Hasil untuk "Microbial ecology"

R. Amann

Archana Pant, T. Maiti, Dinesh Mahajan et al.

The efficacy of drugs widely varies in individuals, and the gut microbiota plays an important role in this variability. The commensal microbiota living in the human gut encodes several enzymes that chemically modify systemic and orally administered drugs, and such modifications can lead to activation, inactivation, toxification, altered stability, poor bioavailability, and rapid excretion. Our knowledge of the role of the human gut microbiome in therapeutic outcomes continues to evolve. Recent studies suggest the existence of complex interactions between microbial functions and therapeutic drugs across the human body. Therapeutic drugs or xenobiotics can influence the composition of the gut microbiome and the microbial encoded functions. Both these deviations can alter the chemical transformations of the drugs and hence treatment outcomes. In this review, we provide an overview of (i) the genetic ecology of microbially encoded functions linked with xenobiotic degradation; (ii) the effect of drugs on the composition and function of the gut microbiome; and (iii) the importance of the gut microbiota in drug metabolism.

C. Matz, S. Kjelleberg

Dongdong Wei, Ke Ke, Shuangyan Xiao et al.

The present study aimed to elucidate the relationship between gut microbiota composition and enteritis in bullfrogs, which is a species of significant economic value in aquaculture. By comparing the gut microbiota of healthy bullfrogs (HG), bullfrogs with enteritis (DG), and bullfrogs in the wild (WG), we sought to identify the microbial community changes associated with enteritis and understand the dynamics of bacterial and fungal interactions in different environments. Utilizing high-throughput sequencing of 16S rRNA gene and ITS amplicons, we analyzed the gut microbiota of the three groups. Our findings showed that the Shannon index of bacterial communities in diseased bullfrogs was lower than that in healthy ones. Dominant bacterial phyla such as Proteobacteria, Bacteroidetes, and Firmicutes had varying abundances among the groups. Opportunistic pathogens like Aeromonas and Vibrio were enriched in DG, while beneficial bacteria were more abundant in HG. The bacterial network complexity is the highest in the WG group, the fungal network complexity is the highest in the HG group, and the complexity of bacteria-fungus network interaction is the highest in the DG group. Our research demonstrates significant alterations in the gut microbiota composition and interactions in bullfrogs with enteritis. The findings highlight the importance of maintaining a balanced microbial community in the gut to prevent enteritis. This study provides foundational insights into the microbial ecology of bullfrog intestines and offers potential strategies for managing and preventing enteritis in bullfrog aquaculture. This study reveals the microbial shifts in bullfrog intestines associated with enteritis, showing a disrupted bacterial and fungal balance that exacerbates disease. By identifying the enriched pathogens and the reduced beneficial bacteria in diseased bullfrogs, our research underscores the critical role of gut microbiota in health and disease. These insights are essential for developing targeted interventions to restore the microbial balance and prevent enteritis in bullfrog aquaculture, thereby enhancing economic sustainability.

Mingxi Zou, Jiaxiang Chen, Aotian Luo et al.

Conventional financial strategy evaluation relies on isolated backtests in static environments. Such evaluations assess each policy independently, overlook correlations and interactions, and fail to explain why strategies ultimately persist or vanish in evolving markets. We shift to an ecological perspective, where trading strategies are modeled as adaptive agents that interact and learn within a shared market. Instead of proposing a new strategy, we present FinEvo, an ecological game formalism for studying the evolutionary dynamics of multi-agent financial strategies. At the individual level, heterogeneous ML-based traders-rule-based, deep learning, reinforcement learning, and large language model (LLM) agents-adapt using signals such as historical prices and external news. At the population level, strategy distributions evolve through three designed mechanisms-selection, innovation, and environmental perturbation-capturing the dynamic forces of real markets. Together, these two layers of adaptation link evolutionary game theory with modern learning dynamics, providing a principled environment for studying strategic behavior. Experiments with external shocks and real-world news streams show that FinEvo is both stable for reproducibility and expressive in revealing context-dependent outcomes. Strategies may dominate, collapse, or form coalitions depending on their competitors-patterns invisible to static backtests. By reframing strategy evaluation as an ecological game formalism, FinEvo provides a unified, mechanism-level protocol for analyzing robustness, adaptation, and emergent dynamics in multi-agent financial markets, and may offer a means to explore the potential impact of macroeconomic policies and financial regulations on price evolution and equilibrium.

