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PubMed2026

Multi-omics reveal microbial functional traits and antifungal metabolites associated with lower Pseudogymnoascus destructans loads in bat cave soils.

White-nose syndrome, caused by Pseudogymnoascus destructans (Pd), is a major fungal disease threatening hibernating bats. Cave soils can serve as environmental reservoirs for Pd, yet the microbial and biochemical mechanisms underlying naturally low Pd burdens in some cave environments remain poorly understood. Here, we integrated soil microbiome profiling, metagenomics, metabolomics, multi-omics network analysis, and in vitro validation to investigate the ecological and functional basis of differential Pd loads in hibernating bat caves in Northeast China. The three caves shared cold, humid, and weakly acidic microenvironments, but differed significantly in electrical conductivity, soil water content, nutrient availability, and extracellular enzyme activities. Soil microbial communities showed significant inter-cave variation in composition, diversity, and niche breadth, with stochastic processes contributing substantially to community assembly. Environmental variables, particularly pH and Pd load, were important predictors of microbial community structure. Functional analyses revealed that the low-Pd Gezi Cave was enriched in genes associated with organic carbon degradation, nitrogen input and retention, and secondary metabolism. Metabolomic profiling further identified cave-specific metabolite signatures, among which Biochanin A, 4-Hydroxybenzaldehyde, Vanillin, and Arachidonic acid were negatively correlated with Pd loads. Integrated pathway and network analyses showed that differential genes and metabolites jointly mapped to secondary metabolite biosynthesis, aminobenzoate degradation, and flavonoid degradation pathways, forming a microbe-metabolite-functional gene coupling network involving key taxa such as Rhodococcus, Pseudorhodoplanes, and Rhodoplanes. In vitro assays confirmed that 4-Hydroxybenzaldehyde, Coumarin, and Vanillin inhibited Pd growth. Structural equation modelling further indicated that environmental heterogeneity was associated with variation in Pd loads through microbial functional attributes and metabolite profiles. These findings suggest that naturally low-Pd cave soils are associated with coordinated environmental filtering, microbial functional specialization, and antifungal metabolite production, providing mechanistic insight into microbial and biochemical constraints on Pd persistence in cave reservoirs.

Animals↗

PubMed2025

Breaking the reproducibility barrier with standardized protocols for plant-microbiome research.

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

Plants↗

PubMed2006

Fragments as islands: a synthesis of faunal responses to habitat patchiness.

Scientific interest in the impact of habitat fragmentation on biodiversity is increasing, but our understanding of fragmentation is clouded by a lack of appreciation for fundamental similarities and differences across studies representing a wide range of taxa and landscape types. In an effort to synthesize data describing ecological responses of animals to fragmentation across two classes of independent variables (taxonomic group and landscape), we sampled 148 studies offive major faunal groups from the primary literature and analyzed data on 13 variables extracted from those studies. We focused our analyses on three classes of dependent variables (effects of area and isolation on species richness, z values, and nestedness and species composition). Area ranged over more orders of magnitude than isolation and tended to explain more variation in species richness than isolation. There were few matrix or taxon effects on the patterns we investigated, although we did find that sky islands tended to manifest isolation effects on both species richness and nestedness more frequently than other patch types. Sky islands may offer insight into the future of habitat patches fragmented by contemporary habitat loss, and because they show a stronger effect of isolation than other patch types, we suggest that isolation will play an increasing role in the biology of habitat fragments. We use multiple lines of evidence to suggest that our understanding of the role of isolation on community assembly in fragmented landscapes is inadequate. Finally, our observation that consistent taxonomic differences in community patterns were minimal suggests that conservation actions intended to mitigate the negative effects of extinction may have far-reaching effects across taxonomic groups.

Animals↗

PubMed2003

Patterns of association, nestedness, and species co-occurrence of helminth parasites in the greater kudu, Tragelaphus strepsiceros, in the Kruger National Park, South Africa, and the Etosha National Park, Namibia.

