ISME communications最新文献

Phaeobacter are marine alphaprotebacteria capable of producing a potent antibacterial compound, tropodithietic acid. Here we demonstrate that they are part of the microbiome of marine bryozoans where they during warmer months reach 10⁵ CFU/g. The levels exhibited a bimodal fluctuation, in both bryozoans and seawater across seasons. However, the population of Phaeobacter sp. was already established in the bryozoans prior to the peak in seawater and did not accumulate as a function of filter feeding on phytoplankton biomass, suggesting that the seawater population is likely seeded from the bryozoan-associated Phaeobacter sp. population rather than the opposite. By comparing whole-genome sequences of more than 100 bryozoan-associated Phaeobacter isolates sampled over a 12-year period, we found that all belonged to the same novel species and no systematic genetic changes occurred within it over the 12 year sampling period despite the fact that the population oscillated from below the limit of detection and across five orders of magnitude to 5.2 Log₁₀ CFU g^-1 bryozoan within individual years and hence were subject to drift. All isolates had the genetic capacity to produce tropodithietic acid (TDA) and the algicidal compounds, roseobacticides. The genes encoding the enzymes for TDA biosynthesis remained stable over time, indicating a conserved phenotype important in the ecophysiology of the bacteria. TDA biosynthetic genes were actively transcribed within the bryozoan host further corroborating the notion that the secondary metabolites of this novel host-associated Phaeobacter sp. may be central to its role within the bryozoan microbiome.

The deep biosphere encompasses life beneath the Earth's surface and constitutes a substantial portion of the planet's microbial biomass. This study analyzed nucleic acid datasets from low-carbon and low-energy deep terrestrial subsurface groundwaters across four continents and revealed four core global populations. These populations exhibited metabolic strategies and adaptations reflecting depth and environmental constraints. Erythrobacter featured heterotrophic metabolism; Thiobacillus demonstrated sulfur oxidation coupled to denitrification along with carbon and nitrogen fixation; Methanobacteriaceae were methanogenic autotrophs using the Wood-Ljungdahl pathway (WL); and Candidatus Desulforudis audaxviator functioned as a sulfate-reducer also encoding the WL pathway. Depth-related adaptations suggested heterotrophic dominance at shallower depths with increasing contributions from autotrophy with depth. Finally, comparative genomics revealed minimal evolutionary changes among these populations, suggesting functional conservation since diverging from their ancestral lineages. These findings underscore a global deep biosphere core community.

A major barrier for most fungal species to infect humans is their inability to grow at body temperature (37°C). Global warming and more frequent extreme heat events may impose selection pressures that allow fungal adaptation to higher temperatures. As fungi adapt to warmer environments, they may overcome the thermal barrier that limits infection of warm-blooded hosts, including humans. Cities are heat islands that are up to 8°C warmer than their suburban counterparts and may thus be an important reservoir of thermotolerant fungi that inhabit environments near humans. Here, we describe a novel and inexpensive technique to collect fungal samples from various sites in Baltimore, MD using commercially available taffy candy. Our results show that fungal isolates from warmer neighborhoods show greater thermotolerance and lighter pigmentation relative to isolates of the same species from cooler neighborhoods, suggesting local adaptation. Lighter pigmentation in fungal isolates from warmer areas is consistent with known mechanisms of pigment regulation that modulate fungal temperature. The opportunistic pathogen Rhodotorula mucilaginosa from warmer neighborhoods had a higher resistance to gradual exposure to extreme heat than those from cooler neighborhoods. Our results imply fungal adaptation to increased temperatures in warmer areas of cities. The acquisition of thermotolerance poses a potential risk for humans, as it is necessary for fungal survival within humans.

Food webs govern interactions among organisms and drive energy fluxes within ecosystems. With an increasing appreciation for the role of symbiotic microbes in host metabolism and development, it is imperative to understand the extent to which microbes conform to, and potentially influence, canonical food web efficiencies and structures. Here, we investigate whether bacteria and their taxa and functional genes are compositionally nested within a simple model food web hierarchy, and the extent to which this is predicted by the trophic position of the host. Using shotgun and amplicon sequencing of discrete food web compartments within replicate tank bromeliads, we find that both taxonomy and function are compositionally nested and largely mirror the pyramid-shaped distribution of food webs. Further, nearly the entirety of bacterial taxa and functional genes associated with hosts are contained within host-independent environmental samples. Community composition of bacterial taxa did not significantly correlate with that of functional genes, indicating a high likelihood of functional redundancy. Whereas bacterial taxa were shaped by both location and trophic position of their host, functional genes were not spatially structured. Our work illustrates the advantages of applying food web ecology to predict patterns of overlapping microbiome composition among unrelated hosts and distinct habitats. Because bacterial symbionts are critical components of host metabolic potential, this result raises important questions about whether bacterial consortia are shaped by the same energetic constraints as hosts, and whether they play an active role in food web efficiency.