Shuo Jiao, Yiqin Xu, Jie Zhang et al.

Disentangling the roles of the core microbiota in community maintaining and soil nutrient cycling is an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the spatial atlas and ecological roles of the core microbiota. A systematic, continental-scale survey was conducted using agro-soils in adjacent pairs of maize (dryland) and rice (wetland) fields across eastern China. The results indicate that the core microbiota play major ecological roles in maintaining complex connections between bacterial taxa and are associated with belowground multinutrient cycling. A continental atlas was built for mapping the bacterial spatial distributions in agro-soils through identifying their habitat preferences. This study represents a significant advance in forecasting the responses of agricultural ecosystems to anthropogenic disturbance and thus helps manage soil bacterial communities for better provisioning of key ecosystem services—the ultimate goal of microbial ecology. ABSTRACT Revealing the ecological roles of the core microbiota in community maintaining and soil nutrient cycling is crucial for understanding ecosystem function, yet there is a dearth of continental-scale studies on this fundamental topic in microbial ecology. Here, we collected 251 soil samples from adjacent pairs of maize and rice fields at a continental scale in eastern China. We revealed the major ecological roles of the core microbiota in maintaining complex connections between bacterial taxa and their associations with belowground multinutrient cycling. By identifying the habitat preferences of the core microbiota, we built a continental atlas for mapping the spatial distributions of bacteria in agro-soils, which helps forecast the responses of agricultural ecosystems to anthropogenic disturbance. The multinutrient cycling index for maize and rice soils was related to bacterial α-diversity and β-diversity, respectively. Rice soils exhibited higher bacterial diversity and closer bacterial cooccurrence relationships than maize soils. In contrast to the macro- or microecological latitudinal richness patterns in natural terrestrial ecosystems, the bacteria in maize soils showed higher richness at high latitudes; however, this trend was not observed in rice soils. This study provides a new perspective on the distinct bacterial biogeographic patterns to predict the ecological roles of the core microbiota in agro-soils and thus helps manage soil bacterial communities for better provisioning of key ecosystem services. IMPORTANCE Disentangling the roles of the core microbiota in community maintaining and soil nutrient cycling is an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the spatial atlas and ecological roles of the core microbiota. A systematic, continental-scale survey was conducted using agro-soils in adjacent pairs of maize (dryland) and rice (wetland) fields across eastern China. The results indicate that the core microbiota play major ecological roles in maintaining complex connections between bacterial taxa and are associated with belowground multinutrient cycling. A continental atlas was built for mapping the bacterial spatial distributions in agro-soils through identifying their habitat preferences. This study represents a significant advance in forecasting the responses of agricultural ecosystems to anthropogenic disturbance and thus helps manage soil bacterial communities for better provisioning of key ecosystem services—the ultimate goal of microbial ecology.