The helminth parasites of the greater kudu from the Kruger National Park (KNP), South Africa, and the Etosha National Park (ENP), Namibia, were examined to determine the major patterns of spatial and demographic variation in community structure and to evaluate nonrandomness in parasite community assembly. Nonmetric multidimensional scaling ordination procedures were used to test for differences in parasite community composition between hosts of the 2 parks and between hosts of different demographic groups within KNP. Infracommunities within KNP were also examined for patterns of nonrandomness using 2 null models, i.e., nestedness and species co-occurrence. Infracommunities of KNP and ENP were significantly different from each other, as were infracommunities of different host demographic groups within KNP. Parasite species in the greater kudu from KNP displayed significant levels of nestedness and were found to co-occur less frequently than expected by chance; however, this lack of co-occurrence was significant only when all demographic groups were considered. When restricted to any particular age class, co-occurrence patterns could not be distinguished from random. Overall, these data suggest that biogeography and host demographics are important factors in determining community organization of helminth parasites in the greater kudu.

Age Factors↗

PubMed2006

The problem and promise of scale dependency in community phylogenetics.

The problem of scale dependency is widespread in investigations of ecological communities. Null model investigations of community assembly exemplify the challenges involved because they typically include subjectively defined "regional species pools." The burgeoning field of community phylogenetics appears poised to face similar challenges. Our objective is to quantify the scope of the problem of scale dependency by comparing the phylogenetic structure of assemblages across contrasting geographic and taxonomic scales. We conduct phylogenetic analyses on communities within three tropical forests, and perform a sensitivity analysis with respect to two scaleable inputs: taxonomy and species pool size. We show that (1) estimates of phylogenetic overdispersion within local assemblages depend strongly on the taxonomic makeup of the local assemblage and (2) comparing the phylogenetic structure of a local assemblage to a species pool drawn from increasingly larger geographic scales results in an increased signal of phylogenetic clustering. We argue that, rather than posing a problem, "scale sensitivities" are likely to reveal general patterns of diversity that could help identify critical scales at which local or regional influences gain primacy for the structuring of communities. In this way, community phylogenetics promises to fill an important gap in community ecology and biogeography research.

Biodiversity↗

PubMed2006

Quantifying the roles of immigration and chance in shaping prokaryote community structure.

Naturally occurring populations of bacteria and archaea are vital to life on the earth and are of enormous practical significance in medicine, engineering and agriculture. However, the rules governing the formation of such communities are still poorly understood, and there is a need for a usable mathematical description of this process. Typically, microbial community structure is thought to be shaped mainly by deterministic factors such as competition and niche differentiation. Here we show, for a wide range of prokaryotic communities, that the relative abundance and frequency with which different taxa are observed in samples can be explained by a neutral community model (NCM). The NCM, which is a stochastic, birth-death immigration process, does not explicitly represent the deterministic factors and therefore cannot be a complete or literal description of community assembly. However, its success suggests that chance and immigration are important forces in shaping the patterns seen in prokaryotic communities.

Archaea↗

PubMed2004

Plant community responses to resource availability and heterogeneity during restoration.

