ISME communications最新文献

Plants produce a plethora of specialized metabolites that often play important roles in their defence against pathogenic microbes or herbivorous insects. Exposure of leaf-colonizing microbes to these metabolites influences their growth, and we hypothesize that it also has consequences for microbe-microbe interactions. In Brassicaceae plants like the model plant Arabidopsis thaliana, glucosinolates and their biologically active derivatives, the isothiocyanates, are major defence metabolites. Adapted plant pathogens like Pseudomonas spp. use the hydrolase SaxA to convert the antimicrobial isothiocyanate sulforaphane to a non-toxic amine, whereas non-adapted commensal microbes are inhibited by this plant toxin. We used Plantibacter sp. 2H11-2 as a model commensal in co-culture with either Pseudomonas viridiflava 3D9 wildtype or a saxA-knock-out mutant. Both strains were isolated from the same wild A. thaliana population. Without isothiocyanate, Plantibacter grew better alone than with Pseudomonas, a potential competitor. At high isothiocyanate concentrations, however, the commensal was dependent on SaxA-mediated isothiocyanate degradation in both solid and liquid medium. At intermediate isothiocyanate concentrations, Plantibacter's transcriptome changed in response to sulforaphane in monoculture but not in co-culture with Pseudomonas, suggesting that it was fully protected from this toxin. In return, Plantibacter caused transcriptional changes in Pseudomonas, suppressing biofilm formation and increasing amino acid metabolism gene expression which might suppress virulence and so contribute to plant health. Together, we find that degradation of an antimicrobial plant metabolite can protect a commensal to depend on a pathogen-produced virulence factor, suggesting effects on community composition in environments where microbes are exposed to ITCs.

Global agricultural dependence on blended saline and freshwater irrigation mandates a mechanistic understanding of how salinity influences microbial biofilms within distribution networks, which are pivotal mediators of water quality and pathogen viability. Here, we examine the architectural, mechanical, and operational reactions of multi-species biofilms to saline exposure (0.6% NaCl) utilizing a regulated laboratory-scale irrigation model. Through a cohesive methodology combining confocal microscopy, atomic force microscopy, 16S rRNA sequencing, and meta-transcriptomics, we elucidate that salinity instigates a pivotal trade-off in biofilm maturation. While salt stress consistently suppressed live and dead cell biovolumes, it induced a significant enhancement of extracellular polymeric substances (EPS), leading to a thicker, EPS-rich biofilm architecture. These saline biofilms exhibited a lower adhesive force and Young's modulus, indicating a softer and less sticky surface. A community analysis revealed a reduction in taxonomic heterogeneity, along with an increase in specialized taxa associated with hydrocarbon decomposition functionalities, such as Hydrogenophaga and Nakamurella. Consequently, transcriptomic characterization revealed substantial upregulation of genes implicated in lipid distribution, ionic equilibrium, and oxidative stress mitigation, in conjunction with a downregulation of intercellular adhesion pathways. Our findings reveal that salinity drives biofilm adaptation towards a protected, EPS-dominated state with a functionally specialized community, suggesting a potential increase in the resilience of biofilms and risk of pathogen shielding in saline irrigation systems.

The Montseny brook newt, Calotriton arnoldi, is a Critically Endangered amphibian species endemic to the Montseny Massif in Catalonia, Northeastern Spain. Due to population declines and threats to its natural habitat, an ex-situ breeding program was initiated in 2007. A key goal of the program is to ensure the survival of captive-bred individuals after reintroduction, which in amphibians heavily relies on the specimens' microbiome being capable of protecting them from environmental microorganisms, especially considering the global Chytridiomycosis pandemic caused by the fungi Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal). This study aims to characterize the skin microbiome of wild and captive C. arnoldi specimens and identify differences in their composition, contributing to future research on the microbiome's impact in captive-bred individuals upon reintroduction. Up to 5996 ASVs (Amplicon Sequence Variants) were identified from 138 samples from 21 and 61 wild and captive-bred individuals, respectively. Results indicate that wild populations from different subspecies have significantly different skin microbiome composition, as do wild and captive-bred groups from the same subspecies. Additionally, dissimilarities in skin microbiome variability were only found within each subspecies, between wild and captive-bred groups. In terms of composition, certain bacteria were identified as potential markers for both wild and captive environments. Enhancing skin microbiome variability might improve the survival prospects of reintroduced specimens. Thus, exposing captive specimens to a more natural environment while in captivity or a soft-release procedure could potentially mitigate the absence of exposure to other bacteria and potential pathogens from their native environment.