G. Lopez, J. Levinton

M. Rillig, Ludo A. H. Muller, A. Lehmann

Soil aggregation, a key component of soil structure, has mostly been examined from the perspective of soil management and the mediation of ecosystem processes such as soil carbon storage. However, soil aggregation is also a major factor to consider in terms of the fine-scale organization of the soil microbiome. For example, the physico-chemical conditions inside of aggregates usually differ from the conditions prevalent in the bulk soil and aggregates therefore increase the spatial heterogeneity of the soil. In addition, aggregates can provide a refuge for microbes against predation since their interior is not accessible to many predators. Soil aggregates are thus clearly important for microbial community ecology in soils (for example, Vos et al., 2013; Rillig et al., 2016) and for microbially driven biogeochemistry, and soil microbial ecologists are increasingly appreciating these aspects of soil aggregation. Soil aggregates have, however, so far been neglected when it comes to evolutionary considerations (Crawford et al., 2005) and we here propose that the process of soil aggregation should be considered as an important driver of evolution in the soil microbial community. There are several features that make soil aggregates specifically interesting, and perhaps even unique, in terms of a setting for microbial evolution (Table 1). Soil aggregation is a continuous and dynamic process in which the formation and disintegration of individual microand macroaggregates are separated in time by periods of relative stability. Each individual soil aggregate may provide a unique environmental compartmentalization of the soil microbial community that is, to a large extent, isolated from its surroundings and that can be thought of as an ‘incubator’ for microbial evolutionary change. Because of their isolation, different aggregates can be regarded as ‘concurrent incubators’ that allow enclosed microbial communities to pursue their own independent evolutionary trajectories during their lifetime (‘incubation period’). The huge number of aggregates that exists at any moment in time validates their conceptualization as ‘massively concurrent incubators’ for microbial evolutionary change (Figure 1). Upon disintegration of soil aggregates (‘incubation cycle ends’), formerly enclosed microbial communities are released and allowed to interact with the microbial community of the soil at large. This combination of features (isolation, large number and relative stability) sets soil aggregates apart from other microbial habitats that may also provide temporary isolation of microbial communities, such as the animal intestinal tract and other parts of the animal body (see also Cordero and Datta, 2016), leaves, roots, and many aquatic habitats (Table 1). However, these habitats do not provide the same combination of extent of isolation, duration of isolation and number of concurrent ‘incubators’ as soil aggregates do. We discuss these specific characteristics of soil aggregates next, before describing how evolutionary change in aggregates can occur and explaining how this system can be tackled empirically.

J. Gilbert, Brent E. Stephens

Ruiwen Hu, Hai-Ming Zhao, Xihui Xu et al.

The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats to human health, it is urgent to develop efficient strategies to eliminate them from environments. Bacteria-driven PAE biodegradation has been considered as an inexpensive yet effective strategy to restore the contaminated environments. Despite great advances in bacterial culturing and sequencing, the inherent complexity of indigenous microbial community hinders us to mechanistically understand in situ PAE biodegradation and efficiently harness the degrading power of bacteria. The synthetic microbial ecology provides us a simple and controllable model system to address this problem. In this review, we focus on the current progress of PAE biodegradation mediated by bacterial isolates and indigenous bacterial communities, and discuss the prospective of synthetic PAE-degrading bacterial communities in PAE biodegradation research. It is anticipated that the theories and approaches of synthetic microbial ecology will revolutionize the study of bacteria-driven PAE biodegradation and provide novel insights for developing effective bioremediation solutions.

Si Ming Man, Rajendra Karki, T. Kanneganti

Julie N Chuong, Nadav Ben Nun, Ina Suresh et al.

Copy number variants (CNVs) are an important source of genetic variation underlying rapid adaptation and genome evolution. Whereas point mutation rates vary with genomic location and local DNA features, the role of genome architecture in the formation and evolutionary dynamics of CNVs is poorly understood. Previously, we found the GAP1 gene in Saccharomyces cerevisiae undergoes frequent amplification and selection in glutamine-limitation. The gene is flanked by two long terminal repeats (LTRs) and proximate to an origin of DNA replication (autonomously replicating sequence, ARS), which likely promote rapid GAP1 CNV formation. To test the role of these genomic elements on CNV-mediated adaptive evolution, we evolved engineered strains lacking either the adjacent LTRs, ARS, or all elements in glutamine-limited chemostats. Using a CNV reporter system and neural network simulation-based inference (nnSBI) we quantified the formation rate and fitness effect of CNVs for each strain. Removal of local DNA elements significantly impacts the fitness effect of GAP1 CNVs and the rate of adaptation. In 177 CNV lineages, across all four strains, between 26% and 80% of all GAP1 CNVs are mediated by Origin Dependent Inverted Repeat Amplification (ODIRA) which results from template switching between the leading and lagging strand during DNA synthesis. In the absence of the local ARS, distal ones mediate CNV formation via ODIRA. In the absence of local LTRs, homologous recombination can mediate gene amplification following de novo retrotransposon events. Our study reveals that template switching during DNA replication is a prevalent source of adaptive CNVs.

