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bioRxiv2024

Virophage replication mode determines ecological and evolutionary changes in a host-virus-virophage system

Giant viruses can control their eukaryotic host populations, shaping the ecology and evolution of aquatic microbial communities. Understanding the impact of the viruses own parasites, the virophages, on their control of microbial communities remains a challenge. Most virophages have two modes of host infection and replication. They can exist as free particles that co-infect a host cell with the virus and replicate but inhibit viral replication. Virophages can also integrate into the host genome and remain dormant until the host is infected with a virus, leading to virophage reactivation and replication that does not immediately inhibit viral replication. Both replication modes are present within host-virus-virophage communities, and their relative contributions are expected to be context dependent and dynamic over time. The consequences of this dynamic regime for ecological and evolutionary dynamics remain unexplored. Here, we test whether and how the relative contribution of virophage replication modes influences the ecological dynamics of an experimental host-virus-virophage system and the evolutionary responses of the virophage. To do this, we indirectly manipulated the level of virophage (Mavirus) integration into the host (Cafeteria burkhardae) in the presence of the giant Cafeteria roenbergensis virus (CroV) (later identified as Cafeteria burkhardae, Schoenle et al. 2020). Our results show that higher virophage integration is positively correlated with host survival, but negatively correlated with virophage reactivation. In addition, communities with higher virophage integration were characterised by lower population densities and reduced fluctuations in both host and viral populations, whereas virophage fluctuations were increased. This study reveals the complex interplay between virophages, viruses and hosts, in which the virophage dual replication mode is a dynamic and reactive mechanism contributing to persistence of the microbial community.

evolutionary biology↗

bioRxiv2024

Ecological divergence is marked by specific plastic gene expression and distinct rhizosphere among sibling allopolyploid marsh orchids (Dactylorhiza)

Phenotypic plasticity, the dynamic adjustment of traits to environmental variations, is crucial for enabling species to exploit broader niches and withstand suboptimal conditions. This adaptability is particularly relevant for newly formed allopolyploids, which possess redundant gene copies and must become established in diverse environments distinct from their parents and other relatives. By evaluating gene expression and root mycobiome among two ecologically divergent sibling allopolyploid marsh orchids (Dactylorhiza majalis and D. traunsteineri) in reciprocal transplants at localities where both species are native, we aimed to understand the drivers of species persistence in the face of interspecific gene flow. Despite consistent abiotic differences characterising the alternative environments at each locality, the majority of gene expression differences between the allopolyploids appears to be plastic. Ecologically relevant processes, such as photosynthesis and transmembrane transport, include some genes that are differentially expressed between the two orchids regardless of the environment, while others change their activity plastically in one species or the other. This suggests that although plasticity helps define the specific ecological range of each sibling allopolyploid, it also mediates gene flow between them, thereby preventing differentiation. Extending our investigations to the root mycobiome, we uncover more diverse fungal communities for either species when grown in the environment with nutrient-poor soils, indicating that both abiotic and biotic factors drive the distribution of sibling marsh orchids. Altogether, our results indicate that plasticity can simultaneously promote diversification and homogenization of lineages, influencing the establishment and persistence of recurrently formed allopolyploid species. Significance statementThis study highlights the role of phenotypic plasticity in the persistence and distribution of sibling allopolyploid marsh orchids (Dactylorhiza majalis s.l.). By examining gene expression and the diversity of root mycobiome across reciprocal transplantations in native environments, we uncover high plasticity that facilitates adaptation and gene flow, thereby promoting both diversification and homogenization. These findings underscore the importance of plasticity in the establishment and long-term survival of allopolyploid species across the landscape.

evolutionary biology↗

bioRxiv2024

Ecological drivers of CRISPR immune systems

1CRISPR-Cas is the only known adaptive immune system of prokaryotes. It is a powerful defense system against mobile genetic elements such as bacteriophages. While CRISPR-Cas systems can be found throughout the prokaryotic tree of life, they are distributed unevenly across taxa and environments. Since adaptive immunity is more useful in environments where pathogens persist or reoccur, the density and/or diversity of the host/pathogen community may drive the uneven distribution of CRISPR system. We directly tested hypotheses connecting CRISPR incidence with prokaryotic density/diversity by analyzing 16S rRNA and metagenomic data from publicly available environmental sequencing projects. In terms of density, we found that CRISPR systems are significantly favored in lower abundance (less dense) taxa and disfavored in higher abundance taxa, at least in marine environments. When we extended this work to compare taxonomic diversity between samples, we found CRISPR system incidence strongly correlated with diversity in human oral environments. Together, these observations confirm that, at least in certain types of environments, the prokaryotic ecological context indeed plays a key role in selecting for CRISPR immunity. 2 ImportanceMicrobes must constantly defend themselves against viral pathogens, and a large proportion of prokaryotes do so using the highly effective CRISPR-Cas adaptive immune system. However, many prokaryotes do not. We investigated the ecological factors behind this uneven distribution of CRISPR-Cas immune systems in natural microbial populations. We found strong patterns linking CRISPR-Cas systems to prokaryotic density within ocean environments and to prokaryotic diversity within human oral environments. Our study validates previous within-lab experimental results that suggested these factors might be important and confirms that local environment and ecological context interact to select for CRISPR immunity.

