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[This corrects the article DOI: 10.1093/ismeco/ycaf063.].
[This corrects the article DOI: 10.1093/ismeco/ycag013.].
[This corrects the article DOI: 10.1093/ismeco/ycae108.].
[This corrects the article DOI: 10.1093/ismeco/ycaf143.].
Bifidobacterium species and strains are key members of the human gut microbiota, appearing soon after birth and persisting into adulthood. Resistant starch is an important dietary substrate for adult-associated bifidobacteria, where its fermentation supports host health. However, less is known about how different starch structures interact with bifidobacteria. Here we show that growth kinetics and gene expression differ depending on starch structure. Using detailed growth assays, genomics, and metabolomic analyses, bifidobacterial starch hydrolysis capabilities were closely associated with their CAZyme profiles. In one isolate of Bifidobacterium globosum, we identified a gene cluster encoding three multi-functional amylase enzymes complemented by several starch-binding modules, the genes and proteins of which were significantly upregulated in response to starch. Homologs of genes in the cluster were found in the genomes of bifidobacterial isolates from weaning infants providing insights into their role in the maturation process of the microbiota. Uncovering mechanisms of metabolic interaction between starch structures and bifidobacteria underscores the importance of this ecological function and potential health implications.
Prochlorococcus is the most numerically abundant photosynthetic organism in the oligotrophic ocean; yet, it is vulnerable to damage by the reactive oxygen species (ROS) hydrogen peroxide (H2O2). Detoxifying microbes and abiotic decay are thought to mitigate the most harmful impacts of H2O2, but the ecological impacts of ROS on ocean microbial community composition are not fully understood. Here, we introduce ROS dynamics within a resource competition model to investigate H2O2 impacts on a community with one catalase negative Prochlorococcus analogue, one catalase positive Synechococcus analogue, and a heterotrophic bacterium. Model parameters defining resource utilization, H2O2 detoxification, and H2O2-mediated cell death are constrained with data from laboratory experiments. With these ecologically realistic parameter values, we investigate the community composition for a range of ammonium and H2O2 supply rates. In the absence of a heterotrophic bacterium, Synechococcus' modest ability to detoxify H2O2 facilitates the survival of Prochlorococcus under conditions that would otherwise be fatal. However, in the absence of a strong bacterial detoxifier, unrealistically high Synechococcus concentrations (>106 mL-1) are required for it to coexist with Prochlorococcus on a single limiting nutrient. Coexistence among Prochlorococcus and Synechococcus at ecologically realistic cell densities and H2O2 concentrations is observed when heterotrophic bacteria with high detoxification rates reach cell densities on the order of 105 cells mL-1. Our analysis suggests that environmentally relevant ROS concentrations have the potential to determine whether Prochlorococcus and Synechococcus coexist on ammonium and points to the importance of ROS supply and degradation for understanding marine cyanobacteria ecology.
Northern peatlands store approximately one-third of all terrestrial carbon, making their belowground microbial communities key regulators of peatland carbon cycling and climate feedbacks. We examined how climate drivers alter microbial community composition across peat and porewater habitats over a 0-200 cm depth profile by leveraging the SPRUCE (Spruce and Peatland Responses Under Changing Environments) experiment. SPRUCE uses whole-ecosystem warming to simulate temperature increases from 0°C to +9°C above ambient as well as elevated carbon dioxide (CO₂) treatments. Through small subunit ribosomal ribonucleic acid amplicon sequencing, we found significant differences in taxonomic diversity, abundance, and community composition between attached (peat) and free-living (porewater) microbial assemblages. Porewater communities exhibited significantly higher microbial diversity, lower abundance, and were more responsive to ecosystem-level manipulations (warming and CO₂) than their peat counterparts. The relative abundance of putative methane-cycling microorganisms, methanogens, and methanotrophs was comparable in surface peat and porewater, but at deeper depths, methanotrophs were far more abundant in porewater. Additionally, warming more strongly stimulated putative methanotrophs than methanogens, particularly in porewater, resulting in a more abundant methanotrophic community across all depths. Our results show that peat and porewater habitats harbor distinct microbial communities that respond differently to climate change drivers. The distinct nature of porewater communities, particularly the observed dynamics of methanotrophs, underscores their role in peatland carbon cycling and highlights their potential as sensitive indicators of environmental change, with significant implications for peatland restoration and carbon management in a changing climate.
