ISME communications最新文献

As the most abundant marine microorganisms, SAR11 bacteria contribute significantly to global carbon and nutrient cycling. Pelagiphages, viruses that infect SAR11, are potential drivers in structuring the communities, shaping the evolution, and reprogramming the metabolism of SAR11. However, interactions between SAR11 and pelagiphages remain poorly understood. In this study, we investigated and compared the transcriptional dynamics of the SAR11 strain, Candidatus Pelagibacter communis HTCC1062, under independent infection with two phylogenetically distinct pelagiphages: the temperate HTVC019P-type pelagiphage HTVC022P and the lytic HTVC023P-type pelagiphage HTVC027P. These two pelagiphages exhibited distinct infection kinetics, with HTVC022P showing a shorter latent period and a faster host takeover. Transcriptome profiling revealed that infection with HTVC022P and HTVC027P led to the differential expression of 136 and 460 host genes, respectively. Compared to the uninfected control, both pelagiphage infections enhanced host transcription, upregulating the majority of differentially expressed genes. Both pelagiphages induced upregulation of host genes involved in DNA metabolism, transcription, translation, central carbon and nitrogen metabolism. Notably, HTVC027P infection led to the upregulation of 56 genes involved in phosphate, sulfur, and iron metabolism, as well as oxidative phosphorylation and one-carbon metabolism. In contrast, HTVC022P had minimal effects on these pathways. These results suggest that distinct pelagiphages exert unique effects on host metabolic processes, implying divergent ecological implications. Collectively, our study provides new insights into SAR11-pelagiphage interactions, enhancing our understanding of the metabolic states of phage-infected SAR11 bacteria and the ecological functions of phages in marine systems.

The evolutionary adaptation of archaea to ecologically diverse habitats remains poorly understood. Ammonia-oxidizing archaea (AOA) exhibit significant diversification across various environmental conditions; however, their ecological dynamics, diversification, and associated evolutionary processes are still largely unexplored in coastal environments, which contain extensive ecosystem heterogeneity. Combining newly assembled metagenomic data from Chinese marginal seas (2059 km coverage) with global datasets (spanning over 16 000 km), these knowledge gaps were explored across a continental-scale latitudinal gradient. It revealed that coastal AOA genomic diversity is latitude-dependent, with predicted optimum growth temperatures and substrate metabolic pathways explaining the geographical distribution. The two dominant genus-level clades exhibited significantly distinct benthic-pelagic niches, associated with specific genes involved in nutrient uptake and stress resistance. Phylogenomic reconstructions suggest that AOA initially colonized the coastal ocean sediments around 718 million years ago (Mya), and subsequent purifying selection and low recombination facilitated the AOA niche expansion into marine coastal environments. By revealing the evolutionary trajectories of Nitrososphaeria and their differential colonization patterns, our findings offer a novel perspective on the mechanisms of AOA diversification in the coastal ocean. This work advances our understanding of microbial diversification and niche differentiation of AOA in coastal ecosystems as well as the evolutionary forces shaping their global biogeography.

An unbiased and accurate estimation of intraspecies diversity, i.e. the extent of genetic diversity within species (or microdiversity), is crucial for clinical and environmental microbiome studies. Although it is well appreciated that sequencing depth (or coverage depth) below 10X can provide biased estimates of microdiversity, typically underestimating diversity due to the random sampling of alleles, there is a widely accepted convention that microdiversity estimates tend to be relatively stable at sequencing depth exceeding 10X. Therefore, discarding species with <10X or rarefying to 10-20X sequencing depth are generally used to compare microdiversity among taxa and samples. Our findings showed that these biases may persist even at depth levels above 50-200X for all popular sequencing platforms, including Illumina, PacBio, and Oxford Nanopore. The biases mostly, but not always, represent an underestimation of diversity and were attributable to the incomplete recovery of Single Nucleotide Variants (SNVs) at lower sequencing depth levels. To address this issue, we recommend using rarefaction-based approaches to standardize data at least 50X, and ideally at 200X sequencing depth, which reduces differences between observed and expected microdiversity values to <0.5%. Furthermore, the Average Nucleotide Identity of reads (ANIr) metric is significantly less sensitive to sequencing depth variability than nucleotide diversity (π), making it a robust alternative for estimating microdiversity at sequencing depth close or exceeding 10X, without a need to rarefying data. Therefore, the sequencing depth thresholds proposed herein provide a more standardized framework for direct comparisons of microdiversity across samples and studies.

The bacterial-type Wood-Ljungdahl (WL) pathway and reductive tricarboxylic acid (rTCA) cycle are the dominant chemolithotrophic CO₂ fixation pathways in bacteria inhabiting aphotic geothermal and deep-sea hydrothermal ecosystems. However, the activity of these bacterial metabolic systems in ecosystems with available organic carbons remains unclear. Here, we examined the impact of extracellular acetate on the CO₂-fixation pathways of three thermophilic hydrogen-oxidizing and non-acetogenic bacteria using ¹³C tracer-based metabolomics. Under chemolithoautotrophic conditions, Thermodesulfatator indicus and Hydrogenobacter thermophilus fixed CO₂ through the WL pathway and rTCA cycle, respectively, whereas Thermovibrio ammonificans, which has been suggested to operate both of these pathways, exhibited significant CO₂ fixation through only the rTCA cycle. Under chemolithomixotrophic conditions with acetate, H. thermophilus and T. ammonificans assimilated both CO₂ and acetate via the rTCA cycle. In contrast, acetate suppressed CO₂ fixation through the WL pathway in T. indicus and was used as the primary carbon source under chemolithomixotrophic conditions. These results suggest that the contribution of the WL pathway for CO₂ fixation might be overestimated in ecosystems where acetate is available. Moreover, the present findings indicate that simultaneous CO₂ fixation through both the WL pathway and rTCA cycle in a cell, which has been proposed as a possible metabolic strategy for CO₂-fixation in ancestral life, is not advantageous in extant microorganisms.

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.