microbiology↗

bioRxiv2024

Herbicidal interference: glyphosate drives both the ecology and evolution of plant-herbivore interactions

The coevolution of plants and their insect herbivores reflects eco-evolutionary dynamics at work-- ecological interactions influence adaptive traits, which feed back to shape the broader ecological community. However, novel anthropogenic stressors like herbicide, which are strong selective agents, can disrupt these dynamics. Little is known about how the evolution of herbicide resistance may impact plant-herbivore interactions. We performed a common garden field experiment using Ipomoea purpurea (common morning glory) and the herbicide glyphosate (Roundup) to investigate the ecological effects of herbicide exposure on insect herbivory patterns and assess the potential evolutionary consequences. We find that plants treated with glyphosate experienced higher levels of herbivory and altered chewing herbivory damage patterns. Additionally, we found that glyphosate resistance is positively associated with herbivory resistance, and uncovered positive selection for increased glyphosate resistance, suggesting that selection for increased glyphosate resistance has the potential to lead to increased herbivory resistance. Positive selection for glyphosate resistance, coupled with the detection of genetic variation for this trait, suggests there is potential for glyphosate resistance--and herbivory resistance via hitchhiking-- to further evolve. Our results show that herbicides can not just influence, but potentially drive the eco-evolutionary dynamics of plant-herbivore interactions.

evolutionary biology↗

bioRxiv2024

Repeated evolution of reduced visual investment at the onset of ecological speciation in high-altitude Heliconius butterflies.

Colonisation of new habitats is typically followed by divergent selection acting on traits that are immediately important for fitness in the new habitat. For example, shifting sensory environments are often associated with variation in sensory traits critical for navigation and foraging. However, the extent to which the initial response to novel sensory conditions is mediated by phenotypic plasticity, and its contribution to early species divergence remains unclear. We took advantage of repeated cases of speciation in Heliconius butterflies with independent allopatric distributions in the west of the Colombian and Ecuadorian Andes. Using volumetric brain measurements, we analysed patterns of investment in sensory processing in brain components across different localities and habitats. We find that a higher-altitude species, H. chestertonii, differs in levels of investment in visual and olfactory brain centres compared to its lower altitude relative H. erato venus, mainly attributable to heritable variation as inferred from comparisons between wild and common-garden reared individuals. We compared these shifts with those reported for another high-altitude species, H. himera, and its parapatric lowland counterpart, H. erato cyrbia, and demonstrate parallel reductions in the size of specific optic lobe neuropils. Conversely, for the antennal lobe, we detected disparate trait shifts in H. himera and H. chestertonii in respect to their lowland erato neighbours. Overall, our findings add weight to the adaptive potential for neuroanatomical divergence related to sensory processing during early species formation. Lay summaryRepeated associations between trait variation and environmental shifts may indicate adaptation to local sources of natural selection. For instance, in fish, the presence of certain morphological traits in specific ecological conditions across independent populations is well documented, suggesting equivalent phenotypic responses to shared sources of natural selection. We compared independent cases of ecological divergence in Heliconius butterflies distributed along altitude gradients from sea level to mid mountain in the west of the Colombian and Ecuadorian Andes. Shifts in altitude involve repeated, abrupt transitions from wet, large-leaved, warm forests to higher dry, open, cold scrubs. We tested hypotheses about the role of these ecological shifts in driving adaptive evolution in neuroanatomical traits during early speciation. We showed that in Heliconius, independent changes in forest-type have been accompanied by heritable parallel patterns of divergence in sensory investment in visual processing in the brain. We propose these differences likely facilitate species divergence in the face of ongoing geneflow.

