Ecological Niche Research Articles (Page 1)

Gut microbiome and rheumatoid arthritis: Revisiting the gut-joint axis.

DNA methylation is a key epigenetic mark that impacts gene expression and represses transposable elements in eukaryotes. Numerous examples of cis elements targeted by DNA methylation, particularly at CG sites (mCG), have been reported to be under selective pressure in animals and plants. By contrast, there is limited knowledge of trans regulators of mCG leading to adaptation. Here, a genome-wide association study identifies CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 (CDCA7) as a major trans determinant of mCG in natural populations of Arabidopsis thaliana. CDCA7 or its paralogue physically binds the chromatin remodeller DECREASE IN DNA METHYLATION 1 (DDM1), which facilitates access of methyltransferases to DNA. Epigenomic analysis shows that while CDCA7 proteins control all DDM1-dependent processes, their predominant function is the maintenance of mCG. We identify a 26-bp promoter indel modulating CDCA7 expression in natural populations and determining the degree of mCG and transposable element silencing. The geographic distribution of CDCA7 alleles suggests that new alleles have repeatedly expanded to novel ecological niches, indicating a potential role in local adaptation. Our findings establish CDCA7 proteins as dedicated regulators of mCG and imply that DDM1 relies on alternative partners to regulate other chromatin features. Broadly, they illustrate how changes in global DNA methylation levels through transcriptional regulation of the epigenetic machinery have the capacity to facilitate local adaptation.

Comparative surveys allow us to characterize the influence of specific factors on population genetic diversity and structure. We conducted a comparative phylogeographic study for three Mexican oak species to identify how their climatic niche preferences and breadth may have influenced historical demography and range shifts during Pleistocene climatic oscillations. We estimated genetic diversity and structure for Quercus deserticola, Q. glaucoides, and Q. peduncularis. We inferred historical demographic changes using approximate Bayesian computation and used ecological niche models to determine present potential distribution of the species and used past climatic scenarios to estimate range and altitudinal shifts. We also measured the niche breadth of each species and evaluated niche similarity among species. We identified differences in population history, which we related to the climatic niche of individual species. For Q. deserticola, we inferred a historical bottleneck consistent with the interglacial refugia hypothesis. Quercus glaucoides, which is characterized by a narrow niche breadth, had high levels of genetic structure based on plastid DNA. Quercus peduncularis had high genetic diversity and low structure. We found correlations between niche breadth and values of genetic structure and diversity. Interglacial contraction and glacial expansion in the three species differed in magnitude, with Q. deserticola exhibiting the most drastic contraction during the interglacial. Mexican oak species responded differently to historical climatic changes since they have distinct distributions in geographic and climatic space. Levels and patterns of genetic variation agreed with the population history of each species inferred using niche modeling.

Genome sequences of extant and extinct gibbons reveal their phylogeny, demographic history, and conservation status.

Herbivorous insects can shape the epidemiology of disease in plants by vectoring numerous phytopathogens. While the consequences of infection are often well-characterized in the host plant, the extent to which phytopathogens alter the physiology and development of their insect vectors remains poorly understood. In this review, we highlight how insect-borne phytopathogens can promote vector fitness, consistent with theoretical predictions that selection should favor a mutualistic or commensal phenotype. In doing so, we define the metabolic features predisposing plant pathogens to engage in beneficial partnerships with herbivorous insects and how these mutualisms promote the microbe's propagation to uninfected plants. For the vector, the benefits of co-opting microbial pathways and metabolites can be immense: from balancing a nutritionally deficient diet and unlocking a novel ecological niche to upgrading its defensive biochemistry against natural enemies. Given the independent origins of these tripartite interactions and a number of convergent features, we also discuss the evolutionary and genomic signatures underlying microbial adaptation to its dual lifestyle as both a plant pathogen and an insect mutualist. Finally, as host association can constrain the metabolic potential of microbes over evolutionary time, we outline the stability of these interactions and how they impact the virulence and transmission of plant pathogens.

