mSystems最新文献

Tibetan antelopes, native to high-altitude plateau regions, play an important role in the local ecosystem. Their gut harbors antimicrobial-resistant microbes, including potential pathogens. To explore this, we analyzed 33,925 metagenome-assembled genomes (MAGs), including 7,318 from 68 Tibetan antelopes sequenced in our laboratory. We first profiled the composition of antibiotic resistance genes (ARGs) and then examined their associations with virulence factor genes (VFGs). In total, 2,968 ARGs were identified, conferring resistance to 23 antibiotic classes, with elfamycin resistance being most prevalent. Two ARGs were located on phage-derived sequences, though their phage taxonomy could not be resolved. ARGs were significantly correlated with VFGs, particularly genes linked to adherence and effector delivery systems. Given potential dissemination risks, we further assessed associations between ARGs and mobile genetic elements (MGEs), finding that insertion elements accounted for the largest number of ARG-MGE links. Comparative analysis with other plateau animals and humans revealed seven ARGs uniquely present in Tibetan antelopes. In summary, this study provides the first comprehensive overview of ARG composition in Tibetan antelope gut microbiomes, establishing a baseline for future hypothesis-driven studies and antimicrobial resistance surveillance in wildlife.

Importance: Investigating the drug resistance of Tibetan antelope (Pantholops hodgsonii) gut microbiota serves as a critical biological indicator for assessing the impact of human activities (particularly antibiotic contamination) on the fragile ecosystem of the Qinghai-Tibet Plateau. This study untangles the invasion of antibiotic resistance genes (ARGs) into remote conservation areas, suggesting that Tibetan antelopes may act as potential vectors for ARG dissemination across plateau environments. Such findings not only highlight threats to wildlife health but also provide an ecological warning regarding the pervasive environmental risks posed by the global antimicrobial resistance crisis in natural ecosystems.

Microbial iron (Fe) redox cycling underpins key biogeochemical processes, yet the functional diversity, ecological roles, and trait architectures of iron-transforming microbes remain poorly synthesized across global environments. Here, we present a systematic review and trait-based meta-analysis of 387 microbial taxa spanning 314 studies and 76 years of research, integrating phenotypic, genomic, and environmental data to define ecologically coherent microbial iron redox cycle guilds. Rather than relying on taxonomy, our framework delineates first-order functional guilds-Fe(III) reducers, Fe(II) oxidizers, and dual-capacity Fe oxidizers/reducers-and resolves second-order guilds based on trait syndromes, such as acidophily, redox flexibility, or metabolic breadth. Trait profiling revealed that iron-cycling capacities frequently transcend phylogenetic boundaries, with multiple guilds converging in chemically stratified hotspots like hot springs, hydrothermal vents, and acid mine drainages. Dual-capacity Fe oxidizers/reducers (e.g., Acidithiobacillus ferrooxidans and Metallosphaera sedula) emerged as overlooked mediators of "cryptic" iron cycling, possessing genomic repertoires capable of toggling between oxidative and reductive modes in response to redox oscillations. Hierarchical clustering and kernel density analyses of ecophysiological traits highlighted niche partitioning along key environmental filters, including pH, iron availability, salinity, and temperature. Collectively, this work introduces the Guild Exploitation Pattern as a conceptual lens for understanding iron microbiome assembly, providing a data-driven foundation for predicting microbial contributions to iron cycling under changing environmental conditions.

Importance: Iron redox reactions shape nutrient turnover, contaminant mobility, and primary productivity, yet the microbes driving these processes are often studied in isolation. By integrating decades of data into a trait-based guild framework, we reveal the ecophysiological diversity and niche differentiation of microbial iron redox cycling taxa across environments. Our synthesis exposes major gaps, such as limited trait data for >80% of dual-capacity Fe oxidizing/reducing species and highlights the need for functional trait surveys to complement metagenomics and cultivation efforts. The guild framework presented here advances predictive microbial ecology by linking metabolic traits with environmental gradients, offering a robust foundation for incorporating iron cycling into ecosystem models and biogeochemical forecasts.