Primer bias in 16S rRNA gene amplicon sequencing can distort microbial diversity estimates by underrepresenting key taxa. We introduce a modified primer pair (V4-EXT) targeting the hypervariable V4 region of bacterial and archaeal 16S rRNA genes, with improved in silico taxonomic inclusivity. To benchmark performance, we analyzed 938 samples from terrestrial, aquatic, and host-associated habitats, comparing microbial community profiles derived with V4-EXT and the currently most widely used V4-targeted primers. V4-EXT substantially improved the detection of Patescibacteria and other underrepresented lineages, such as Chloroflexi and Iainarchaeota, while enhancing recovery of novel amplicon sequence variants across sample types. Overall, V4-EXT provides broader taxonomic coverage and more inclusive microbial community profiles, particularly in high-diversity ecosystems such as groundwater and soils. We propose V4-EXT as a robust successor for comprehensive microbial community analysis across diverse habitats.
Deep-sea hydrothermal vents are archetypal chemosynthetic ecosystems, yet the intense geothermal near-infrared (NIR) radiation emitted by black smoker chimneys remains a largely unexplored environmental factor. While infrared (IR)-driven photosynthesis has been described in vent-associated bacteria, whether deep-sea eukaryotes can biologically respond to geothermal NIR radiation has remained unknown. Here, we demonstrate that the vent yeast Rhodotorula mucilaginosa F-J1 exhibits wavelength-specific growth stimulation under NIR exposure through a previously unrecognized mitochondria-centered metabolic response. NIR exposure significantly enhanced growth beyond the effects of glucose supplementation and reduced the apparent activation energy for growth, consistent with enhanced cellular metabolism. Mechanistically, targeted inhibition and ultrastructural analyses identified mitochondrial oxidative phosphorylation and mitochondrial ribosomal activity as essential components of this response. Proteomic and heterologous expression analyses further identified the mitochondrial ribosomal protein MRPS18b as a key mediator of NIR-stimulated growth. These findings reveal a previously unrecognized capacity of deep-sea eukaryotic microbes to biologically respond to geothermal IR radiation and expand the known energetic framework of hydrothermal vent ecosystems beyond canonical chemosynthesis and photosynthesis.
Microbial communities play a fundamental role in lake nutrient cycling, yet their composition and functional diversity in response to environmental gradients remain poorly understood. Specifically, little is known about how the supply of dissolved macronutrients, including inorganic and bioavailable organic fractions, shape microbial community structure, and functional diversity in lakes that are strongly subsidized by terrestrial inputs. Boreal lakes, with varying concentrations of total and bioavailable dissolved organic carbon (DOC), nitrogen (N) and phosphorus (P), provide an ideal setting to investigate these dynamics. Here, we hypothesize that microbial pathways related to N and P acquisition, as inferred from marker-gene data, are more represented under relative deficiency of available N and P resources, respectively. To test this, we analysed the rRNA-inferred microbial community composition and metabolic functional diversity across 34 south-Swedish lake outlets in relation to bioavailable nutrient supply. Results show that DOC and P were key drivers of microbial community structure, with bulk DOC concentrations being most relevant for bacteria (16S rRNA), while bioavailable fractions of DOC and P were relatively more influential for eukaryotic communities (18S rRNA). Predicted N- and P-related metabolic pathways correlated with nutrient ratio imbalances, supporting our hypothesis that microbial communities adjust their metabolic strategies in response to relative nutrient demand. These findings demonstrate that accounting for nutrient ratios and bioavailability, in addition to bulk concentrations, helps provide an improved mechanistical understanding of microbial functional potentials in lakes.