Understanding species distribution and environmental niches is crucial for conserving endangered taxa. The recent taxonomic split of the European freshwater mussels U. crassus and U. nanus into distinct species requires a reassessment of their distinct ecologies for conservation. This study uses species distribution models (SDMs) to define and compare the environmental niches and reconstruct the distributions across six past time periods, starting from the mid-Pliocene Warm Period (mPWP, ca. 3.205 Ma) to the present. Our results reveal significant environmental niche differentiation between the two species, with U. crassus occupying a broader environmental niche primarily influenced by annual mean temperature and precipitation in the warmest quarter. In contrast, U. nanus shows a narrower niche shaped by temperature seasonality, mean diurnal range, annual mean temperature, and precipitation seasonality. Paleodistribution models indicate that during the Last Glacial Maximum (LGM, ca. 21 ka), U. crassus persisted in multiple southern refugia, whereas U. nanus was restricted to a single western refugium. These contrasting glacial histories led to divergent post-glacial colonization routes, explaining their current genetic patterns and partially overlapping ranges. By identifying present environmental hotspots, this research provides an essential framework for developing targeted, species-specific conservation strategies for these freshwater mussels.

Global climate change-driven poleward shifts in suitable habitat distribution and niche differentiation of benthic euryhaline Lateolabrax species.

Microevolution and macroevolution describe evolutionary change at different scales: short-term genetic and phenotypic variation within populations, and long-term patterns of diversification and extinction. Despite their interconnected nature, they have often been studied separately, and the reciprocal causal links between them remain poorly understood due to their operation on different timescales and the complexity of the processes involved, making mechanistic approaches particularly challenging. To bridge this operational gap, we introduce a novel bottom-up, process-based computational framework that integrates genotype-to-phenotype mapping, fitness evaluation under environmental constraints, and biotic interactions shaping ecological niches and adaptive pressures, while incorporating lower-level mechanisms such as mutation, gene flow, and gene-pool expansion through stochastic duplication of genes. Its modular design accommodates diverse microevolutionary mechanisms to study the emergence of large-scale eco-evolutionary patterns from explicit individual-level processes. The framework allows addressing research questions ranging from the formation of spatiotemporal biodiversity patterns to the role of eco-evolutionary feedbacks in macroevolution. It provides an open-ended platform that serves both as a theoretical tool for testing evolutionary hypotheses and as a flexible environment for exploratory simulations. To illustrate its heuristic potential, we present proof-of-concept simulations under biologically plausible conditions that reproduce multiple well-documented macroevolutionary patterns-such as biphasic diversification, saturating and exponential-like biodiversity trends, speciation-extinction correlations, species duration distributions, and niche structuring-as emergent phenomena. Beyond reproducing patterns, the simulations reveal underlying mechanisms, including trial-and-error dynamics in long-term adaptation, high species turnover maintaining biodiversity equilibrium, and self-organized niche occupancy. These findings establish the framework as a versatile tool for investigating the complex interplay of ecological and evolutionary forces shaping biodiversity. By capturing emergent dynamics from mechanistic microevolutionary processes without imposing predefined constraints, the model provides a unique perspective on long-term evolutionary change, contributing to a broader theoretical toolkit for studying macroevolutionary patterns under controlled conditions. Future extensions could assess how variations in environmental dynamics, genomic architecture, or species interactions influence evolutionary trajectories, refining our understanding of biodiversity evolution.