[Formula: see text]-diversity is central to microbial ecology, yet commonly used metrics overlook changes in microbial load (or "absolute abundance"), limiting their ability to detect ecologically meaningful shifts. Popular for incorporating phylogenetic relationships, UniFrac distances currently default to relative abundance and therefore omit important variation in microbial abundances. As quantifying absolute abundance becomes more accessible, integrating this information into [Formula: see text]-diversity analyses is essential. Here, we introduce "Absolute UniFrac" ([Formula: see text]), a variant of Weighted UniFrac that incorporates absolute abundances. Using simulations and a reanalysis of four 16S rRNA metabarcoding datasets (from a nuclear reactor cooling tank, the mouse gut, a freshwater lake, and the peanut rhizospere), we demonstrate that Absolute UniFrac captures microbial load, composition, and phylogenetic relationships. While this can improve statistical power to detect ecological shifts, we also find Absolute Unifrac can be strongly correlated to differences in cell abundances alone. To balance these effects, we also incorporate absolute abundance into the generalized extension ([Formula: see text]) that has a tunable, continuous ecological parameter ([Formula: see text]) that modulates the relative contribution of rare versus abundant lineages to [Formula: see text]-diversity calculations. Finally, we benchmark GU^A and show that although computationally slower than conventional alternatives, GU^A is comparably sensitive to noise in load estimates compared to conventional alternatives like Bray-Curtis dissimilarities, particularly at lower [Formula: see text]. By coupling phylogeny, composition, and microbial load, Absolute Unifrac integrates three dimensions of ecological change, better equipping microbial ecologists to quantitatively compare microbial communities.

The rumen microbiome plays a pivotal role in modulating feed efficiency in ruminants, yet the ecological mechanisms mediating the active interactions among microbial adaptations, dietary inputs, and host feed efficiency within the rumen remain poorly understood. To address this gap, we analyzed 120 metatranscriptomic datasets obtained from 30 purebred Angus bulls (each sampled four times) classified as high-feed-efficiency or low-feed-efficiency based on feed conversion ratio, and fed either forage-based (n = 15) or grain-based (n = 15) diets. We constructed a comprehensive active gene catalog comprising 1 744 067 non-redundant genes and compiled a reference set of 25 115 ruminant microbial genomes. Using integrated Neutral Community Model analysis and carbohydrate-active enzyme profiling, we examined how ecological processes and functional capacities differed across host phenotypes and diets. Neutral Community Model fits revealed that stochastic processes broadly governed rumen microbial community structures (R² = 0.779 for high-feed-efficiency; R² = 0.781 for low-feed-efficiency). Within the predominantly stochastic processes, however, high-feed-efficiency bulls exhibited strong positive selection for diet-responsive microbial lineages: Fibrobacter spp. (positively selected species-level genome bins: 61.3%-76.0%; negatively selected: 0%-1.3%), Butyrivibrio spp. (positively selected: 13.3%-46.0%; negatively selected: 1.0%-11.2%) under forage feeding, and UBA1067 spp. (positively selected: 33.3%-48.5%; negatively selected: 0%-8.3%) under grain feeding. These lineages encoded catalytic domains appended with carbohydrate-binding modules, such as tandem carbohydrate-binding modules linked to glycoside hydrolases, thereby enhancing substrate adhesion and degradation. In contrast, low-feed-efficiency bulls showed more random community structures and reduced functional specialization. Therefore, these suggest that cattle hosts with higher feed efficiency promote microbial populations functionally aligned with dietary inputs, a process we define as efficient host-mediated microbial amplification. These findings offer new insight into how ecological assembly and functional adaptation of the microbiome contribute to feed efficiency and lay the foundation for microbiome-informed strategies to enhance ruminant production sustainability.