Conifers are a challenging host for herbivores since their tissues are very low in essential nutrients but high in chemical defenses. For herbivorous insects, such as phloem-colonizing bark beetles, mutualistic fungi may improve their diet by providing a nutritious mycelium. A recent study revealed that two filamentous fungi are mutualists of the European fir engraver beetle Pityokteines vorontzowi, but a potential nutritional contribution of the fungi, as well as their capability to degrade plant antiherbivore defenses remains unknown. We analyzed the nutrient content of the fungal mutualists Ophiostoma piceae and Geosmithia sp. F1 and examined their ability to degrade the constitutive chemical defenses of silver fir phloem in comparison to other fungi. Both mutualists turned out to be rich in amino acids, sugars, and B vitamins and were found to efficiently deplete their phloem media of several defenses. Strikingly, O. piceae not only accumulated the highest amounts of the B vitamin nicotinic acid of the 17 tested fungi but also showed a high ability to deplete its medium of chemical defenses, similar to the behavior of the Ips typographus mutualist Endoconidiophora polonica. Beetle-vectored, non-mutualistic fungi isolated from P. vorontzowi showed similar capacities to deplete defensive compounds, whereas non-fir-associated fungi were less effective in reducing their concentrations in the phloem medium. The nutritious mycelium of O. piceae and Geosmithia sp. F1 and the ability of these fungi to deplete the medium of major fir defense compounds likely facilitates the colonization of silver fir phloem by P. vorontzowi.
[This corrects the article DOI: 10.1093/ismeco/ycaf009.].
Long-term changes in phytoplankton communities are key to understanding and predicting ecosystem responses to climate-driven circulation change. By analyzing sedimentary ancient DNA from two sediment cores in the Yellow Sea, we reconstructed mid-late Holocene phytoplankton dynamics during the intensification of the Yellow Sea Warm Current (YSWC). We found that phytoplankton communities differed significantly between sites, with stronger spatial differentiation in eukaryotes than in cyanobacteria. Dinoflagellates and chlorophytes dominated overall, while Dictyochophyceae (silicoflagellates) were unexpectedly abundant relative to diatoms. Phylogenetic reconstruction recovered diverse Dictyochophyceae lineages (two orders, six genera) dominated by Pseudopedinella, indicating greater regional diversity than previously recognized. The cyanobacterial assemblages comprised SIO2C1, UCYN-A, and PCC-6307 lineages. Following the intensification of the YSWC since ~3 ka BP, eukaryotic community structure shifted in the central basin. 18S rRNA gene abundance increased, whereas diversity and silicifier-to-dinoflagellate ratios declined. Although the absolute age of core B07 remains tentative, a pronounced stratigraphic turnover occurred in the frontal zone around 100 cmbsf, with a shift from chlorophyte to dinoflagellate dominance, consistent with reduced freshwater influence and an enhanced YSWC impact. Numerous indicator species exhibited contrasting abundance patterns before and after these transitions. These findings demonstrate the sensitivity of coastal phytoplankton to circulation-driven regime shifts.
Plastics have been shown in incubation experiments to select for distinct microbial communities from biogenic and inanimate controls, with successional shifts over time. However, few field studies have directly compared microbial communities on free-drifting plastic debris and non-plastic particles. Using shotgun metagenomics, we analyzed the microbial communities adhered to marine microplastics and co-drifting volcanic pumice as a time-tracked control to investigate differences in metabolic potential. Overall, the mature microbial communities on neuston-net collected microplastics and pumice exhibited broad functional and taxonomic similarity, providing suggestive evidence of function convergence. Interestingly, plastic hydrolysis genes, and putative hydrocarbon-degrading bacteria were scarce on both substrates, whereas β-glucan degradation genes were abundant, indicating potential utilization of biofilm-associated carbon sources. Nevertheless, pumice biofilms exhibited substrate-associated enrichment of genes linking to biofilm formation, quorum sensing, nitrogen and phosphonate metabolism, suggesting expanded genomic versatility. Considering the increasing input of anthropogenic and natural inanimate particles may act as environmental perturbations, potentially shaping microbial succession and metabolic potential on floating surfaces. Our findings provide insight into the genomic potential of particle-associated assemblages that stay afloat for months to years, and their metabolic responses to both natural and anthropogenic perturbations.