Hydrothermal systems are widespread in our solar system. Identification of alteration mineral assemblages on Mars and potentially in ocean worlds such as Enceladus suggests the existence of extensive hydrothermal fluid-igneous rock interactions of astrobiological interest in different planetary bodies. Here, we studied the terrestrial analog Cerro Caliente, a band of geothermal alterations located in the glaciovolcanic environment of Deception Island (Antarctica), with the aim of determining the mobility of major chemical elements (e.g., alkalis, phosphorus) and its implications in the habitability potential of such environments. We verified that the rock texture, particularly rich in volcanic glass, plays a major role in geochemical mobility, with permafrost delimiting the impact of hydrothermal activity by reducing the permeability of the lapilli tuff deposit. We studied the mineralogy and geochemistry of the alteration band by comparing borehole samples in different locations that represent different thermal regimes along the hydrothermal alteration band. The alteration products are characteristic of palagonitization processes, which favor the release of elements useful for life, such as phosphorus, although the basic alkalinity of the medium caused its precipitation in the form of tricalcium phosphate. In addition, lipid biomarker analyses were performed to assess the existence of possible potential ecological niches associated with these environments. On Mars, the circulation of low-temperature CO2-rich hydrothermal fluids through glass-bearing volcanic rocks results in a loss of silica content and a secondary mineral assemblage composed of palagonite, phyllosilicates, and zeolites, which establishes Cerro Caliente as a valid Mars analog for understanding such environments. In addition, our results support the hypothesis of a hydrothermal origin of phosphorous for the formation of Enceladus' phosphates recently detected in the plumes. We also determined that a fraction of the calcium in Cerro Caliente was sequestered as carbonates of biogenic origin, which produced a distinctive Raman signal that, together with the lipid content, would make it a relevant potential biosignature if similar findings were made in the search for life in such low-temperature hydrothermal environments. Key Words: Hydrothermal systems-Palagonitization-Phosphates-Lipid biomarkers-Mars-Ocean worlds. Astrobiology xx, xxx-xxx.

Plains rough fescue, a native species of North America's central plains, has experienced a decline due to land conversion and population fragmentation. To assess the historical distribution of this species, we employed ecological niche modeling. Presence records of Festuca hallii were collected from the SEINet Portal Network, iNaturalist, herbaria in The United States and Canada, and Canadian conservation data centers. A model was developed using MaxEnt with 1048 records, seven climatic variables and nine soil variables. A habitat suitability map was generated illustrating the likely distribution of F. hallii before European settlement in 19th century. The species has a high probability of occurrence across the Canadian prairies, with fragmented distribution in regions of the Rocky Mountains of Alberta and United States. Good habitat for F. hallii is characterized by soil bulk density between 1.07–1.25 g cm-3, annual mean temperature between 0.64–4.14 °C, precipitation during the warmest quarter between 149.72–228.19 mm, soil water content between 38.9–45.85%, and precipitation seasonality between 51.53–77.08%, which were the most important predictors in the model. Of the 450,206 km2 historic range, approximately 63,273 km2, or 14.1% remains intact with land cover/land use data indicating grassland conversion to agriculture as the main cause of habitat loss.

Tetracladium spp. represent a group of fungi that inhabit various ecological niches, including soil and aquatic environments, where they are considered to have a saprotrophic lifestyle and within plant roots as endophytes. To date, a lack of sequenced Tetracladium spp. genomes has inhibited our understanding of their metabolic potential and ecological interactions. In this study, we aimed to elucidate the genetic differences between aquatic saprotrophic and endophytic strains of Tetracladium spp. by sequencing and analysing the genomes of T. maxilliforme (isolated from Brassica napus roots) and T. marchalianum (isolated from freshwater), alongside 41 publicly available saprotrophic and endophytic Ascomycetes. Genomic sequencing revealed that T. maxilliforme possesses a genome size of 35.5 Mbp with 9657 predicted genes, while T. marchalianum has a genome size of 33.2 Mbp with 15,230 predicted genes. Our analyses primarily focused on carbohydrate-active enzymes (CAZymes). Both genomes possessed the full range of enzymatic machinery for cellulose degradation, as well as the complete repertoire of genes necessary to degrade plant cell walls. Notably, the genomes lacked essential enzymes for lignin degradation or modification. Furthermore, we observed a complete repertoire of known fungal chitin-degrading enzymes in both genomes, which might be related to potential interactions with other fungi. Enzyme composition profiles revealed distinct groupings, with T. maxilliforme primarily clustering with endophytic or ecologically versatile species, while T. marchalianum was predominantly associated with saprotrophic species. We also identified secondary metabolite biosynthetic gene clusters in both genomes, including several that showed high homology to those of known bioactive compounds. In summary, our findings offer valuable insights into the genomic adaptations of Tetracladium spp. to various ecological niches, highlighting their enzymatic capabilities for carbohydrate degradation and potential interactions within fungal communities.