Bénédicte Madon, Rachel Haderlé, Emma Arotcharen et al.

ABSTRACT This paper provides a pioneering study case on monitoring fish biodiversity in ports through the eDNA and citizen science approach. eDNA samples were collected in the spring and in fall 2022 in the ports of Calvi, L'Île‐Rousse, STARESO, Saint‐Florent. Samples collected led to the identification of 73 taxa. These ports appeared to harbor at least 20% of the known teleost biodiversity in Corsica and 11% of the Mediterranean teleost biodiversity. The ports of Calvi and L'Île‐Rousse displayed the highest taxonomic, phylogenetic, and functional diversities and appeared the most similar. However, taxonomic turnover highlighted that none of the 4 ports was a subset of any of the others. In August 2022, an extreme climate event (ECE) struck Corsica, offering a unique opportunity to collect data under abnormal conditions. Although it is not possible to distinguish the seasonal effect from the ECE effect in the fall, we detected in all ports but Saint‐Florent an increase in taxonomic richness, phylogenetic, and functional diversity: we did not only detect new species but also showed that these species led to an increase in the local representativeness of phylogenetic diversity, most likely correlated with new functional traits. The port of Saint‐Florent displayed the highest relative phylogenetic diversity, that is, a smaller but evolutionarily more distinct group of species. Our study demonstrated the robustness and relevance of eDNA citizen science coupled with relevant indicators for port biodiversity monitoring and emphasized the need for more research and targeted conservation efforts to better understand and mitigate the ecological impacts of ports while exploring their potential as habitats.

Haiyue Yu, Yongjing Guo, Jialu Li et al.

BackgroundBronchopulmonary dysplasia (BPD) remains a major cause of morbidity in preterm infants, yet current diagnostic criteria are delayed and underlying mechanisms are incompletely defined. Evidence suggests that intestinal dysbiosis may influence pulmonary outcomes via the gut–lung axis, but the metabolic mediators of this interaction remain unclear.MethodsWe conducted a prospective cohort study of 50 preterm infants (≤ 32 weeks gestation), stratified by BPD severity at 36 weeks. Stool samples collected on postnatal day 7 underwent 16S rRNA sequencing and targeted bile acid metabolomics. Differential features were identified via multivariate statistics and LEfSe. Spearman correlation analysis explored bile acid–microbiota interactions. An interpretable machine learning model (XGBoost) incorporating bile acid and microbial features was developed and validated using five-fold cross-validation and an independent test set.ResultsInfants with severe BPD showed significantly reduced levels of 16 bile acids—including primary, secondary, and sulfated species—compared to non-BPD controls. Gut microbiome β-diversity differed significantly among groups, with enrichment of opportunistic Proteobacteria (e.g., Brevundimonas) in severe BPD. Negative correlations were observed between depleted bile acids and enriched bacterial genera. The XGBoost model predicted BPD severity with 80% accuracy (AUC = 0.91), leveraging key features such as chenodeoxycholic acid (CDCA), hyocholic acid (HCA), and Brevundimonas.ConclusionsPreterm infants who develop severe BPD exhibit early disruption of the bile acid–microbiota axis, characterized by reduced bile acid levels and enrichment of opportunistic taxa. Integrating these features within interpretable machine-learning models enables accurate early risk stratification and provides mechanistic insights beyond traditional inflammation-based frameworks. Validation in larger, multicenter cohorts is warranted to refine biomarker panels and explore targeted interventions that modulate bile acid signaling or microbial ecology to prevent or attenuate BPD.

Robert M. Bowers, Shayna Bennett, Robert Riley et al.