Biotic interactions, including competition among bacteria mediated by phage-derived weapons, can profoundly shape microbial genomes. We found that compared to genomes across domain Bacteria, genomes from the animal-associated Xenorhabdus genus contain among the highest proportions of phage-related genes, and variation among strains in their total number of protein-coding genes was largely predicted by variation in total number of non-cargo phage genes per genome. A universal yet highly variable Xenorhabdus phage-related locus encoded xenorhabdicin tailocins, a key weapon in bacterial competition. The xenorhabdicin tailocin locus ranged in length from 12 to 41 kilobases and varied markedly within species. Concomitant with this variation, xenorhabdicins produced by six strains of X. nematophila differed in killing profiles towards each other. Mutants from two X. nematophila strains whose tailocin tail fibre genes were deleted lost their killing ability, while complementation experiments restored or shifted killing profiles, demonstrating that the tailocin locus is responsible for intraspecific killing and the tail fibre gene its specificity. We demonstrated the ecological importance of xenorhabdicin diversity by significantly associating broad differences in intraspecific killing profiles of mitomycin-induced cell lysates from 37 regionally sympatric X. bovienii strains with genes within the tailocin locus. The diversity of these genes and their rearrangements within the locus challenges our understanding of tailocin mechanics. We propose that frequent coinfection of insect hosts by multiple Xenorhabdus strains promotes strong selection for within-host competitive dominance as well as opportunities for genomic rearrangements, making this genus a valuable resource for examining bacterial evolution in an ecological context.
The soil matrix is a heterogeneous mixture composed of aggregates-three-dimensional complexes composed of organic materials and mineral particles. Soil aggregates vary considerably in physical and chemical properties by size, making them unique habitats for distinct microbial communities and metabolic pathways. Yet, this microscale spatial variability is often overlooked in studies that use homogenized soil cores. We investigated the microbial taxonomy, functional gene composition, and metabolic products observed in four aggregate size fractions ranging from 8 mm to free particles (below 53 μm) collected from agricultural soils under two different management practices. The functional gene composition differed significantly among aggregate sizes, with higher abundances of genes for the degradation of plant-derived compounds in the macroaggregates and for biomass recycling in the two smallest size fractions. These differences were corroborated by significant differences in the composition of the metabolome but not in specific enzyme activities. Both taxonomic profiling and reconstruction of genomes from metagenomes revealed a higher abundance of ammonia-oxidizing archaea in the macroaggregates in comparison to other aggregate sizes, and analysis of their genomes revealed complementary metabolisms potentially enabling them to colonize different niches within the same habitat. Together, our results show that soil microbial communities and their functions are shaped by the size of soil aggregates, likely driven by differences in resource availability between macro- and microaggregates.
Extreme anoxic environments are hotspots of sulfur cycling and harbor numerous novel uncharacterized microbial lineages. Although the phylum Joyebacterota was recently proposed, its internal phylogenetic architecture and evolutionary adaptations remain poorly understood. Here, we significantly expand the genomic diversity and metabolic framework of this phylum by integrating recovered metagenome-assembled genomes, and propose a novel genus, Cavimicrobium. Phylogenomic analysis placed Cavimicrobium as a distinct clade and further divided into four species-level subgroups associated with diverse anoxic sources, including sediments from the Salton Sea, the Eastern Gotland Basin, and the anoxic waters of the Sansha Yongle Blue Hole (SYBH). Unlike previous broad surveys, our study revealed that this lineage evolved from a facultatively anaerobic ancestor and underwent adaptive gene gain and loss through phylogenetic reconstruction. Genomic evidence suggested that this lineage harbored a previously overlooked anaerobic sulfite reduction (asrABC) pathway that likely mediating thiosulfate uptake and conversion to sulfite and sulfide. Notably, Cavimicrobium was particularly abundant in the anoxic waters of SYBH, comprising up to one-third of the bacterial community in particle-associated fraction below 100 m, where it is likely a major contributor to sulfide accumulation. Analysis of MAGs and global amplicon datasets revealed that Cavimicrobium is widespread across anoxic environments, comprising up to 0.32% of the bacterial community in 354 200 publicly available 16S rRNA gene amplicon samples. Together, these findings reveal a new lineage dominant in certain anoxic environments where they are likely important mediators of sulfur cycling, and broaden our understanding of biogeochemical potential of Joyebacterota.