Understanding the spatial dynamics of plant-associated microbial communities is increasingly urgent in the context of habitat loss and the biodiversity crisis. However, the influence of reduced habitat size and connectivity on the assembly mechanisms underlying microbial associations is fundamental to advancing microbial ecology and conservation. In the Brazilian Amazon, we investigated nitrogen-fixing (diazotrophic) bacterial communities associated with two epiphyllous liverworts, Cololejeunea surinamensis and Radula flaccida, across 11 forest sites within the Biological Dynamics of Forest Fragments Project landscape. Using amplicon sequencing targeting the nitrogenase gene (nifH), we characterized diazotroph community diversity, inferred assembly mechanisms through null models, and analyzed co-occurrence network structure. Host-specific associations were evident: C. surinamensis predominantly hosted Hassallia, while R. flaccida was primarily associated with Fischerella. Despite habitat fragmentation, diazotrophic richness and composition remained similar across habitats of different sizes, consistent with strong homogenizing dispersal. Network analyses revealed that smaller fragments harbored more modular communities with fewer module hubs, pronounced shifts in key species relative abundance, and reduced network robustness. Our findings underscore the influence of habitat size on the stability of liverwort-associated diazotrophs, with smaller fragments exhibiting lower key species specificity and disruption of microbe-microbe interactions. Our results emphasize the importance of conserving large, connected forest habitats to maintain the functional integrity of phyllosphere N-fixing microbiota.

The rapid advancement of technologies and methods in the life sciences has significantly increased the availability of big data, presenting new challenges for its analysis. Microbiome datasets, in particular, are characterized by extensive feature sets with defined but complex hierarchical structures that are often overlooked or underutilized. Here we introduce a novel metric, UniCor, to identify UNIquely CORrelated eNtities (UNICORNs) in quantitative datasets associated with continuous target variables. These datasets may include microbiome community structures in relation to environmental factors (e.g., temperature, pH, salinity) or biotic variables (e.g., thermal tolerance, oxidative stress). The UniCor metric combines the uniqueness of a given feature within a dataset with its correlation to a target variable of interest. To further enhance its utility, we developed a propagation algorithm (UniCorP), which exploits inherent dataset hierarchies, such as taxonomic levels in microbiome datasets, by selecting and propagating features based on their UniCor metric. Using bacterial community datasets with hierarchical taxonomic annotations and various continuous environmental variables, we demonstrate the ability of the novel metric to reduce features and increase predictive performance in cross-validated Random Forest Regressions. After propagating features with UniCorP and enriching the hierarchical levels with UNICORNs, the predictive performance consistently outperformed control trials for taxonomic aggregation, even at the least granular hierarchical level, allowing a substantial reduction of the feature space. We also compared the metric to existing methods for feature aggregation, showing that it offers stable, competitive predictive performance and feature reduction, within a simple and adaptable framework.

Diatoms, a diverse and abundant group of microalgae, play a crucial role in the functioning of rivers, and are widely used as indicators of ecological quality. This microalgae group has an intraspecific genetic diversity that is poorly understood on a global scale. We examined their genetic diversity using metabarcoding data from Nordic to Equatorial rivers (n = 1103 samples). Notably, 61% of genetic variants were endemic to a single climate zone, including 33% from the Equatorial zone. Looking at the genetic diversity within species, one third of the species showed geographic pattern between climate zones and the phylogenetic structure of their communities indicated that they were shaped by environmental filtering. Another third showed no geographic pattern, and their communities were in majority shaped by neutral processes. A final group was between these two situations. Interestingly, no geographic pattern was observed within the same climate zones, even in regions over 10 000 km apart. We conclude that the numerous species showing allopatric diversification between climate zones, would deserve to be separated into new species to improve diatom-based biomonitoring tools. For future studies, expanding geographical sampling coverage, together with using multi-markers or metagenomes approaches would enable to go beyond these results.