evolutionary biology↗

bioRxiv2024

Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems

Viruses are ubiquitous in deep-sea hydrothermal environments, where they exert a major influence on microbial communities and biogeochemistry. Yet, viral ecology and evolution remain understudied in these environments. Here, we identified 49,962 viruses from 52 globally distributed hydrothermal vent samples (10 plumes, 40 deposits, and 2 diffuse flow), and reconstructed 5,708 viral metagenome-assembled genomes (vMAGs), the majority of which were bacteriophages. Hydrothermal viruses were largely endemic. However, some viruses were shared between geographically separated vents, predominantly between the Lau Basin and Brothers Volcano in the Pacific Ocean. Geographically distant viruses often shared proteins related to core functions such as structural proteins, and rarely, proteins of auxiliary functions. Common microbial hosts of viruses included members of Campylobacterota, Alpha-, and Gammaproteobacteria in deposits, and Gammaproteobacteria in plumes. Campylobacterota- and Gammaproteobacteria-infecting viruses reflected variations in hydrothermal chemistry and functional redundancy in their predicted microbial hosts, suggesting that hydrothermal geology is a driver of viral ecology and coevolution of viruses and hosts. Our study indicates that viral ecology and evolution in globally distributed hydrothermal vents is shaped by endemism, and thus may have increased susceptibility to the negative impacts of deep-sea mining and anthropogenic change in ocean ecosystems.

microbiology↗

bioRxiv2024

Genomic stability in the Galapagos Scalesia adaptive radiation: Consistent transposable element accumulation despite hybridization and ecological niche shifts

Transposable elements (TEs) have been hypothesized to play a pivotal role in driving diversification by facilitating the emergence of novel phenotypes and the accumulation of divergence between species. Hybridization and adaptation to novel niches are hypothesized to influence TE accumulation in genomes by disrupting genomic regulation, including the suppression of TE replication. The rapid speciation and ecological diversification characteristic of adaptive radiations offer a unique opportunity to examine the link between TE accumulation and speciation, diversification, hybridization and adaptation. Here, focusing on all 15 species of the genus Scalesia (Asteraceae), a radiation endemic to the Galapagos Islands, we test whether hybridization or shifts in ecological niche are associated with changes in TE accumulation in genomes. Our analyses reveal little to no variation in TE accumulation among Scalesia species nor its hybrid populations. Shifts in ecological niches, linked to climatic variation, did not result in discernible changes in TE accumulation, a surprising finding given the anticipated selective pressure imposed by aridity, a factor often linked to genome size reduction. We found no distinct patterns in the temporal accumulation of TEs, and no effects at the class or superfamily level. Our findings challenge the assertion that TEs have directly driven diversification, speciation and local adaptation. Instead, we suggest that TEs may simply be along for the ride, rather than actively contributing to plant diversification.

evolutionary biology↗

bioRxiv2024

Integration of multi-level dental diversity links macro-evolutionary patterns to ecological strategies across sharks.

Sharks are notorious for their exceptional dental diversity, which is frequently used as a proxy for ecological function. However, functional inferences from morphology need to consider morphological features across different organizational scales, from small cusplets to patterns at the level of the entire jaw. Here, we deploy a set of classic and novel morphometric approaches to quantify morphological features ranging from sub-dental features to whole dentitions within a large ensemble of species encompassing all extant orders of sharks. We then correlate these measures with habitat, feeding and body size traits and track their variation as a function of genetic distance, a measure of trait adaptability. Intriguingly, sharks tend to either explore tooth-level or dentition-level complexity, resulting in two distinct groups with key differences in tooth symmetry, graduality of heterodont change, and depth of habitat. Overall, we find that intermediate levels of resolution, namely monognathic heterodonty in comparison with dignathic heterodonty and tooth-level shape descriptors, show the strongest predictive power for ecological traits, while exhibiting low phylogenetic signal, which suggests a more dynamic adaptability on shorter evolutionary timescales. This raises macro-evolutionary interpretations about the evolvability of nested modular phenotypic structures, with likely important implications for paleo-ecological inferences from sequentially homologous traits.

systems biology↗

bioRxiv2024

The Microbial Ecology of Serpentinites

Serpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that are challenging for life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, serpentinite-hosted biospheres offer insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the ability of serpentinites to support abundant microbial communities was only recognized [~]20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of marine and continental serpentinite-hosted biospheres in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo of in situ evolution, and the extent to which modern serpentinites serve as analogs for those on early Earth. These topics are explored herein from a microbial perspective to outline key knowledge-gaps that should be a focus of future research.