Abstract Background The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers, no previous study has applied shotgun metagenomics to their phyllosphere microbiomes. Results This study uses metagenomic sequencing to explore the microbial phyllosphere communities of subalpine Western conifer needle surfaces from 67 trees at six sites spanning the Rocky Mountains, including 31 limber pine, 18 Douglas fir, and 18 Engelmann spruce. Sites span ~ 1,075 km and nearly 10° latitude, from Glacier National Park to Rocky Mountain Biological Laboratory, capturing broad environmental variation. Metagenomes were generated for each of the 67 samples, for which we produced individual assemblies, along with three large coassemblies specific to each conifer host. From these datasets, we reconstructed 447 metagenome-assembled genomes (MAGs), 417 of which are non-redundant at the species level. Beyond increasing the total number of extracted MAGs from 153 to 294, the three coassemblies yielded three large MAGs, representing partial sequences of host genomes. Phylogenomics of all microbial MAGs revealed communities predominantly composed of bacteria (n = 327) and fungi (n = 117). We show that both microbial community composition and metabolic potential differ significantly across host tree species and geographic sites, with site exerting a stronger influence than host. Conclusions This dataset offers new insights into the microbial communities inhabiting the conifer needle surface, laying the foundation for future research on needle microbiomes across temporal and spatial scales. Variation in functional capabilities, such as volatile organic compound (VOC) degradation and polysaccharide metabolism, closely tracks shifts in taxonomic composition, indicating that host-specific chemistry, local environmental factors, and regional microbial source pools jointly shape ecological roles. Moreover, the observed patterns of mobile genetic elements and horizontal gene transfer suggest that gene exchange predominantly occurs within microbial lineages, with occasional broader transfers dispersing key functional genes (e.g., those involved in polysaccharide metabolism), which may facilitate microbiome adaptation.

Michaela Caboňová, Marisol Sanchez-Garcia, Miroslav Caboň et al.

The majority of members of the fungal genus Dermoloma have been described, based on morphology and without molecular support. Sequencing most Dermoloma type specimens has been unsuccessful, probably due to degraded DNA, leaving their taxonomy primarily reliant on morphological characters. In this study, we re-described nine Dermoloma types, providing standardised morphological descriptions that include observations of previously undocumented microscopic structures.The pileipellis structure of D. hybridum, D. inconspicuum and D. intermedium var. coniferarum differs strongly from the typical Dermoloma pileipellis and these taxa do not belong to this genus. Dermoloma atrobrunneum and D. hymenocephalum are distinct taxa which have not been reported recently. The concept of Dermoloma cuneifolium var. punctipes is based on the presence of dark spots on the stipe. However, our examination of the type material reveals that its spores are more consistent with those of D. atrocinereum, a species that can also exhibit dark dots. Dermoloma longibasidiatum is likely a synonym of this species as well. The name D. pseudocuneifolium has been misapplied for a species with amyloid spores, but the type has inamyloid narrow spores characteristic for D. bellerianum. Dermoloma pragense probably represents a distinct, but recently unrecorded European species defined by large basidiomata and small spores. The data presented here are essential for future nomenclatural treatments within Dermoloma, as current phylogenetic studies suggest the presence of a large number of undescribed species.