Interkingdom interactions are crucial for community and ecosystem function; however, the secondary metabolites mediating interactions between plant beneficial bacteria and fungi remain understudied. Beneficial Penicillium and Bacillus species can individually suppress soilborne phytopathogens and promote plant growth. Here, we showed that Penicillium hordei and Bacillus subtilis co-culture led to precipitation of B. subtilis lipopeptides, observed as white lines in agar. Metabolomic analysis revealed that the presence of B. subtilis enhanced the production of fungal terrestric acid and its biosynthetic intermediates, which in turn induced lipopeptide precipitation, preventing P. hordei inhibition through chemical inactivation and physical barrier formation. Besides lipopeptide precipitation, terrestric acid-mediated acidification progressively reduced production of antifungal plipastatins. The lack of lipopeptide production permitted P. hordei to invade and overgrow the B. subtilis colony. We demonstrated that the white line phenomenon was conserved among closely related fungi via secretion of terrestric, fulvic, or barceloneic acids. Furthermore, terrestric acid at specific concentrations acted as a universal metabolite that drives B. subtilis lipopeptide precipitation even in distantly related fungi. This study provides new insights into acidification as a fungal defensive strategy that may promote co-existence with beneficial bacteria exhibiting strong antagonistic potential, thereby contributing to the formation of a stable rhizosphere community.

Blastocystis is a prevalent gut eukaryote intricately associated with the gut microbiota. This genetically diverse protozoan exhibits significant intra-host subtype heterogeneity, yet the implications of this diversity for the host gut microbiome remain poorly understood. Here, we investigated the interactions between Blastocystis and gut microbiota in non-human primates at the level of subtypes, using a comprehensive investigation of gut microbiota for Blastocystis carriers of captive Macaca fascicularis (discovery cohort, n = 100) and Macaca mulatta (validation cohort, n = 26). We identified highly prevalent intra-host co-occurrence patterns of Blastocystis SSU rRNA-based subtypes, primarily dominated by Subtype 1 (ST1) or ST3. These patterns were associated with compositional and structural variations in the gut microbiome but were not significantly influenced by host covariates such as sex, age, or BMI. Specifically, Ruminococcaceae-enterotype was enriched in the patterns dominated by ST1, whereas Limosilactobacillus-enterotype was predominantly identified in the patterns dominated by ST3. Variance partitioning and mediation analyses revealed that the absolute abundance of Blastocystis was a critical determinant in elucidating this microbiota association across subtype concurrent patterns. In vivo experiments in a new cohort (n = 11) demonstrated that lactic acid bacteria, enriched in the Limosilactobacillus-enterotype, were sufficient to reduce Blastocystis load. We validated the strong association between gut microbiome composition and Blastocystis load in M. mulatta, confirming that specific microbial features could quantitatively predict Blastocystis status in both species. These findings highlight the close links of the gut microbiome with within-host subtype diversity patterns and absolute abundance of Blastocystis.

Unveiling the soil biological communities ecologically associated with crop wild progenitors (CWPs) in their habitats of origin is essential for advancing productive and sustainable agriculture. A field survey was conducted to investigate the edaphoclimatic conditions and soil bacterial, fungal, protist, and invertebrate communities of 125 populations of direct progenitors of major crops for world agriculture. The wild populations clustered into four ecoregions shaped by two edaphoclimatic dimensions: one summarizing variations in soil sand contents and nutrients concentrations, and the other featuring changes in aridity, soil pH, and carbon storage potential. We identified a common soil core community across CWPs that varied significantly along deserts to tropical seasonal forests and savannas. The assembly of the soil core community was driven by varying environmental preferences amongst soil biodiversity kingdoms, reflecting potential shifts in their functional profiles. The tropical ecoregion exhibited higher proportion of acidophilic bacteria, fungal, and protist parasites, whilst desert ecosystems harboured greater abundances of saprophytic fungi and heterotrophic protists. Moreover, CWPs displayed unique microhabitats that incorporate variability into the soil community assembly. Our work reveals the biogeography of soil communities associated with CWPs, the first step towards the development of microbial rewilding initiatives.