ISME communications最新文献

Analyzing past ecosystems can improve our understanding of the mechanisms linking biodiversity with environmental changes. Sedimentary ancient DNA (sedaDNA) opens a window to past biodiversity, beyond the fossil record, that can be used to reconstruct ancient environments and ecosystems functions. To this end, modern biodiversity and environmental conditions are used to calibrate transfer functions, that are then applied to past biodiversity data to reconstruct environmental parameters. Doing this with sedaDNA can be challenging, because ancient DNA is often obtained in limited quantities and fragmented into smaller molecules. This leads to noisy datasets, with a low alpha diversity relative to modern DNA, patchy taxa detection patterns and/or skewed relative abundance profiles. How this affects beta-diversity measures, and the performance of transfer functions remain untested. Here we simulated ancient DNA reads counts matrices from synthetic and empirical datasets, and tested 464 combinations of counts transformations (n = 13), beta-diversity indices (n = 16), and ordinations methods (n = 4), and assessed their performance in (i) separating the ecological signal from the noise introduced by DNA degradation and in (ii) predicting ground-truth environmental conditions. Our results show that commonly used workflows in DNA-based community ecology studies are sensitive to the noise associated to ancient DNA signal. Instead, combinations of methods that include more recent ordination methods proved robust to ancient DNA noise and produced better transfer functions. Our study provides a framework for designing postprocessing workflows that are better suited for sedaDNA studies.

Microbial-mediated litter decomposition drives carbon and nutrient cycling. This process can be top-down regulated by microbiome predators, particularly the diverse protists. Size has been suggested to determine predation impacts, but how protists of different size categories affect microbial-mediated litter decomposition remains unknown. Using a litter decomposition experiment with three protist size categories, we investigated protist size-dependent effects on microbial-driven litter decomposition. We found that protists of the large-size category created more structurally similar bacterial communities compared to the no-protist control. These protists of the large size category also reduced litter mass loss by 40%, while increasing microbial respiration by 17% compared to the no-protist control after five weeks of decomposition. In contrast, protists of the small-size category and protists of the medium-size category had no measurable impact on bacterial communities, litter mass loss, or microbial respiration. Random forest analysis identified Streptomyces as a major contributor to litter mass loss (explained 8% of litter mass), while the potential protist symbionts Taonella and Reyranella explained 8% and 6% of microbial respiration, respectively. These likely predation-resistant bacterial taxa were primarily enriched by protists of the large-size category. Our results indicate that protists, especially large ones, can alter litter decomposition by shaping microbiome composition. Future studies on litter decomposition and carbon cycling should incorporate protists and their traits, particularly size, to enhance our understanding of global carbon and nutrient cycling.

Microorganisms associated with insects play crucial roles in mediating the host plant adaptation of their insect hosts. Although oral microbiota are the primary interface with ingested plant material, we still poorly understand their diversity, their function, and their ecological relationship with insect performance. Here, we investigated the diversity and function of the oral microbiota in two generalist lepidopteran pests (Spodoptera litura and Spodoptera frugiperda) feeding across three host plants (bok choy, peanut, and maize). Plant species significantly influenced the diversity and composition of oral microbiota in both S. litura and S. frugiperda. Oral microbial communities from insects feeding on bok choy exhibited significantly higher Sobs richness and Shannon diversity compared to those with peanut or maize plants. Community-level analysis revealed overlapping enriched oral taxa-including Brevibacterium, Staphylococcus, Microbacterium, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Brachybacterium, and Rhodococcus-that were enriched in both insect species when consuming bok choy. In contrast, they accumulated distinct bacterial taxa emerged when feeding on peanut and maize. Microbial ligninolysis capacity within the oral microbiota showed positive associations with leaf lignin content and herbivore performance. This functional trait primarily associated with Brevibacterium and Rhodococcus taxa. Accordingly, two isolated strains, Brevibacterium sedimins OS20 and Rhodococcus sp. OS5 demonstrated effective lignin degradation capacity, achieving 41.01% and 17.62% lignin loss in litter, respectively, after 60 days in microcosm experiments. Overall, host plants shape the diversity and composition of insect oral microbiota. Crucially, microbial ligninolysis capacity and leaf lignin content positively correlated with herbivore performance. This study provides novel insights into the function of oral microbiota in plant-insect interactions, potentially informing the complex multitrophic relationships underlying coevolutionary dynamics.

