ISME communications最新文献

Bacterial secondary metabolites are a major source of therapeutics and play key roles in microbial ecology. These compounds are encoded by biosynthetic gene clusters (BGCs), which show extensive genetic diversity across microbial genomes. While recent advances have enabled clustering of BGCs into gene cluster families (GCFs), there is still a lack of frameworks for systematically analysing their internal diversity at a population scale. Here, we introduce "PanBGC", a pangenome-inspired framework that treats each GCF as a population of related BGCs. This enables classification of biosynthetic genes into core, accessory, and unique categories and provides openness metrics to quantify compositional diversity. Applied to over 250 000 BGCs from more than 35 000 genomes, PanBGC maps biosynthetic diversity of more than 80 000 GCFs. Our analysis reveals that gene composition reshuffling, rather than acquisition of new genes, is the dominant driver of diversity within GCFs, with most families exhibiting closed gene repertoires but high compositional variability. Additionally, transporter-related domains were commonly identified among core genes, reflecting the fundamental importance of compound export in BGC function. To facilitate exploration, we present PanBGC-DB (https://panbgc-db.cs.uni-tuebingen.de), an interactive web platform for comparative BGC analysis. PanBGC-DB offers gene- and domain-level visualizations, phylogenetic tools, openness metrics, and custom query integration. Together, PanBGC and PanBGC-DB provide a scalable framework for exploring BGCs at population resolution and for contextualizing newly discovered BGCs within the global landscape of secondary metabolism.

Phytoplankton help control the habitability of Earth by serving as the base of marine food webs, producing approximately half of the planet's oxygen, and sequestering carbon dioxide from the atmosphere. As global changes accelerate through the Anthropocene, phytoplankton communities face multiple stressors, such as shifting patterns in ocean circulation, and associated changes in light exposure. The health of the oceans depends on phytoplankton responses to these stressors; however, the physiological processes involved in light stress are not fully understood. Here, we surveyed 16 representative phytoplankton and show that most produce extracellular superoxide, an otherwise damaging reactive oxygen species, as a widespread strategy to acclimate to light stress. Indeed, all species adjusted extracellular superoxide production as a function of light exposure, which was modeled with a modified photosynthesis-irradiance (PI) curve. Furthermore, the flavoenzyme inhibitor diphenyl iodonium (DPI) quenched extracellular superoxide production and led to declines in viability and photosynthetic health in 13 out of 16 species. The negative effect of DPI on photosynthetic health was stronger with increasing light, consistent with inhibition of a photoprotective process. Taken together, these results support the hypothesis that phytoplankton mitigate light stress through enzyme-mediated production of extracellular superoxide. These results imply that daytime rates of biological superoxide production in the marine environment are substantially underestimated by dark measurements. Furthermore, phytoplankton photoacclimation may alter superoxide production rates in future oceans impacted by changes in water column structure and light exposure.

The gut microbiota of wild animals is characterized by both stability and adaptive shifts in composition and prevalence in response to variation in food availability, nutrient intake, host physiology, temperature, and rainfall. Here, over a 12-month period, we investigated seasonal interactions between diet, weather, and gut microbiota in a wild group of Tibetan macaques in Huangshan by recording feeding behavior, monitoring weather, and analyzing 209 fecal samples using plant DNA metabarcoding (trnL region) and 16S rRNA gene sequencing. Based on the field observations and plant DNA metabarcoding, results revealed marked seasonal shifts in plant types and species consumed by Tibetan macaques. Despite dietary variability, only two enterotypes were presented throughout the year and gut microbiota composition exhibited lower dissimilarity within and across seasons compared to diet, except in autumn when low dietary diversity correlated with reduced microbial diversity. In addition, we also found that the enrichment of seasonal indicator bacterial genera and functions was related to the temperature or the nutrients of the food consumed by Tibetan macaques during that season. This study highlights the microbiota's resilience and metabolic plasticity in buffering seasonal dietary shifts, underscoring its role in maintaining host energy homeostasis under fluctuating resource availability.

