ABSTRACT Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on “species” richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO2 enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO2 and ambient CO2 (aCO2) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO2 and aCO2, at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO2 dramatically altered the network interactions among different microbial functional genes/populations. Such a shift in network structure is also significantly correlated with soil geochemical variables. In short, elucidating network interactions in microbial communities and their responses to environmental changes is fundamentally important for research in microbial ecology, systems microbiology, and global change. IMPORTANCE Microorganisms are the foundation of the Earth's biosphere and play integral and unique roles in various ecosystem processes and functions. In an ecosystem, various microorganisms interact with each other to form complicated networks. Elucidating network interactions and their responses to environmental changes is difficult due to the lack of appropriate experimental data and an appropriate theoretical framework. This study provides a conceptual framework to construct interaction networks in microbial communities based on high-throughput functional gene array hybridization data. It also first documents that elevated carbon dioxide in the atmosphere dramatically alters the network interactions in soil microbial communities, which could have important implications in assessing the responses of ecosystems to climate change. The conceptual framework developed allows microbiologists to address research questions unapproachable previously by focusing on network interactions beyond the listing of, e.g., the number and abundance of species. Thus, this study could represent transformative research and a paradigm shift in microbial ecology. Microorganisms are the foundation of the Earth's biosphere and play integral and unique roles in various ecosystem processes and functions. In an ecosystem, various microorganisms interact with each other to form complicated networks. Elucidating network interactions and their responses to environmental changes is difficult due to the lack of appropriate experimental data and an appropriate theoretical framework. This study provides a conceptual framework to construct interaction networks in microbial communities based on high-throughput functional gene array hybridization data. It also first documents that elevated carbon dioxide in the atmosphere dramatically alters the network interactions in soil microbial communities, which could have important implications in assessing the responses of ecosystems to climate change. The conceptual framework developed allows microbiologists to address research questions unapproachable previously by focusing on network interactions beyond the listing of, e.g., the number and abundance of species. Thus, this study could represent transformative research and a paradigm shift in microbial ecology.
Most of the Human diseases affecting westernized countries are associated with dysbiosis and loss of microbial diversity in the gut microbiota. The Western way of life, with a wide use of antibiotics and other environmental triggers, may reduce the number of bacterial predators leading to a decrease in microbial diversity of the Human gut. We argue that this phenomenon is similar to the process of ecosystem impoverishment in macro ecology where human activity decreases ecological niches, the size of predator populations, and finally the biodiversity. Such pauperization is fundamental since it reverses the evolution processes, drives life backward into diminished complexity, stability, and adaptability. A simple therapeutic approach could thus be to reintroduce bacterial predators and restore a bacterial diversity of the host microbiota.
The 16S ribosomal RNA gene is the most widely used marker gene in microbial ecology. Counts of 16S sequence variants, often in PCR amplicons, are used to estimate proportions of bacterial and archaeal taxa in microbial communities. Because different organisms contain different 16S gene copy numbers (GCNs), sequence variant counts are biased towards clades with greater GCNs. Several tools have recently been developed for predicting GCNs using phylogenetic methods and based on sequenced genomes, in order to correct for these biases. However, the accuracy of those predictions has not been independently assessed. Here, we systematically evaluate the predictability of 16S GCNs across bacterial and archaeal clades, based on ∼ 6,800 public sequenced genomes and using several phylogenetic methods. Further, we assess the accuracy of GCNs predicted by three recently published tools (PICRUSt, CopyRighter, and PAPRICA) over a wide range of taxa and for 635 microbial communities from varied environments. We find that regardless of the phylogenetic method tested, 16S GCNs could only be accurately predicted for a limited fraction of taxa, namely taxa with closely to moderately related representatives (≲15% divergence in the 16S rRNA gene). Consistent with this observation, we find that all considered tools exhibit low predictive accuracy when evaluated against completely sequenced genomes, in some cases explaining less than 10% of the variance. Substantial disagreement was also observed between tools (R2<0.5) for the majority of tested microbial communities. The nearest sequenced taxon index (NSTI) of microbial communities, i.e., the average distance to a sequenced genome, was a strong predictor for the agreement between GCN prediction tools on non-animal-associated samples, but only a moderate predictor for animal-associated samples. We recommend against correcting for 16S GCNs in microbiome surveys by default, unless OTUs are sufficiently closely related to sequenced genomes or unless a need for true OTU proportions warrants the additional noise introduced, so that community profiles remain interpretable and comparable between studies.