Soils act as both reservoirs and filters of antimicrobial resistance genes (ARGs); however, the ecological and genetic traits of antibiotic-degrading bacteria (ADB) and their interactions with nondegrading bacteria (NADB) across soil types remain poorly understood. In particular, the role of ADB in ARG dynamics and their potential contribution to horizontal gene transfer (HGT) are still underexplored. Here, we applied ¹³C-DNA stable isotope probing (DNA-SIP) combined with metagenomic sequencing to resolve active ADB from NADB in two contrasting soils: Ultisol and Mollisol. ADB harbored significantly more abundant and diverse chromosomal ARGs - especially multidrug and tetracycline resistance genes - often co-localized with mobile genetic elements (MGEs) and degradation genes, suggesting robust and regulated resistance strategies. In contrast, NADB relied more on plasmid-borne ARGs, reflecting flexible but potentially transient adaptation. Soil properties shaped both resistome composition and host taxa. Mollisol enriched enzymatic degraders such as Lysobacter and Nocardioides, while Ultisol favored stress-tolerant Burkholderia, which carried up to 34 ARGs and exhibited membrane-associated resistance. Notably, 89 ARGs or MGEs were found co-localized with degradation genes on assembled contigs, highlighting a strong potential for HGT. In addition, 24 high-potential ARG hosts were identified, including Ralstonia pickettii and Saccharomonospora viridis. These findings reveal that antibiotic degradation is embedded within complex, soil-specific resistome networks. This work enhances our understanding of ARG ecology and supports targeted mitigation strategies based on soil microbiome characteristics.

Nitrobacter strain NHB1 is a nitrite-oxidizing bacterium previously demonstrated to form a consortium capable of nitrification under acidic conditions when cocultivated with a neutrophilic ammonia-oxidizing bacterium. Here, we characterize the growth of isolated NHB1 under different pH and nitrite (NO₂ ^-) concentrations, as well as its influence on the activity of obligately acidophilic soil ammonia-oxidizing archaea (AOA) isolated from acidic soils when grown in coculture. NHB1 is acidotolerant with optimal growth at pH 6.0 (range: 5.0-7.5) at an initial NO₂ ^- concentration of 500 μM. However, at lower NO₂ ^- concentrations, closer to those found in soil, its pH optimum decreases to 5.0 and with detectable growth extended to pH 3.5. In coculture, NHB1 enhances the growth of the acidophilic AOA Nitrosotalea devaniterrae Nd1 and Nitrosotalea sinensis Nd2, which are highly sensitive to NO₂ ^-derived compounds and typically oxidize only ~200 to 300 μM ammonia (NH₃) when grown in batch cultures as isolates. However, in coculture with NHB1, both strains oxidized up to ~3 mM NH₃, limited only by the buffering capacity of the medium, and their pH range was also extended downward by ~0.5 units. NHB1 also possesses a cyanase, enabling reciprocal cross-feeding through cyanate-derived NH₃ production while utilizing AOA-derived NO₂ ^-. These findings suggest that NO₂ ^- removal is essential for ammonia oxidizer growth in acidic soils and emphasize the importance of considering substrate and metabolic product concentrations when characterizing ecophysiology. Genome analysis reveals that NHB1 is distinct from validated species, and we propose the name "Nitrobacter laanbroekii."