Sphagnum mosses maintain peatland ecosystem stability through intimate associations with their microbiomes. As the foundational component of these communities, the core microbiome enables ecosystems to resist, absorb, and recover from environmental changes, yet the roles and processes of Sphagnum core members remain poorly understood, particularly in subtropical ecosystems. Here, we identified different components of core microbiomes and found that host-specific and environmental core microbiomes differentially shape the stability and function of Sphagnum phyllosphere bacteria by examining vertical stratification within a litter-Sphagnum-soil system in a subtropical mountain forest. Sphagnum harbors a microbial community that is significantly distinct from its surrounding environment (i.e. litter and soil), with community assembly primarily driven by deterministic processes, whereas litter and soil communities are more strongly shaped by stochastic processes. Sphagnum host-specific core taxa, enriched in carbon- and nitrogen-cycling lineages (i.e. Ca. Eremiobacterota), stabilized microbial composition, whereas environmental core taxa enhanced interaction strength and network robustness, and these groups responded differently to environmental filters (e.g. pH and elevation). Our framework highlights that core microbiomes are not functionally homogeneous, but instead reflect contrasting strategies that collectively shape ecosystem stability.

Microorganisms drive biogeochemical cycling. Therefore, examining environmental change through the lens of microbial ecology is particularly useful for developing a mechanistic understanding of the biogeochemical consequences and feedbacks of perturbations to ecosystems. When aquatic systems with deep anoxic waters undergo eutrophication, the resulting surface productivity impacts the anaerobic microbial community below. The increase in sinking organic carbon can shift the anaerobic community function from inorganic nitrogen (N) loss to N retention, amplifying eutrophication as a positive feedback. However, we lack a mechanistic understanding of this transition, which is critical for anticipating these impacts in aquatic environments where microbial community composition is unknown. Here, we provide a first-principles, quantitative model of this transition from N loss to retention by linking ecological dynamics to the energetics underlying microbial metabolisms. We develop and analyze an ecosystem model in which redox chemistry constrains the traits of key anaerobic N-cycling microbial functional types: denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonium oxidation (anammox). The model captures the transition from N loss to N retention with increasing organic carbon supply, consistent with observations for specific systems and species. Results identify characteristics of the microbial community composition at the "net zero N loss" point at which N loss balances N retention, providing testable hypotheses for sequencing data and other observations. By tying microbial ecological dynamics to environmental chemical potential, results provide a broadly applicable framework for better predicting the biogeochemical impacts of eutrophication, deoxygenation, and other perturbations.

Bacterioplankton communities are characterized by varying distributions of cell size, shape and internal complexity, and macromolecular composition, yet there have been few attempts to quantitatively describe this complex community structure and to assess how it varies among communities and habitats. Here we present a framework to assess this morphological structure, based on the analysis of dot clouds resulting from flow cytometric measurements of side and forward scatter and cell fluorescence of individual bacterioplankton cells. Each community has a characteristic cytometric dot cloud, which forms an ellipsoid that can be described by a combination of metrics that quantify its shape, elongation, volume, orientation, and internal complexity. We apply this framework to assess how the bacterioplankton morphological structure (BMS) varies in 637 lakes distributed across Canada, covering a wide range of limnological, watershed, and climatic features. We show that there is a BMS core, which is characterized by small, simple and oblate shapes, and low overall fluorescence i.e. present in all lakes but is prevalent in oligotrophic lakes with hydrologically less evaporated water and low retention time, likely reflecting mass effects and allochthonous bacterial inputs. We further show that along gradients of increasing network water residence time, system productivity and dissolved organic carbon enrichment, there is a clear succession wherein BMS becomes increasingly dispersed, complex, and prolate shapes, likely reflecting environmental selection of aquatic taxa.

Extracting and directly amplifying DNA from small-volume, low-biomass samples would enable rapid, ultra-high-throughput analyses, facilitating the study of microbial communities where large-volume sample collection is challenging. This can aid where 'conventional' filtrater-based methods miss capturing smaller microbes, or where microscale variability matters, such as the ocean. Here, we develop and validate physical and chemical-based DNA extractions from microvolumes with universal rRNA gene amplicons and metagenomic sequencing of all domains and viruses, on natural surface seawater and experimentally manipulated marine waters. Compared to 500-mL filter-based extraction, direct PCR of 3 μL of lysate from seawater microvolume extractions ranging from 100-1000 μL consistently captured comparable microbial community composition and diversity, with reliable amplification and little to no contamination. Metagenomic results of 10 μL lysates from 15 microvolume samples (100 μL) captured 83 high- and draft-quality, diverse bacterial genomes and 430 complete, high and medium quality viral contigs. Our approach enables scaling of rRNA gene sequencing and metagenomic library prep for high-throughput experimentation for a fraction of the cost of conventional methods and builds upon existing microvolume approaches by removing unnecessary expenses, like excess plasticware and expensive bead clean-up. The method expands opportunities for more comprehensive microbial community monitoring and controlled laboratory experiments by facilitating higher sample numbers and lowering sample volume needs. However, its potential bias against Gram-positive bacteria should be considered when applying to environments where these taxa are abundant.