Availability and heterogeneity of resources have a strong influence on plant community structure in undisturbed systems, as well as those recovering from disturbance. Less is known about the role of resource availability and heterogeneity in restored communities, although restoration provides a valuable opportunity to test our understanding of factors that influence plant community assembly. We altered soil nitrogen (N) availability and soil depth during a prairie restoration to determine if the availability and/or heterogeneity of soil resources influenced plant community composition in restored grassland communities. Plant community responses to three levels of N availability (ambient, enriched by fertilization, and reduced by carbon amendment) and two levels of soil depth (deep and shallow) were evaluated. In addition, we evaluated plant community responses to four whole plot heterogeneity treatments created from the six possible combinations of soil N availability and soil depth. The soil depth treatment had little influence on community structure during the first 3 years of restoration. Total diversity and richness declined over time under annual N enrichment, whereas diversity was maintained and richness increased over time in soil with reduced N availability. Non-native species establishment was lowest in reduced-N soil in the initial year, but their presence was negligible in all of the soil N treatments by the second year of restoration. Panicum virgatum, a native perennial C(4) grass, was the dominant species in all soil N treatments by year three, but the magnitude of its dominance was lowest in the reduced-N soil and highest in enriched-N soil. Consequently, the relative cover of P. virgatum was strongly correlated with community dominance and inversely related to diversity. The differential growth response of P. virgatum to soil N availability led to a higher degree of community similarity to native prairie in the reduced-N treatment than in the enriched-N treatment. There were no differences in plant community structure among the four whole plot-level heterogeneity treatments, which all exhibited the same degree of similarity to native prairie. Diversity and community heterogeneity in the whole-plot treatments appeared to be regulated by the dominant species' effect on light availability, rather than soil N heterogeneity per se. Our results indicate that a strong differential response of a dominant species to resource availability in a restored community can regulate community structure, diversity, and similarity to the native (or target) community, but the importance of resource heterogeneity in restoring diversity may be dampened in systems where a dominant species can successfully establish across a range of resource availability.

Conservation of Natural Resources↗

PubMed2006

Taxa-area relationships for microbes: the unsampled and the unseen.

The recent observation of a power-law relationship, S proportional A(z), between number of taxa, S, and area, A, for microbial eukaryotes and bacteria suggests that this is one of the few generic relationships in ecology, applicable to plants, animals and microbes. However, the rate of increase in the number of species with area varies from approximately the fourth (z = 0.26) to as little as the 50th root (z = 0.0019) in microbes. This is an enormous range for which no quantitative explanation has been proffered. We show by sampling from synthetic populations that the disparity between sample and community sizes in microbial community surveys means z can be considerably underestimated and accrual of rare taxa with increasing area will not be detectable. Significant microbial taxa-area relationships will only be observed when changes in community structure within samples correlate with area. Thus, the very low z values observed recently cannot be used as the sole evidence in support of any particular community theory of community assembly. More generally, this suggests that our search for patterns and laws in the microbial world will be profoundly influenced and, potentially distorted by the sample sizes that are typical of microbial community surveys.

Bacteria↗

PubMed2006

Bacterial diversity is determined by volume in membrane bioreactors.

It has been proposed that established models and theories developed in classical ecology could be employed to greatly improve the optimization of wastewater treatment plants (WWTP) by placing the microbiological component onto a model-predictive basis. In particular, this could be achieved by better understanding bacterial community assembly and development. The species-area relationship is one of the oldest biological laws and has been used to describe spatial diversity patterns in contiguous habitats and on islands. In the current study, bacterial communities in seven membrane bioreactors (MBR), of increasing size, located across the UK were sampled. A significant linear relationship between bacterial taxa richness and reactor size was observed and was similar to classical species-area relationships of larger organisms colonizing oceanic islands. Rank-abundance plots revealed a gradient of greater evenness in community structure as MBR volume increased. Application of the Raup and Crick probability-based similarity index indicated a strong role for dispersal in MBR colonization and community structure. Our findings demonstrate that the MBR sampled behaved like islands with respect to bacterial colonization in accordance with the theory of island biogeography. In addition this study provides further evidence that biodiversity at the bacterial level is more similar to that of animals and plants than previously postulated.

Bacteria↗

PubMed2004

Patterns in the co-occurrence of fish species in streams: the role of site suitability, morphology and phylogeny versus species interactions.

A number of studies at large scales have pointed out that abiotic factors and recolonization dynamics appear to be more important than biotic interactions in structuring stream-fish assemblages. In contrast, experimental and field studies at small scales show the importance of competition among stream fishes. However, given the highly variable nature of stream systems over time, competition may not be intense enough to generate large-scale complementary distributions via competitive exclusion. Complementary distribution is a recurrent pattern observed in fish communities across stream gradients, though it is not clear which instances of this pattern are due to competitive interactions and which to individual species' requirements. In this study, I introduce a series of null models developed to provide a more robust evaluation of species associations by facilitating the distinction between different processes that may shape species distributions and community assembly. These null models were applied to test whether conspicuous patterns in species co-occurrences are more consistent with their differences in habitat use, morphological features and/or phylogenetic constraints, or with species interactions in fish communities in the streams of a watershed in eastern Brazil. I concluded that patterns in species co-occurrences within the studied system are driven by common species-habitat relationships and species interactions may not play a significant role in structuring these communities. I suggest that large-scale studies, where adequate designs and robust analytical tools are applied, can contribute substantially to understanding the importance of different types of processes in structuring stream-fish communities.