Members of the bacterial phylum Bacteroidota inhabit diverse ecosystems, yet environmental species remain poorly understood compared to clinically relevant ones. Although Bacteroidota are dominant in crop-associated microbiomes, the mechanisms enabling them to thrive in plant and soil environments remain unclear. A key obstacle in understanding gene fitness in Bacteroidota is the lack of genome-wide functional studies, largely due to their inherent resistance to antibiotics, which hinders genetic manipulation. Here, we applied randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) to measure gene fitness in a plant-associated Bacteroidota, Mucilaginibacter yixingensis YX-36. Our data sheds light on pathways involved in rhizosphere colonization, gliding motility, stress tolerance, and carbon metabolism. Notably, we found that phylum-specific genes such as polysaccharide utilization loci and carbohydrate-active enzymes are needed for fitness in the plant niche. Overall, this work advances our understanding of gene functions in environmental Bacteroidota species and provides a foundation for future research on their roles in plant-microbe interactions.
Insect symbionts play essential roles in host biology, influencing nutrition, immunity, reproduction, and environmental adaptation, ultimately shaping insect physiology, ecology, and evolution. With the rapid growth of functional and genomic datasets on insect symbionts, there remains a critical need for a dedicated platform to systematically compile, organize, and analyze these datasets from an integrative ecological perspective. Here, we developed an insect Symbiont database, named as iSymBase, by manually curating functional records and genomic datasets of insect symbionts from published academic literature. Currently, iSymBase contains over 2657 insect symbiont functional records spanning 795 host species, along with 1494 metagenomes, 14 992 amplicon datasets, and standardized genome and gene catalogs, providing a comprehensive resource for ecological and comparative insect symbiont researches. iSymBase offers standardized query functionalities, such as data browsing, keyword associative search, sequence alignment, data download, and submission. Beyond conventional database functionalities, iSymBase provides several innovative tools: insect-symbiont interaction network for host-symbiont ecological relationships, a batch annotation tool for detecting ecologically functional symbionts from microbiome profiles, and an artificial intelligence (AI)-powered chatbot iSymSeek designed to assist researchers with related knowledge queries. Taken together, iSymBase will serve as an open-access and continually updated platform for storing, querying, and analyzing insect symbiont data, supporting ecological exploration of host-symbiont interactions, symbiont functional diversity, and microbiome-driven adaptation. Database URL: http://symbiont.insect-genome.com/.
Microbes frequently navigate the environment with the help of small, excreted metabolites. Iron-binding molecules called siderophores are one such set of secondary metabolites that are commonly used by microbes to access the essential trace element iron. Although many marine microbes produce siderophores, a substantial number, including the highly abundant SAR11 clade of Pelagibacterales, do not and it has remained unclear whether such nonproducers can access siderophore-bound iron. Here, we show that iron-limited SAR11 cultures fail to grow in the presence of the hydroxamate siderophore ferrichrome but exhibit robust growth in the presence of the catechol siderophore enterobactin. We confirm that this is linked to iron availability using transcriptomic and 55Fe radio tracer uptake experiments. This phenotype can be explained by the relative lability of enterobactin-bound iron in seawater, a phenomenon that has been previously observed in field studies and which we demonstrate with a simple kinetic model. Further experiments with the marine heterotrophs Phaeobacter inhibens and Vibrio harveyi suggest that enterobactin-Fe is unlikely to support the faster growth rates of these organisms without the use of biochemical uptake mechanisms. Overall, our work provides a model of siderophore use that considers bioavailability conferred through both kinetic and biochemical mechanisms and shows that some catechol-bound Fe may be widely available to small, slow growing marine organisms.