Acetosyringone (AS), a prototypical syringyl-type monomer of lignin, functions as a model compound for the study of microbial catabolism of S-lignin-derived aromatics. In this study, we present the discovery of a novel metabolic pathway for AS catabolism, initiated by a previously uncharacterized FAD-dependent oxidoreductase, designated AsdA. In contrast to the sole previously documented AS funneling route, which entails side chain modification and conversion to syringic acid, AsdA catalyzes direct hydroxylation of the aromatic core. This represents a mechanistically distinct entry into central metabolism. The identification of this enzyme was achieved through metagenomic and functional analyses of a bacterial consortium enriched on AS as the sole carbon source. The consortium, predominantly comprising Pseudomonas rhizophila, exhibited co-metabolic transformation of the chlorinated pollutants 2,4,6-trichlorophenol (2,4,6-TCP) and 2,6-dichlorophenol. Subsequent functional assays substantiated the hypothesis that AsdA facilitates the transformation of both AS and 2,4,6-TCP. Induction assays employing a biosensor strain derived from the bacterial isolate Pseudomonas rhizophila AS1 confirmed AS-specific upregulation of the asd gene cluster. A survey of publicly available metagenomes has revealed that asdA is narrowly distributed but enriched in rhizosphere environments, pointing to its ecological significance. In summary, the present study unveils a hitherto unrecognized route for AS transformation and identifies an enzyme that exhibits dual functions in lignin-derived aromatic catabolism and environmental pollutant transformation. While the mechanisms underlying TCP degradation are well-established, the specific enzyme responsible for the conversion to 2,6-dichloro-p-hydroquinone had remained elusive-a knowledge gap that has now been addressed by AsdA.IMPORTANCEThe microbial conversion of lignin monomers is central to the global carbon cycle, yet pathways for syringyl-derived aromatics remain poorly resolved. Here, we identify AsdA, an enzyme initiating a previously unrecognized route for acetosyringone catabolism, providing new insight into how this abundant plant-derived compound is integrated into microbial metabolism. Beyond expanding the mechanistic diversity of lignin degradation, AsdA also catalyzes a key step in the transformation of the chlorinated pollutant 2,4,6-trichlorophenol, linking natural and anthropogenic compounds within a shared metabolic framework. The restricted yet rhizosphere-enriched distribution of asdA underscores its specialized role in plant-microbe interactions. By integrating enzyme function, microbial community context, and metagenomic distribution, we demonstrate how a single catalytic activity connects metabolic pathways and ecosystem processes, illustrating a multi-scale systems biology perspective on aromatic compound turnover.

Hundreds of thousands of individual microbe-molecule interactions regulate the flux, transformation, and fate of carbon stored in the climatically important reservoir of marine dissolved organic matter (DOM). While marine microbial communities have been characterized at high resolution for over a decade, observations of the molecules cycled by the microbial-chemical network at similar resolution are limited. In addition, bulk characterizations of DOM can mask the complex network of interactions comprised of rich chemical diversities. Here, we present a three-year, depth-resolved, molecular time-series of DOM and prokaryoplankton at the Bermuda Atlantic Time-series Study (BATS) site. Both time-series exhibited seasonality that was compositionally distinct and primarily endemic to one sampling depth. We also putatively identified four exometabolites (gonyol, glucose-6-sulfate, succinate, and trehalose) that exhibit seasonal accumulation. We hypothesize these patterns result from environmental conditions that alter community composition on a seasonal timescale and thus shift the relative proportions of microbial functions that produce and consume the substrates. Critically, we observed the interannual composition of seasonal DOM molecules to be more stable than the taxonomy of the microbial community. This points to an important role of functional redundancy in regulating DOM composition. We tested this observation by querying metagenomes for pathways that utilize metabolic by-products putatively identified in the DOM time-series. We find that core microbial metabolisms, either those required by all or by a subset of marine microbes, are important predictors of DOM composition. The molecular-level characterization of DOM herein highlights the potential imprint of microbial activity on seasonal DOM composition.IMPORTANCEMarine dissolved organic matter (DOM) is a major carbon reservoir that acts as a critical control on the Earth's climate. DOM dynamics are largely regulated by a complex web of chemical-microbial interactions, but the mechanisms underpinning these processes are not well understood. In a three-year time-series, we found that the identity of the microbes is more likely to change between years than the composition of the DOM molecules. The taxonomic variability suggests that metabolisms shared across taxa, encoded by genes that conduct core microbial functions, are responsible for the more stable composition of DOM. While more than three decades of marine prokaryoplankton time-series are available, a similar reference for DOM molecules was missing. This time-series provides an improved understanding of the different responses of DOM molecules and microbes to seasonal environmental changes.