Harmful algal blooms negatively impact the ecosystem and fisheries in affected areas. Eutrophication is a major factor contributing to bloom occurrence, and phosphorus is particularly important in limiting the growth of bloom-forming algae. Although algae efficiently utilize orthophosphate (Pi) as a phosphorous source over other molecular forms, Pi is often limited in the marine environment. While uptake and utilization of soluble inorganic and organic phosphorous by bloom-forming algae has been extensively studied, the details of geochemical and biological phosphorous cycling remain to be elucidated. Here, we report for the first time that the bloom-forming alga Heterosigma akashiwo can phagocytose bacteria and grow under phosphate-depleted conditions. The addition of Vibrio comitans to Pi-depleted H. akashiwo enabled the alga propagate to high cell densities, whereas other bacterial strains had only a minor effect. Importantly, V. comitans accumulates polyphosphate-a linear polymer of Pi-at high levels. The extent of algal proliferation induced by the addition of Vibrio species and polyphosphate-accumulating Escherichia coli correlated strongly with their polyphosphate content, indicating that bacterial polyphosphate served as an alternative PO₄ ^3- source for H. akashiwo. The direct uptake of polyphosphate-accumulating bacteria through algal phagocytosis may represent a novel biological phosphorous-cycling pathway in marine ecosystems. The role of polyphosphate-accumulating marine bacteria as a hidden phosphorous source required for bloom formation warrants further investigation.

Because accessing the small intestine is technically challenging, studies of the small intestinal microbiome are predominantly conducted in patients rather than in healthy individuals. Invasive clinical procedures, such as endoscopy or surgery, usually performed for therapeutic purposes, are typically required for sample collection. Although stomas offer a less invasive means for repeated sampling, their use remains restricted to patient populations. As a result, the small intestinal microbiome of healthy individuals remains largely understudied. This study evaluated a novel ingestible medical device for collecting luminal samples from the small intestine. A monocentric interventional trial (NCT05477069) was conducted on 15 healthy subjects. Metagenomics, metabolomics, and culturomics were used to assess the effectiveness of the medical device in characterizing the healthy small intestinal microbiome and identifying potential biomarkers. The small intestinal microbiota differed significantly from the fecal microbiota, displaying high inter-individual variability, lower species richness and reduced alpha diversity. A combined untargeted and semi-targeted LC-MS/MS metabolomics approach identified a distinct small intestinal metabolic footprint, with bile acids and amino acids being the most abundant metabolite classes. Host- and host/microbe-derived bile acids were particularly abundant in small intestinal samples. Using a fast culturomics approach on two small intestinal samples, we achieved species-level characterization and identified 90 bacterial species, including five potentially novel ones. This study demonstrates the efficacy of our novel sampling device in enabling comprehensive small intestinal microbiome analysis through an integrative, multi-omics approach. This approach allows distinct microbiome signatures to be identified between small intestinal and fecal samples.

Stony coral tissue loss disease (SCTLD) is a rapidly spreading lethal coral disease, the etiology of which remains poorly understood. In this study, using deep metagenomic sequencing, we investigated microbial and viral community dynamics associated with SCTLD progression in the Caribbean stony coral Diploria labyrinthiformis. We assembled 264 metagenome-assembled genomes and correlated their abundance with disease phenotypes, which revealed significant shifts in both the prokaryotic microbiome and virome. Our results provide clear evidence of microbial destabilization in diseased corals, suggesting that microbial dysbiosis is an outcome of SCTLD progression. We identified DNA viruses in our dataset that increase in abundance in SCTLD-affected corals and are present in existing coral data from other Caribbean regions. In addition, we identified the first putative instance of asymptomatic/resistant SCTLD-affected corals. These are apparently healthy colonies that share the viral profile of diseased individuals. However, these colonies contain a different prokaryotic microbiome than do diseased corals, suggesting microbe-induced resilience (i.e. beneficial microbiome) to SCTLD. Finally, utilizing differential abundance analysis and gene inventories, we propose a mechanistic model of SCTLD progression, in which viral dynamics may contribute to microbiome collapse. These findings provide novel insights into SCTLD pathogenesis and offer consistent molecular signals of disease across diverse geographic sites, presenting new opportunities for disease monitoring and mitigation.

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.