Yueqing An, Sarahi L. Garcia, Peter A. Hambäck

ABSTRACT Gut microbiomes of holometabolous insects can be strongly affected by metamorphosis. Previous studies suggest that microbiome colonization and community development often rely on specialized transmission routes between host life stages. However, there is a lack of comparative studies of microbial community dynamics from different transmission mechanisms. We compared the gut microbial community dynamics across life stages in five Galerucella species that differ in their potential microbial transfer mechanism by sequencing amplicons of the 16S rRNA gene. Females of three of the studied species place a fecal string on top of the egg, which may enhance the transfer of gut microbes, whereas females of the two other species do not. We found that the α-diversity was more stable between life stages in fecal string-placer species compared with the non-fecal string-placer species. Moreover, there were consistent microbiome differences between species, with multiple taxa in each species consistently appearing in all life stages. Fecal strings placed on eggs seem to play an important role in the diversity and dynamics of gut bacteria in Galerucella species, facilitating the vertical transfer of gut bacteria between host insect generations. Alternative, but less efficient, transmission routes appear to occur in non-fecal string-placer species.IMPORTANCEWe explore the consequences of having different mechanisms for transferring and establishing the gut microbiome between generations on gut microbial community dynamics. This process is often problematic in holometabolous insects, which have a complete metamorphosis between larval and adult stages. In our previous research, we found that females of some species within the genus Galerucella (Chrysomelidae) place a fecal string on the eggs, which is later consumed by the hatching larvae, whereas other species in the same genus do not have this behavior. In this paper, we therefore quantify the microbial community dynamics across all life stages in five Galerucella beetles (three with and two without fecal strings). Our results also indicate that the dynamics are much more stable in the species with fecal strings, particularly in the early life stages.

Tianyu Song, Van-Doan Duong, Thi-Phuong Le et al.

Accurate identification of wood species plays a critical role in ecological monitoring, biodiversity conservation, and sustainable forest management. Traditional classification approaches relying on macroscopic and microscopic inspection are labor-intensive and require expert knowledge. In this study, we explore the application of deep learning to automate the classification of ten wood species commonly found in Vietnam. A custom image dataset was constructed from field-collected wood samples, and five state-of-the-art convolutional neural network architectures--ResNet50, EfficientNet, MobileViT, MobileNetV3, and ShuffleNetV2--were evaluated. Among these, ShuffleNetV2 achieved the best balance between classification performance and computational efficiency, with an average accuracy of 99.29\% and F1-score of 99.35\% over 20 independent runs. These results demonstrate the potential of lightweight deep learning models for real-time, high-accuracy species identification in resource-constrained environments. Our work contributes to the growing field of ecological informatics by providing scalable, image-based solutions for automated wood classification and forest biodiversity assessment.

Davide Zanchetta, Deepak Gupta, Sofia Moschin et al.

Ecosystems frequently display the coexistence of diverse species under resource competition, typically resulting in skewed distributions of rarity and abundance. A potential driver of such coexistence is environmental fluctuations that favor different species over time. How to include and treat such temporal variability in existing consumer-resource models is still an open problem. In this work, we study correlated temporal fluctuations in species' resource uptake rates -- i.e. metabolic strategies -- within a stochastic consumer-resource framework. In a biologically relevant regime, we are able to find analytically the species abundance distributions through the path integral formalism. Our results reveal that stochastic dynamic metabolic strategies induce community structures that align more closely with empirical ecological observations. Within this framework, ecological communities show a higher diversity than expected under static competitive scenarios. We find that all species become extinct when the ratio of the number of species to the number of resources exceeds a critical threshold. Conversely, diversity peaks at intermediate values of the same ratio. Furthermore, when metabolic strategies of different species are different on average, maximal biodiversity is achieved for intermediate values of the amplitude of fluctuations. This work establishes a robust theoretical framework for exploring how temporal dynamics and stochasticity drive biodiversity and community structure.

Preet Mishra, Shyam Kumar, Sorokhaibam Cha Captain Vyom et al.

Evolutionary changes impacts interactions among populations and can disrupt ecosystems by driving extinctions or by collapsing population oscillations, posing significant challenges to biodiversity conservation. This study addresses the ecological rescue of a predator population threatened by a mutant prey population using optimal control method. To study this, we proposed a model which incorporates genotypically structured prey comprising of wild-type, heterozygous and mutant prey types and predator population. We proved that this model has both local and global existence and uniqueness of solutions ensuring the model robustness. Then, we applied optimal control method along with Pontryagin Maximum Principle by incorporating a control input in the model to minimize the mutant population and subsequently to stabilize the ecosystem. The numerical results clearly reveal that the undesired dynamics of the model can be controlled showing the suppression of the mutant, rescues the predator, and restores the oscillatory dynamics of the system. These findings demonstrate the efficacy of the control strategy and provide a mathematical framework for managing such ecological disruptions