The role of metabolic state reprogramming in modulating antibiotic susceptibility has attracted growing interest as a promising strategy to combat antimicrobial resistance. Our study revealed that L-arginine potentiates chloramphenicol's bactericidal activity by at least two orders of magnitude against multidrug-resistant Edwardsiella tarda via the coordinated modulation of three interconnected metabolic pathways: the tricarboxylic acid cycle disruption, redox homeostasis alteration, and phenylalanine metabolic suppression. Mechanistically, L-arginine-mediated tricarboxylic acid cycle inhibition diminished NADH production and compromised proton motive force, thereby depleting cellular energy supply and impairing drug efflux capacity. Concurrently, L-arginine disturbed the bacterial redox balance, which normally provides antibiotic resistance, by both lowering total antioxidant capacity and raising reactive oxygen species production. Furthermore, L-arginine suppressed phenylalanine metabolism, whereas trans-cinnamate restored antioxidant defenses and proton motive force, diminishing antibiotic resistance. These findings expanded the understanding of metabolic modulation's role in combating antibiotic resistance and offered theoretical support for the development of new antimicrobial strategies.IMPORTANCEThe global crisis of antimicrobial resistance demands innovative strategies to revitalize existing antibiotics. Our work addresses this urgent need by demonstrating that L-arginine acts as a powerful potentiator of chloramphenicol, enhancing its bactericidal efficacy by over 100-fold against multidrug-resistant Edwardsiella tarda. More significantly, we elucidate a novel, dual-pathway mechanism: arginine concurrently disrupts the TCA cycle and phenylalanine metabolism, which collectively alter the cellular redox state and compromise the proton motive force. This study is the first to uncover this sophisticated metabolic interplay, providing not only a promising adjuvant strategy but also a new conceptual framework for combating resistant bacterial infections by targeting core metabolism. Our findings, therefore, hold substantial potential for both basic science and translational antimicrobial development.

This study aims to characterize the phenotypic behavior and in vivo persistence of a ceftriaxone-tolerant Neisseria gonorrhoeae clinical isolate from a single patient and evaluate the potential role of tolerance in treatment failure. A previously identified ceftriaxone-tolerant vaginal isolate was compared with isogenic and clinical non-tolerant strains. Bacterial growth was assessed in vitro, and tolerance was quantified using the minimum duration required to kill 99% of the population (MDK99), and persistence was evaluated in an in vivo Galleria mellonella infection model. Whole-genome sequencing (WGS) and transcriptomic (RNA-sequencing [RNA-seq]) profiling were performed to identify tolerance-associated genetic and transcriptional signatures. The tolerant strain exhibited prolonged MDK99 values across ceftriaxone concentrations, persisting for up to 24 hours under drug exposure. It also showed delayed early-phase growth, suggesting a fitness cost. In vivo, the tolerant strain remained viable up to 8 hours after treatment, whereas non-tolerant strains were cleared. WGS revealed identical gene content across all isolates, but non-synonymous mutations in pilE_3, a type IV pilin gene, were exclusively present in tolerant strains. RNA-seq analysis showed upregulation of pilin-associated genes and downregulation of zinc-independent ribosomal paralogs (rpmE2 and ykgO), suggesting a combined mechanism of surface remodeling and translational suppression associated with the tolerant phenotype. Ceftriaxone tolerance enables prolonged survival of N. gonorrhoeae despite apparent susceptibility by standard MIC-based testing. This phenotype may contribute to treatment failure, recurrent infection, and ongoing transmission, indicating the need for revised diagnostic and therapeutic strategies.IMPORTANCECeftriaxone remains the last reliable option for gonorrhea therapy, yet recurrent infections can occur despite isolates being classified as susceptible by MIC testing. One possible explanation is antibiotic tolerance, a phenotype that allows survival during drug exposure without changes in MIC. Although tolerance has been described in other pathogens, its role in gonococcal infection has remained poorly defined. In this study, we provide the first detailed characterization of a ceftriaxone-tolerant Neisseria gonorrhoeae clinical isolate associated with repeated treatment failure. By combining in vitro killing assays, an in vivo Galleria mellonella infection model, whole-genome sequencing, and transcriptomic profiling, we demonstrate that tolerance enables prolonged survival under ceftriaxone and is linked to pilin gene variation and ribosomal remodeling. These findings illustrate how a clinically observed phenomenon can be mechanistically dissected and emphasize tolerance as a hidden factor contributing to gonococcal persistence and potential treatment failure.