Animals↗

PubMed2004

Introduction and synthesis: Plant phylogeny and the origin of major biomes.

Phylogenetic trees based upon DNA sequence data, when calibrated with a dimension of time, allow inference of: (i) the pattern of accumulation of lineages through time; (ii) the time of origin of monophyletic groups; (iii) when lineages arrived in different geographical areas; (iv) the time of origin of biome-specific morphologies. This gives a powerful new view of the history of biomes that in many cases is not provided by the incomplete plant fossil record. Dated plant phylogenies for angiosperm families such as Leguminoaceae (Fabaceae), Melastomataceae sensu stricto, Annonaceae and Rhamnaceae indicate that long-distance, transoceanic dispersal has played an important role in shaping their distributions, and that this can obscure any effect of tectonic history, previously assumed to have been the major cause of their biogeographic patterns. Dispersal from other continents has also been important in the assembly of the Amazonian rainforest flora and the Australian flora. Comparison of dated biogeographic patterns of plants and animals suggests that recent long-distance dispersal might be more prevalent in plants, which has major implications for community assembly and coevolution. Dated plant phylogenies also reveal the role of past environmental changes on the evolution of lineages in species-rich biomes, and show that recent Plio-Pleistocene diversification has contributed substantially to their current species richness. Because of the critical role of fossils and morphological characters in assigning ages to nodes in phylogenetic trees, future studies must include careful morphological consideration of fossils and their extant relatives in a phylogenetic context. Ideal study systems will be based upon DNA sequence data from multiple loci and multiple fossil calibrations. This allows cross-validation both of age estimates from different loci, and from different fossil calibrations. For a more complete view of biome history, future studies should emphasize full taxon sampling in ecologically important groups, and should focus on geographical areas for which few species-level phylogenies are available, such as tropical Africa and Asia. These studies are urgent because understanding the history of biomes can both inform conservation decisions, and help predict the effects of future environmental changes at a time when biodiversity is being impacted on an unprecedented scale.

Demography↗

PubMed2006

Inedible producers in food webs: controls on stoichiometric food quality and composition of grazers.

Ecological stoichiometry and food web theories focus on distinct mechanisms that shape communities. These mechanisms, however, likely interact in ways that neither theory alone addresses. To illustrate, we show how a model that tracks flow of energy and nutrients through two producers and two grazers reveals two indirect, interrelated roles for "neutrally inedible" producers. First, inedible producers can exert controls over the nutrient content of edible producers and indirectly influence whether grazers are nutrient or energy limited. Second, through these controls, inedible producers can shape community assembly by excluding grazers that are weak competitors for nutrients contained in edible producers. A mesocosm experiment revealed patterns consistent with both predictions: high abundances of inedible algae were accompanied by low phosphorus contents of edible algae and low abundances of the grazer Daphnia. Both lines of inference suggest that interactions between stoichiometry and plant heterogeneity may shape plankton communities.

Animal Nutritional Physiological Phenomena↗

PubMed2026

Methane and carbon dioxide emissions from wastewater treatment units linked to DOM stabilization and phosphonate-scavenging microbiomes.

