therefore, we conducted a second experiment with strains that were pre-adapted to the abiotic conditions before being co-cultured. We find that even after [~]400 generations of pre-adaptation, evolution is surprisingly non-partner-specific. Further work is required in order to elucidate the factors that influence partner-specificity of coevolution, but our results suggest that selection imposed by the biotic environment may play a secondary role to that imposed by abiotic conditions, making predictions regarding coevolutionary dynamics less challenging than previously thought.

evolutionary biology↗

bioRxiv2023

A Simple Subcortical Feeding Circuit Linking Interoceptive Inputs to Consummatory Behavior

The brain processes an array of stimuli enabling the selection of an appropriate behavioural response but the neural pathways linking interoceptive inputs to outputs for feeding are poorly understood. Here we delineate a subcortical circuit in which brain-derived neurotrophic factor (BDNF) expressing neurons in the ventromedial hypothalamus (VMH) directly connect interoceptive inputs to motor centers controlling food consumption and jaw movements. VMHBDNF neuron inhibition increases food intake by gating motor sequences of feeding through projections to premotor areas of the jaw. When food is unavailable, VMHBDNF inhibition elicits consummatory behaviors directed at inanimate objects such as a wooden block and inhibition of mesencephalic trigeminal area (Me5) projections evokes rhythmic jaw movements. The activity of these neurons is decreased during food consumption and increases when food is in proximity but not consumed. Activity is also increased in obese animals and after leptin treatment. VMHBDNF neurons receive monosynaptic inputs from both agouti-related peptide (AgRP) and proopiomelanocortin (POMC) neurons in the arcuate nucleus (Arc) and constitutive VMHBDNF activation blocks the orexigenic effect of AgRP activation. These data delineate an Arc[->]VMHBDNF[->]Me5 circuit that senses the energy state of an animal and regulates consummatory behaviors in a state dependent manner.

neuroscience↗

bioRxiv2022

Interactions between culturable bacteria are highly non-additive

Microorganisms are found in diverse communities whose structure and function are determined by interspecific interactions. Just as single species seldom exist in isolation, communities as a whole are also constantly challenged and affected by external species. Though much work has been done on characterizing how individual species affect each other through pairwise interactions, the joint effects of multiple species on a single (focal) species, remain under explored. As such, it is still unclear how single species effects combine to a community-level effect on a species of interest. To explore this relationship, we assayed over 14,000 communities of two, three, and four bacterial species, measuring the effect of single, pairs of, and trios of 61 affecting species on six different focal species. Our results demonstrate that joint effects of multiple species on a focal species are typically not given by the sum of the effects of individual affecting species. Rather, they are dominated by the strongest individual-species effect. Therefore, while joint effects of multiple species are often highly non-additive, they can still be derived from the effects of individual species, making it plausible to map complex interaction networks based on pairwise measurements. This finding is important for understanding the fate of species introduced into an occupied environment, and is relevant for applications in medicine and agriculture, such as probiotics and biocontrol agents, as well as for ecological questions surrounding migrating and invasive species.

microbiology↗

bioRxiv2022

Interactions between culturable bacteria are predicted by individual species' growth

Predicting interspecies interactions is a key challenge in microbial ecology, as such interactions shape the composition and functioning of microbial communities. However, predicting microbial interactions is challenging since they can vary considerably depending on species metabolic capabilities and environmental conditions. Here, we employ machine learning models to predict pairwise interactions between culturable bacteria based on their phylogeny, monoculture growth capabilities, and interactions with other species. We trained our models on one of the largest available pairwise interactions dataset containing over 7500 interactions between 20 species from 2 taxonomic groups that were cocultured in 40 different carbon environments. Our models accurately predicted both the sign (accuracy of 88%) and the strength of effects (R2 of 0.87) species had on each others growth. Encouragingly, predictions with comparable accuracy could be made even when not relying on information about interactions with other species, which are often hard to measure. However, species monoculture growth was essential to the model, as predictions based solely on species phylogeny and inferred metabolic capabilities were significantly less accurate. These results bring us a step closer to a predictive understanding of microbial communities, which is essential for engineering beneficial microbial consortia.

microbiology↗

bioRxiv2022

Arabidopsis thaliana induces multigenerational stress tolerance against biotic and abiotic stressors and memorization of host colonization in Bacillus subtilis

Bacillus subtilis is a beneficial bacterium that supports plant growth and protects it from bacterial, fungal, and viral infections. Here using a simplified system of B. subtilis, and Arabidopsis thaliana interactions, we found that history-dependent behavior is a potentially important manifestation of host colonization, worth classifying and quantifying. To study history-dependent adaptation to plant hosts, we develop a simple framework for measuring the physiological memory of B. subtilis following its interaction with Arabidopsis thaliana. We found that A. thaliana secretions reduce the lag time in pre-exposed bacteria compared with naive B. subtilis cells, even after their complete removal. Pre-exposed B. subtilis cells colonized plant roots more efficiently than naive bacteria, and were more resistant to biotic and abiotic stressors such as salicylic acid, and high salinity. Descendants of bacteria treated with plant secretions had an advantage in the competition against unexposed bacteria for root colonization. The effect of plant secretions was independent of their roles as nitrogen and carbon sources. Transcriptome analysis of both ancestors and descendants revealed that a specific set of plant-induced processes, among them c-di-AMP homeostasis, and the general stress response, maintain the signature of association with the plant in descendants of pre-exposed bacteria. Consistently, plant secretions compensated for the loss of c-di-AMP cyclases but required the general stress response and the master regulator Spo0A to exert their short and long-term effects. Overall, our work demonstrates that bacterial memory manifested by multigenerational reversible adaptation to plant hosts confirms an advantage to symbiotic bacteria during competition.

microbiology↗