Temperate-zone Geometridae moths, active across seasons, offer an excellent model for investigating how related species respond to varying environmental conditions, particularly photoperiod-a major Zeitgeber regulating biological oscillators. In this study, we examined the daily cycle of sperm release from the testes in 9 geometer moth species, including univoltine and bivoltine taxa, as well as diurnal and nocturnal species. We found that sperm release into the upper vasa deferentia differs consistently between day-flying and night-flying species. Moreover, we observed marked differences in the diel regulation of sperm release between spring and summer generations of the same species. Experimental evidence suggests that these intergenerational differences are photoperiod-dependent. Further manipulation confirmed that a long photoperiod not only abolishes rhythmic sperm release but also significantly reduces the number of eupyrene sperm bundles transferred into the vasa deferentia. This is the first demonstration, under near-natural conditions, of photoperiodic regulation of a physiological rhythm in a peripheral organ via its suppression. These findings underscore the importance of environmental timing cues in reproductive physiology and provide new insights into the temporal plasticity of insect reproductive systems. Importantly, they also highlight the potential for integrating agro-chronobiological knowledge with mechanistic studies of temporal regulation in insect pests. Finally, this work adds to our understanding of how peripheral oscillators may be shaped by selective pressures in closely related species occupying distinct ecological niches, where differences in the timing of life-history processes serve as key axes of divergence.

Due to global warming and intensified anthropogenic impacts, mountainous areas are increasingly being colonised by alien plant species. The diversity patterns of these species have not been sufficiently studied in the Central Balkans. The aims of this study were to determine the occurrence and richness of alien plant species in relation to habitat type and geological substrates, and to identify the factors with the greatest influence on the composition and abundance of these species on Zlatibor Mountain (Central Balkans). This area is known as an important tourist centre and a large mountainous massif in Serbia. Principal Component Analysis (PCA) and distance-based Redundancy Analysis (db-RDA) were employed to examine the influence of environmental factors on the abundance and composition of 18 alien plant taxa. Data on altitude, habitat type, bedrock type, bioclimatic variables, and indicator values (light regime, soil moisture, acidity, nitrogen and temperature) of dominant plant species within the habitats were used as explanatory variables. Erigeron annuus, Reynoutria × bohemica, Robinia pseudoacacia, and Erigeron canadensis were the most common alien taxa and had the highest abundances. Residential and tourist facilities and the peripheries of asphalt roads are the habitat types where most alien species occur, while the lowest number of species was found in natural and semi-natural herbaceous habitats. Most taxa were found on serpentine substrates, while the number of taxa was lower on siliceous and carbonate substrates. This study emphasises the predominant role of habitat type in the partitioning of ecological niches of alien plant species. Furthermore, habitat type has a much greater influence on species composition and abundance than climatic factors and bedrock type, suggesting that the diversity pattern of alien plant species is related to the type and intensity of anthropogenic influences. Our results provide a useful basis for developing effective strategies to protect native habitats from invasion by alien plants.