Municipal wastewater treatment plants (WWTPs) are major engineered facilities for urban carbon removal, yet methane (CH4) formation and source mechanisms in downstream stages after aeration and biological nutrient removal remain poorly resolved. Process resolved monitoring at a full-scale WWTP showed that CH4 emissions were concentrated upstream, while measurable fluxes persisted in downstream sedimentation and denitrification units. Dissolved CH4 profiles showed strong attenuation of influent derived CH4 during upstream treatment, followed by a local increase after secondary clarification. Carbon dioxide (CO2) emissions peaked in the biochemical tank, consistent with rapid oxidation of labile organic carbon. Fluorescence and molecular analyses revealed a shift in dissolved organic matter (DOM) from protein like to more humic and processed molecules, while community assembly remained predominantly deterministic despite greater stochasticity in later stages. The C-P lyase catalytic core was enriched in these units, accompanied by higher phnJ transcript abundance, candidate organophosphonate features, and genomic potential. Together with BES insensitive CH4 formation in independent microcosms, these observations supported C-P lyase mediated organophosphonate utilization as a contributing pathway to local CH4 formation. Integrated evidence indicated that DOM stabilization, deterministic community filtering, potential succinate mediated cross feeding, and phosphonate scavenging jointly shaped this process. These findings show that advanced treatment units are not CH4 hotspots, but neither are they CH4 inactive zones; process resolved GHG assessments should therefore consider persistent local CH4 generation and its association with substrate restructuring and alternative phosphorus acquisition.

Dissolved organic matter↗

PubMed2002

Clinical profile and spectrum of commotio cordis.

CONTEXT: Although blunt, nonpenetrating chest blows causing sudden cardiac death (commotio cordis) are often associated with competitive sports, dangers implicit in such blows can extend into many other life activities. OBJECTIVE: To describe the comprehensive spectrum of commotio cordis events. DESIGN AND SETTING: Analysis of confirmed cases from the general community assembled in the US Commotio Cordis Registry occurring up to September 1, 2001. MAIN OUTCOME MEASURE: Commotio cordis event. RESULTS: Of 128 confirmed cases, 122 (95%) were in males and the mean (SD) age was 13.6 (8.2) years (median, 14 years; range, 3 months to 45 years); only 28 (22%) cases were aged 18 years or older. Commotio cordis events occurred most commonly during organized sporting events (79 [62%]), such as baseball, but 49 (38%) occurred as part of daily routine and recreational activities. Fatal blows were inflicted with a wide range of velocities but often occurred inadvertently and under circumstances not usually associated with risk for sudden death in informal settings near the home or playground. Twenty-two (28%) participants were wearing commercially available chest barriers, including 7 in whom the projectile made direct contact with protective padding (baseball catchers and lacrosse/hockey goalies), and 2 in whom the projectile was a baseball specifically designed to reduce risk. Only 21 (16%) individuals survived their event, with particularly prompt cardiopulmonary resuscitation/defibrillation (most commonly reversing ventricular fibrillation) the only identifiable factor associated with a favorable outcome. CONCLUSIONS: The expanded spectrum of commotio cordis illustrates the potential dangers implicit in striking the chest, regardless of the intent or force of the blow. These findings also suggest that the safety of young athletes will be enhanced by developing more effective preventive strategies (such as chest wall barriers) to achieve protection from ventricular fibrillation following precordial blows.

Adolescent↗

PubMed2000

Gilbert's conjecture: the search for DNA (cytosine-5) demethylases and the emergence of new functions for eukaryotic DNA (cytosine-5) methyltransferases.

In 1985 Walter Gilbert challenged members of the DNA methylation community assembled at a National Institutes of Health meeting organized by Giulio Cantoni and Ahron Razin with the following words: "The most exciting aspect about the methyl groups on DNA is the thought that they might provide a locally inherited change in a DNA structure. However, for that to be interesting, those changes have to be different in different cells. Furthermore, the alterations in methylation have to be freely imposable and have to be maintained. It is not yet clear that all these properties are true. So I don't think one will find that methylation ever is one of the primary, top-level controls on gene expression."In essence, Gilbert's conjecture, that DNA methylation is not one of the top-level controls on gene expression, assumes that evidence in favor of both of its testable propositions will not be obtained. Evidence for the first proposition, that alterations in methylation status associated with gene-expression states have to be maintained, was already available in 1985 and has been strengthened by a number of very recent experiments. However, the extensive effort to obtain evidence for the second proposition, that alterations in methylation status be freely imposable, has not been successful in its original intent. The effort has, on the other hand, resulted in the emergence of new functions for 5-methylcytosine and the cytosine methyltransferases in eukaryotic DNA repair, recombination and chromosome stability.