Environmental microbiota are essential yet often overlooked, with urbanization driving microbial diversity loss and diseases of civilization. Public misconceptions, exacerbated by COVID-19, have widened the gap between microbiologists and society, highlighting the need for science-society integration. The Bicocca Sampling Days (BSDs) model offers a reproducible "citizen science" framework integrating research, education, and public engagement through large-scale microbiome sampling. Tested while assessing environmental microbiomes in different urbanized outdoors, 76 undergraduates participated in four sampling events, collecting 2429 samples in 8 h of effective sampling, achieving over than 303 samples/hour in 29 288.74 m². Manual metadata curation revealed only 0.58% critical errors and no data loss, emphasizing the effectiveness of structured submission forms in ensuring data quality. Educational outcomes, assessed through a validated survey, significant gains in participants' perceived skills, understanding, and knowledge of microbiome sampling compared to non-participants. The BSDs model, including a step-by-step guide, illustrated protocol, and templates, is freely available for replication. Our findings demonstrate that citizen science can rival or complement traditional microbiome research in efficiency, scale, and data quality while broadening accessibility. BSDs offers a scalable tool to advance educational and societal, empower participation, and support informed decision-making.

Nucleocytoplasmic large DNA viruses (NCLDVs), also called giant viruses, are widespread in marine systems and infect a broad range of microbial eukaryotes (protists). Recent biogeographic work has provided global snapshots of NCLDV diversity and community composition across the world's oceans, yet little information exists about the guiding "rules" underpinning their community dynamics over time. We leveraged a five-year monthly coupled metagenomic-viromic time-series to quantify the community composition of NCLDVs off the coast of Southern California and characterize their temporal population dynamics. NCLDVs were dominated by Algavirales (Phycodnaviruses, 59%) and Imitervirales (Mimiviruses, 36%). We identified clusters of NCLDVs with distinct classes of seasonal and nonseasonal temporal dynamics. Overall, NCLDV population abundances were often highly dynamic, showing strong seasonal signals. The Imitervirales group had the highest relative abundance in the more oligotrophic late summer and fall, while Algavirales did so in winter. Generally, closely related strains had similar temporal dynamics, suggesting that evolutionary history is an important driver of the temporal niche partition of marine NCLDVs. However, a few closely-related strains had drastically different seasonal dynamics, suggesting that while phylogenetic proximity often indicates ecological similarity, occasionally phenology can shift rapidly, possibly due to host-switching. We also identified distinct functional content and possible interactions of two major NCLDV orders with diverse eukaryotes in the study environment- revealing their putative hosts that include both primary producers and heterotrophic grazers. Together, our multiannual time-series study captures diverse temporal patterns among marine giant viruses and demonstrates that evolutionary history plays a key role in shaping their temporal niche partitioning.

Diel light cycles profoundly influence estuarine biogeochemical processes, yet the mechanistic responses of planktonic prokaryotic communities to these rhythmic cues remain incompletely understood. This study employed an integrative multi-omics approach-combining high-frequency sampling, 16S rRNA gene sequencing, metagenomics, and metatranscriptomics-to elucidate diel dynamics in microbial diversity, interaction networks, and metabolic functions in the Pearl River Estuary. The results revealed significant temporal partitioning in microbial organization: nocturnal communities exhibited higher α-diversity and formed more densely connected co-occurrence networks, indicative of enhanced heterotrophic processes, whereas daytime assemblages were dominated by Cyanobacteria (particularly Synechococcales) with enriched pathways for photoautotrophic carbon fixation and nitrogen assimilation. Metabolic profiling further demonstrated distinct diel oscillations in key biogeochemical processes, including daytime enhancement of Calvin cycle-mediated CO₂ fixation and nocturnal upregulation of dissimilatory sulfate reduction. Network topology analysis showed that nighttime communities displayed increased clustering coefficients and reduced path lengths, suggesting more efficient resource utilization under dark conditions. Through reconstruction of 786 metagenome-assembled genomes, we identified Cyanobiaceae as key mediators of diel carbon and nitrogen transformations, while diverse heterotrophic taxa facilitated nighttime nutrient remineralization. This study provides mechanistic insights into how light-driven diel oscillations shape microbial metabolic partitioning and ecological interactions, advancing our understanding of the temporal dynamics that underpin biogeochemical resilience in estuarine ecosystems.