The Lactobacillaceae family encompasses microorganisms of exceptional ecological and biotechnological importance, serving as central agents in food fermentations, health applications, and nutrient cycling across diverse environments. Despite their broad functional and phylogenetic diversity, the global distribution and ecological specialization of Lactobacillaceae are not yet fully understood. In this study, we performed a comprehensive analysis of over 2 million records from the NCBI database to survey and trace the ecological landscape of Lactobacillaceae across thousands of distinct habitats. Our results reveal that food products and animal hosts represent the primary ecological niches for members of this family. The examined taxa exhibit a broad spectrum of ecological strategies, ranging from generalists with wide environmental adaptability to specialists with strict niche preferences. Notably, our findings highlight a profound geographical and ecological sampling bias, with unclassified taxids frequent in animal gastrointestinal tracts, soils, and especially in living plant tissues—habitats identified as promising frontiers for discovering novel biodiversity. The obtained results emphasize the urgent need for expanded sampling efforts in underexplored geographic regions such as Africa, Antarctica, the Arctic, South America, and Central Asia to capture a more complete picture of Lactobacillaceae diversity. The study underscores the necessity of implementing standardized, metadata-rich data deposition practices to enable unbiased, large-scale ecological and evolutionary analyses. Ultimately, these insights not only deepen our fundamental knowledge of Lactobacillaceae diversity but also provide a strategic framework for future bioprospecting, fostering the discovery of novel strains and expanding the biotechnological potential of this influential bacterial family.

Climate change is increasingly recognized as a critical driver influencing the global epidemiology of malaria. Rising temperatures, changing rainfall patterns, and altered humidity levels have reshaped the geographical distribution, intensity, and seasonality of malaria transmission. This review synthesizes current evidence on the complex interplay between climate variability and malaria dynamics, emphasizing how warmer climates expand vector habitats, modify parasite development rates, and extend transmission seasons. Particular attention is given to regions at high altitude and those previously unsuitable for malaria, where climate change is creating new ecological niches for vectors. The paper also examines methodological approaches to studying climate–malaria linkages, highlights the uncertainties and challenges in predicting future disease patterns, and underscores the role of adaptive strategies in mitigating the health burden. Ultimately, the integration of climate science, epidemiological data, and public health interventions is essential to address the evolving threats posed by malaria in a warming world. Keywords: Climate change; Malaria epidemiology; Vector-borne diseases; Anopheles mosquitoes; Global health; Disease modeling; Public health adaptation

This study investigates the biogeographic barriers and environmental gradients that influence the distribution and niche segregation of seven Hynobius salamander species in South Korea. Using Ecological Niche Models (ENMs) developed with the Maxent software and 48 environmental variables, we conducted four niche overlap tests for each species pair: niche identity tests and background similarity tests to assess niche differentiation, lineage-breaking tests to evaluate species boundaries in relation to environmental shifts, and ribbon tests to determine whether unsuitable habitats serve as distributional barriers. The results indicated that significant biogeographic barriers, including both physical features such as rivers and mountains and environmental gradients, influence the range segregation of these salamanders. The study also identified distinct ecological niches among the species, with environmental gradients and unsuitable habitats acting as key factors shaping their distributions. These findings highlight the crucial role of biogeographic barriers in the distribution and speciation of Hynobius salamanders, emphasizing the need to consider these factors in conservation strategies aimed at preserving their ecological diversity and evolutionary trajectories.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-22226-5.

Introduction This study elucidated how different plantation types in limestone mountains shape the community structure and co-occurrence networks of soil fungal habitatspecialization groups, offering a habitat-adaptation perspective on the assembly mechanisms of soil microbial diversity during ecological restoration. Methods In this study, we grouped soil fungi from plantations of coniferous forests (CF), mixed forests (MF) and broad-leaved forests (BF) into habitat-generalists, specialists and opportunists based on niche breadth, and examined how forest type shapes their diversity, community structure and co-occurrence networks along a habitat-specialization gradient. Results We found that: (1) The number and abundance of habitat-specialists significantly exceeded those of generalists. Habitat-generalists exhibited the highest abundance and ecological niche width in BF, whereas habitat-specialists were most abundant in CF. (2) The diversity index was the highest in BF across all habitat specialization groups. Differences in community structure among forest types increased with habitat specialization, and the composition of dominant tree species significantly influenced the community structure of each group. Soil properties primarily affected the community structure of habitat generalists and opportunists between BF and other forest types. (3) The network structure of habitat specialists exhibited high modularity, while habitat generalists formed independent subnetworks with more fragile structures. CF and BF exhibited strong intra-module connections and high modularity, whereas MF displayed high intermodule connectivity, which reduced their modularity. Both within-module (Zi) and between-module connectivity (Pi) of increased with habitat specialization and the proportion of broadleaved tree species. Discussion We concluded that broad-leaved plantations, by increasing soil environmental heterogeneity, promoted the diversity of habitat-specialists and enhancing their network hub roles, representing the optimal strategy for optimizing below-ground biodiversity and stability in limestone mountain forest restoration.