White band disease (WBD) has decimated the Caribbean staghorn coral, Acropora cervicornis, since its emergence in 1979, but its etiology remains unknown. Numerous WBD pathogen candidates from over nine bacterial families have been implicated, with a multi-year field study recently identifying Cysteiniphilum litorale as the likely pathogen. Here, we use 16S rRNA gene amplicon sequencing to profile changes in the bacterial communities in a tank-based transmission experiment in the Florida Keys using 50 nursery-raised staghorn coral genotypes with varying disease resistances to determine whether any bacteria in the native staghorn coral microbiomes were associated with WBD resistance and to identify bacterial amplicon sequencing variants (ASVs) associated with WBD exposure and transmission. We found no significant associations, positive or negative, between any bacterial ASV, genus, or family and disease resistance in native staghorn coral microbiomes but did identify nine bacterial ASVs strongly associated with disease outcome in the tank-based transmission experiment. ASV 65, classified as Cysteiniphilum litorale, showed strong disease associations consistent with pathogenicity, including being significantly associated with WBD transmission within disease-exposed tanks (i.e. more abundant on diseased fragments) and being significantly more abundant on the diseased experimental dose than the healthy dose. The V3-V4 16S rRNA gene sequence for ASV 65 differed by only 1 of 415 bp from the C. litorale ASV identified as the putative WBD pathogen in the recent multi-year study from Panama, suggesting a rare Caribbean-wide strain-level pathogen association. Eight additional disease-associated ASVs were identified as potential opportunistic pathogens and included ASVs from the families Vibrionaceae and Colwelliaceae.

Coastal lagoons are dynamic transitional ecosystems shaped by complex hydrodynamic and biogeochemical processes. Their sediments host diverse microbial communities essential for nutrient cycling, organic matter sequestration, and pollutant degradation. However, the taxonomic and functional profiles of these communities remain poorly understood, especially in pristine systems. Here, shotgun metagenomics was used to investigate microbial diversity and functional potential in a seagrass-dominated coastal lagoon on the Mexican Pacific coast, influenced by seasonal upwelling and with minimal anthropogenic impact. Despite pronounced physicochemical gradients and oceanographic variability, these sediments harbored a diverse and taxonomically conserved microbial community. 60% of genera and 38% of species (with relative abundance >0.1%) were consistently shared across sites and the two upwelling seasons, with Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Flavobacteria, and Actinobacteria as dominant taxa. Genes associated with nitrogen and sulfur metabolic pathways were consistently detected, suggesting the presence of a conserved functional core supporting key biogeochemical processes. In contrast, genes related to antibiotic resistance and virulence factors exhibited more heterogeneous distributions. Among measured physicochemical variables, only nitrate and ferric iron significantly influenced microbial community structure and its functional repertoire, suggesting that additional factors likely contribute to the broader distribution of these communities. These findings reveal a high degree of taxonomic and functional stability of microbial communities in a minimally impacted lagoon, providing a valuable baseline for understanding microbial dynamics in coastal sediments primarily shaped by oceanographic processes.

Wastewater-based surveillance has become a powerful tool for monitoring the spread of pathogens, antibiotic resistance genes, and measuring population-level exposure to pharmaceuticals and chemicals. While surveillance methods commonly target small molecules, DNA, or RNA, wastewater also contains a vast spectrum of proteins. However, despite recent advances in environmental proteomics, large-scale monitoring of protein biomarkers in wastewater is still far from routine. Analyzing raw wastewater presents a challenge due to its heterogeneous mixture of organic and inorganic substances, microorganisms, cellular debris, and various chemical pollutants. To overcome these obstacles, we developed a wastewater metaproteomics approach including efficient protein extraction and an optimized data-processing pipeline. The pipeline utilizes de novo sequencing to customize large public sequence databases to enable comprehensive metaproteomic coverage. Using this approach, we analyzed wastewater samples collected over approximately three months from two urban locations. This revealed a core microbiome comprising a broad spectrum of microbes, gut bacteria and potential opportunistic pathogens. Additionally, we identified nearly 200 human proteins, including promising population-level health indicators, such as immunoglobulins, uromodulin, and cancer-associated proteins.