Salinization of inland waters, driven by climate change and human activities, poses a major threat to aquatic ecosystems. While species can swiftly adapt to environmental stress, the molecular mechanisms underpinning this adaptation remain to be fully elucidated. This study seeks to clarify the complex adaptive strategies employed by the freshwater ciliate Tetrahymena thermophila in response to chronic salt stress through the methodologies of experimental evolution and multi-omics integration. The findings indicate that three lineages adapted to salt (ST-4, ST-8, and ST-12), which evolved under a regime of increasing NaCl concentration, demonstrated a trade-off between delayed growth and osmotic resilience. Transcriptomic and proteomic analyses revealed key evolutionary priorities, including (i) the co-upregulation of pathways related to DNA replication, glutathione metabolism, and endoplasmic reticulum (ER) protein processing, (ii) the suppression of lipid catabolism alongside the accumulation of lipid droplets mediated by START2, and (iii) mitochondrial remodeling through the expansion of ER contacts to sustain ATP production. Interestingly, the adaptation to salt appears to tolerate genome instability induced by replication stress through the dysregulation of replisome components, specifically the upregulation of Prim1 and downregulation of LIG, while also evading antioxidant defenses via the compartmentalization of oxidative damage. These results contribute to a framework in which protists effectively balance lipid-mediated osmoregulation, controlled mutagenesis, and organelle metabolism to navigate salinity challenges, thereby offering predictive insights into microbial adaptation thresholds within evolving ecosystems.IMPORTANCESalinization of inland waters is a growing concern due to climate change and human activities. Understanding how organisms adapt to saline environments is vital. Tetrahymena thermophila, a model organism, was studied to explore its adaptation mechanisms. The findings show that through gene regulation, it can acclimate to high salt conditions. The role of mitochondria in metabolic reprogramming during this process is significant. This research contributes to a more profound understanding of how organisms adapt to saline stress and the molecular mechanisms underlying such adaptations, which may aid in predicting and managing the impacts of salinization on aquatic ecosystems.

Bacteria produce a diverse range of specialized metabolites that influence the health and behavior of neighboring cells and, therefore, have potential applications in treating diseases. Deciphering the intended ecological functions of specialized metabolites is challenging due to the small scales at which these interactions occur and the complexity of unraveling simultaneous responses to multiple signals. In this study, we investigated the chemical interactions between two marine bacterial colonies, Vibrio parahaemolyticus PSU5429 and Bacillus pumilus YP001. When the two bacteria were grown in proximity on agar, V. parahaemolyticus exhibited swarming motility toward B. pumilus, but close approach to the B. pumilus colony was impeded by a zone of inhibition. Matrix-assisted laser desorption/ionization time-of-flight imaging mass spectrometry (MALDI-TOF IMS) suggested that lipopeptides produced by Bacillus induced swarming motility, a finding corroborated by genomic and chemical analyses of YP001. Based on activity and metabolomics guidance, the antibiotic amicoumacin B was found to be responsible for the observed antibiosis, while swarming motility by V. parahaemolyticus was induced by lipopeptides and two lipoamides. In this scenario, lipopeptide production by the Bacillus colony induces the Vibrio colony to swarm toward a lysis zone, resulting in a possible "catch and kill" effect. These results demonstrate the complexity of behaviors and outcomes exhibited by microbes under the simultaneous influence of different allelochemicals, suggesting possible interplays between antibiotics and compounds that induce motility.

Importance: Microbes communicate and compete using small molecules, yet linking specific metabolites to visible behaviors is difficult. We combine imaging mass spectrometry, genomics, analytical chemistry, and bioassays to decode an interaction between a marine Bacillus and the pathogen Vibrio parahaemolyticus. Surfactin-like lipopeptides act at a distance to stimulate Vibrio swarming and draw cells toward the colony. Amicoumacin B accumulates at the interface and halts growth, yielding a simple "catch and kill" outcome. This study shows that the spatial localization of natural products shapes microbial behavior on surfaces and provides a general, scalable workflow that maps chemistry to phenotype. Beyond this case, the approach can be applied broadly to understand and, ultimately, tune microbial interactions relevant to marine ecosystems, aquaculture health, and microbiome engineering.