This study investigated the effects of dietary supplementation with composite acidifying agents containing 2-hydroxy-4-methylthiobutyric acid (≥30.0%), lactic acid (≥24.2%), and phosphoric acid (≥23.8%) on production performance, egg quality, serum biochemistry, intestinal health, and cecal microbiota in 300-day-old BIAN chickens. In a 42-day randomized trial, 900 laying hens were randomly allocated to three groups: the control group (basal diet with tap water), test group A (basal diet with 0.05% composite acidifier in drinking water), and test group B (basal diet with 0.20% composite acidifier in drinking water). The results demonstrated that test group B exhibited a significant 4.6% increase in average egg weight compared to the control (p = 0.029), while test group A showed enhanced Haugh unit values (p = 0.010) and eggshell strength (p = 0.010). Serum biochemical analysis revealed marked improvements in immune function, with test group B showing a 65.49% increase in globulin levels (p = 0.010) and 61.76% elevation in total antioxidant capacity (T-AOC) (p = 0.010). Intestinal digestive enzyme activities were significantly enhanced, particularly in test group A with a 61.73% increase in duodenal lipase activity (p = 0.010) and 37.43% elevation in jejunal amylase activity (p = 0.036). Morphological assessment demonstrated improved intestinal architecture in test group B, with a 26.02% reduction in crypt depth (p = 0.025) and a 44.53% increase in the villus-to-crypt ratio (p = 0.030). Microbiota analysis revealed dose-dependent modulation of cecal bacterial communities, with notable increases in beneficial genera including Akkermansia (from 1.8% to 7.2% in test group A) and Lachnospiraceae (from 4.7% to 9.7% in test group B) while maintaining core microbiota stability. Principal component analysis confirmed distinct microbial ecological niches created by acidifier supplementation. These findings demonstrate that composite acidifying agents effectively enhance egg production quality, immune status, digestive function, and gut health in BIAN chickens, supporting their potential as sustainable alternatives to antibiotic growth promoters in laying hen production systems.

ABSTRACT Early detection of plant pathogens is essential to maintain global food production and ecosystem resilience, especially as climate change creates new ecological niches that favour the emergence and spread of novel pathogens. Laboratory‐based diagnostic methods, including ELISA and PCR, while accurate, are unsuitable for on‐site (directly at the point of sample collection) testing. Recent advances in microfluidics, including polydimethylsiloxane (PDMS)‐based chips and paper‐based platforms, offer solutions for this by enabling rapid and sensitive diagnostics with results obtained directly in the field. This mini review gives a short overview of channel‐flow, paper, droplet and digital microfluidics‐based platforms integrated with nucleic acid amplification, immunosensors or morphological methods for fungal, oomycete, bacterial and viral detection. We touch on recent material enhancements and sample preparation strategies that have improved the performance of these devices. Finally, we explore the challenges and opportunities of deploying miniature diagnostic devices across diverse agricultural and environmental settings, emphasising the need for specificity and reliability in detecting plant pathogens, supporting timely disease management.

Rhizosphere microbes enhance plant resistance to cadmium through a root ROS-microbial IAA-root DNA methylation interkingdom signaling pathway.