Scleractinian corals’ microbial symbionts influence host health, yet how coral microbiomes assembled over evolution is not well understood. We survey bacterial and archaeal communities in phylogenetically diverse Australian corals representing more than 425 million years of diversification. We show that coral microbiomes are anatomically compartmentalized in both modern microbial ecology and evolutionary assembly. Coral mucus, tissue, and skeleton microbiomes differ in microbial community composition, richness, and response to host vs. environmental drivers. We also find evidence of coral-microbe phylosymbiosis, in which coral microbiome composition and richness reflect coral phylogeny. Surprisingly, the coral skeleton represents the most biodiverse coral microbiome, and also shows the strongest evidence of phylosymbiosis. Interactions between bacterial and coral phylogeny significantly influence the abundance of four groups of bacteria–including Endozoicomonas-like bacteria, which divide into host-generalist and host-specific subclades. Together these results trace microbial symbiosis across anatomy during the evolution of a basal animal lineage. Associations between corals and symbiotic microorganisms could be driven by the environment or shared evolutionary history. Here, the authors examine relationships between coral phylogenies and associated microbiomes, finding evidence of phylosymbiosis in microbes from coral skeleton and tissue, but not mucus.
Abstract Quorum sensing (QS) orchestrates collective microbial behaviors and functional acclimatization through chemical communication. However, QS in natural waters is challenged by dilution, alkaline hydrolysis, and enzymatic degradation of freely dissolved autoinducers. Here, we demonstrate that extracellular vesicles (EVs) act as selective, durable, and protective vectors for QS signal molecules under environmental stresses. Specifically, EVs preferentially package hydrophobic acyl‑homoserine lactones, concentrate them locally, and shield them from alkaline hydrolysis, and exhibiting long-distance transport. In addition, EVs possess specific affinity to recipients, thus influencing microbial community. Field investigation via multi-omics showed that EV abundance covaried with salinity, nutrients, chlorophyll a, and biomass, which were validated by culture experiments. Our statistical framework demonstrated that organisms producing moderate EV levels contributed significantly to maintaining community stability and ecosystem functions. Distinctively within this group, QS-active species (including Burkholderiaceae, Pseudomonadaceae, Rhodobacteraceae, Roseobacteraceae, Flavobacteriaceae etc.) emerge as key drivers facilitating these crucial ecological roles. Furthermore, metaproteomics of field EVs reveal QS receptor and synthesis proteins, suggesting coordinated transport of signals and proteins, which indicate new routes for QS crosstalk, particularly for taxa bearing luxR/I solos. Our results show that moderately generated EVs are the potentially important QS signal carriers and ecological regulation hubs in natural waters.
Ecological interaction networks are rarely homogeneous: species naturally form communities with distinct interaction structures, resulting in block-structured variance and correlation profiles in the interaction matrix. We study the equilibrium properties of generalized Lotka-Volterra systems whose interaction matrices are random and non-symmetric with variance and correlation profiles. Based on recent advances in approximate message passing (AMP) for heterogeneous and correlated random matrices, we derive a set of self-consistent fixed-point equations that, in the large-$n$ limit, characterize the equilibrium abundance distribution. In particular, we show that this limiting distribution is an explicit mixture of truncated Gaussian, driven by the variance and correlation profiles. We then illustrate the ecological implications of this result through three applications involving two interacting communities. First, we show that local changes in the correlation profile within a single community induce system-wide responses in species persistence, revealing the non-local nature of persistence dynamics. Second, we find that communities dominated by mutualistic or competitive interactions are more robust to increasing inter-community coupling, whereas communities structured by predator-prey interactions are more prone to collapse. Third, we demonstrate that asymmetric interaction variance alone, in the complete absence of correlation, can generate feedback loop between communities.
Emma Phillips, Sizèd vanEnk, Sara Kildgaard
et al.