Alleles↗

PubMed2002

Species positions and extinction dynamics in simple food webs.

Recent investigations on the structure of complex networks have provided interesting results for ecologists. Being inspired by these studies, we analyse a well-defined set of small model food webs. The extinction probability caused by internal Lotka-Volterra dynamics is compared to the position of species. Simulations have revealed that some global properties of these food webs (e.g. the homogeneity of connectedness) and the positions of species therein (e.g. interaction pattern) make them prone to modelled biotic extinction caused by population dynamical effects. We found that: (a) homogeneity in the connectedness structure increases the probability of extinction events; (b) in addition to the number of interactions, their orientations also influence the future of species in a web. Since species in characteristic network positions are prone to extinction, results could also be interpreted as describing the properties of preferred states of food webs during community assembly. Our results may contribute to understanding the intimate relationship between pattern and process in ecology.

Animals↗

PubMed1999

Sustaining Ecosystem Services in Human-Dominated Watersheds: Biohydrology and Ecosystem Processes in the South Platte River Basin.

/ Sustaining ecosystem services important to humans while providing a dependable water supply for agriculture and urban needs is a major challenge faced by managers of human-dominated watersheds. Modification of natural flow regimes alters the abundance and composition of native plant and animal communities, affecting ecosystem services such as water storage and nutrient cycling that depend on particular species or functional groups. Because complete restoration of natural hydrology is generally not an option in human-dominated watersheds, there is a need to determine which specific flow manipulations are necessary to restore species-dependent ecosystem services in particular systems. Here we propose a framework for predicting ecological consequences of flow manipulations that is based on the role of hydrology in linking population, community, and ecosystem processes. We use a case-study approach to examine how interactions among the flow regime and species' functional traits help organize local biotic communities and generate alternate states of ecosystem functioning. Results indicate the importance of integrating hydrology and biology to predict ecological consequences of flow regime manipulations and the need to apply general flow-restoration principles on a case-by-case basis.KEY WORDS: Biohydrology; Aquatic ecosystems; Community assembly; Ecological integrity; Watershed restoration; Ecosystem serviceshttp://link.springer-ny.com/link/service/journals/00267/bibs/24n1p39.html

Journal Article↗

PubMed2026

Microbial diversity, functional activities, and safety risks in fermented tea: a comprehensive review.

Microbial fermented teas are gaining global popularity due to their unique sensory profiles and health benefits. The quality and safety of these products are governed by complex microbial ecosystems that orchestrate the biotransformation of tea leaf components. This review addresses a critical paradox in the field: the same microbial activities that generate desirable bioactive metabolites, such as theabrownins and organic acids, also create ecological niches for mycotoxigenic fungi, posing significant health risks from contaminants like ochratoxin A, citrinin, and aflatoxins. While extensive research has cataloged the microbial diversity in these systems, a comprehensive framework linking processing environments to microbial community assembly, functional outcomes, and quantifiable safety risks remains elusive. This review systematically bridges this gap by synthesizing current knowledge on the microbial consortia-dominated by Aspergillus, Penicillium, Bacillus, and Lactiplantibacillus species-that drive tea fermentation. We critically analyze their functional roles in enhancing flavor, bioactivity, and potential probiotic activity while simultaneously evaluating the mechanisms of mycotoxin production and accumulation. By integrating microbial ecology, biochemistry, and food safety, we propose a forward-looking perspective focused on transitioning the industry from traditional, spontaneous fermentation to modern, controlled biotechnological processes. This approach, centered on the use of defined starter cultures, predictive modeling, and active biocontrol strategies, provides a roadmap for ensuring the consistent quality and safety of fermented tea products, ultimately unlocking their full potential as high-quality functional foods.

Tea↗