Glioblastoma is a highly aggressive brain tumor for which there is no cure. The dire prognosis of this disease is largely attributable to a high level of heterogeneity, including the presence of a subpopulation of tumor‐initiating glioblastoma stem‐like cells (GSCs), which are refractory to chemo‐ and radiotherapy. Here, in an unbiased marine‐derived fungal extract screen, together with bioguided dereplication based on high‐resolution mass spectrometry, we identified malformin C to preferentially induce cell death in patient‐derived GSCs and explore the potential of this cyclic peptide as a therapeutic agent for glioblastoma. Malformin C significantly reduced tumor growth in an in vivo xenograft model of glioblastoma. Using transcriptomics and chemoproteomics, we found that malformin C binds to many proteins, leading to their aggregation, and rapidly induces the unfolded protein response, including autophagy, in GSCs. Crucially, chemical inhibition of translation using cycloheximide rescued malformin C‐induced cell death in GSCs, demonstrating that the proteotoxic effect of the compound is necessary for its cytotoxicity. At the same time, malformin C appears to accumulate in lysosomes, disrupting autophagic flux, and driving cells to death. Supporting this, malformin C synergizes with chloroquine, an inhibitor of autophagy. Strikingly, we observed that autophagic flux is differentially regulated in GSCs compared with normal astrocytes. The sensitivity of GSCs to malformin C highlights the relevance of proteostasis and autophagy as a therapeutic vulnerability in glioblastoma.
Neoplasms. Tumors. Oncology. Including cancer and carcinogens
The mining areas in arid and semi-arid region have become important coal production bases to ensure China’s energy strategic security, however, coal development by large-scale and high-intensity mining has triggered a series of water resources and ecological environment problems. The article analyzes ecological issues from a hydrological perspective, systematically reveals the hydrological and ecological effects caused by coal mining, and develops restoration technologies for damaged hydrological ecology in mining areas based on water. The research results are indicated by the follow. The subsidence caused by coal mining accelerates the infiltration and evaporation of precipitation, and the soil moisture near the soil fractures appears “funnel zone”. The water conducting fracture connects directly with the loose aquifer in typical coal areas, and the groundwater flow field and resource quantity have undergone significant changes. The maximum water level drop exceeds 14 m, the average water level drop exceeds 5m, and the amount of negative balance exceeds 2500×104 m3/a. The decrease in groundwater level leads to a gradual reduction in river flow, with a maximum of 172×104 m3/a. In areas where the groundwater level is less than 5 m, the decrease in groundwater level significantly reduces the ecological water consumption of vegetation. Base on the water resources and ecological environment problems, the hydrological and ecological restoration technologies have been developed, to response to the current situation of water resource shortage, ecological water level reduction, poor soil water retention, and low vegetation water use efficiency. Firstly, the moderate purification technology for mine water by nanofiltration has been developed. The technology has a wide range of desalination rates, and the treated mine water can provide high-quality water sources for hydrological and ecological restoration. Secondly, the ecological reinjection technology has been developed in soil, basing on the large amount of mine water inflow, good mine water quality, and considerable storage space in the Quaternary loose aquifer. The mine water recharge can lift the ecological water level in the mining area. Thirdly, the soil reconstruction technology has been developed, in which a water-resistant soil layer is placed underneath the vegetation root soil layer, which can significantly increase soil moisture and vegetation water consumption in the collapsed area. Fourthly, soil microbial inoculation technology has been developed, and appropriate inoculation treatment can expand the absorption range and area of soil moisture and nutrients by roots, regulate the expression of genes related to photosynthesis, sugar metabolism, glutathione metabolism, and calcium ion signal transduction, and improve the water efficiency and drought resistance of vegetation. The research results provide scientific basis for water resource protection and ecological environment restoration in arid and semi-arid mining areas in western China.
Abstract Non-nucleatum Fusobacterium may play a nonnegligible role in colorectal cancer (CRC) and certain Fusobacterium lineages (namely, L1 and L5) have shown specific associations with CRC. We aim to clarify the complex connections between Fusobacterium and CRC. We found that the widely adopted quantitative PCR (qPCR) method could overestimate F. nucleatum abundance and, in fact, reflect L1 levels in clinical samples. A lineage-specific qPCR assay targeting L1/L5 was developed and validated using mock and clinical samples. Its application in independent cohorts confirmed that L1 was overabundant in CRC, whereas L5 correlated with lymphovascular invasion. Importantly, faecal L1 abundance was more predictive of CRC than F. nucleatum, supported also by cross-population metagenomic data. CRC-associated virulence and colonisation genes were found in various L1 species other than F. nucleatum. Our results highlight the clinical importance of L1/L5 in CRC with high-diversity Fusobacterium contexts and suggest that non-nucleatum Fusobacterium may also contribute to CRC.