microbiology↗

bioRxiv2024

Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes

Understanding the spread of antibiotic-resistant bacteria in human-associated microbial communities, particularly in the gut microbiome, is critical for combating the global resistance crisis. However, the role of various ecological factors, such as intraspecies or interspecies interactions, in modulating this process is poorly understood. We hypothesized that different strains within the same species would exhibit distinct interactions with the resident microbiota, leading to variable invasion outcomes. To test this, we examined the population growth of multiple clinically relevant antibiotic-resistant E. coli strains carrying ESBL and carbapenemase resistance plasmids. We introduced these strains into human gut microbiome samples from healthy individuals, using replicated anaerobic microcosms treated or untreated with antibiotics. We found that while antibiotic exposure significantly influenced the growth of these incoming strains, some were successful even in the absence of antibiotics. The variation in ecological success across strain-microbiome sample combinations was positively associated with the intrinsic growth capacities of the strains in local abiotic conditions and their competitive interactions with resident E. coli. Furthermore, the incoming resistant strains had strain- specific effects on the taxonomic composition of the resident microbiota; different strains not only varied in their growth performance in human microbiomes, in some cases they pushed taxonomic composition of the resident community in different directions. In contrast with phenotypes measured in gut microcosms, metabolic profiles measured across various single-carbon-source environments were not reliable predictors of population growth in human microbiomes. Overall, this controlled design reveals the multi-layered ecological dynamics and strain-specific mechanisms that govern the spread of antibiotic-resistant bacteria in individual human-associated microbiomes.

microbiology↗

bioRxiv2024

Ecological Scaling of Temporal Fluctuations with Bacterial Abundance in Gut Microbiota Depends on Functional Properties of Individual Microbial Species and Bacterial Communities

Macroecological relationships that describe various statistical associations between species abundances, their spatial, and temporal variability are among the most general laws in ecology and biology. One of the most commonly observed relationships is a power-law scaling between means and variances of temporal species abundances, known in ecology as Taylors law. Taylors law has been observed across many ecosystems, from diverse plant and animal ecosystems to complex microbial communities. While many mathematical models have been proposed to explain the potential origins of Taylors law, what determines its scaling exponents across species and ecosystems is not understood. Here, we use temporal trajectories of human and baboon gut microbiota to analyze the relationship between functional properties of individual bacterial species and microbial communities with the scaling of species-specific and community-level Taylors law. The species Taylor law characterizes - for each individual species - the relationship between the species temporal abundance means and temporal abundance variances across host organisms. On the other hand, community-level Taylors law characterizes - in each host organism - the scaling across multiple species between their temporal abundance means and temporal abundance variances. For community Taylors law, we find that the power law scaling is strongly associated with the microbiota abundance of certain nutrient-degrading enzymes in the gut. Notably, our results demonstrate that the availability of enzymes metabolizing starch glycogen significantly increases Taylors law scaling. We also find that species Taylors law depends on the individual species functional properties. Specifically, we observe lower Taylors law scaling for species with larger metabolic networks, for species that are able to grow on a larger number of carbon sources, and for species with particular metabolic functions, such as glutamine and folate metabolism. Overall, our study reveals that Taylors law scaling is strongly associated with the functional capabilities of bacterial communities and individual microbial species biosynthetic properties, which are likely related to their ecological roles in the gut microbiota.

microbiology↗

bioRxiv2024

New isolate genomes and global marine metagenomes resolve ecologically relevant units of SAR11

The bacterial order Pelagibacterales (SAR11) is widely distributed across the global surface ocean, where its activities are integral to the marine carbon cycle. High-quality genomes from isolates that can be propagated and phenotyped are needed to unify perspectives on the ecology and evolution of this complex group. Here, we increase the number of complete SAR11 isolate genomes threefold by describing 81 new SAR11 strains from coastal and offshore surface seawater of the tropical Pacific Ocean. Our analyses of the genomes and their spatiotemporal distributions support the existence of 29 monophyletic, discrete Pelagibacterales ecotypes that we define as genera. The spatiotemporal distributions of genomes within genera were correlated at fine scales with variation in ecologically-relevant gene content, supporting generic assignments and providing indications of speciation. We provide a hierarchical system of classification for SAR11 populations that is meaningfully correlated with evolution and ecology, providing a valid and utilitarian systematic nomenclature for this clade.

microbiology↗

bioRxiv2025

Systematic Metaproteomics Mapping Reveals Functional and Ecological Landscapes of Human Gut Microbiota Responses to Therapeutic Drugs

Therapeutic compounds exert impacts on gut microbiota; however, how they affect the community functional ecology, especially as reflected at the protein level, remains largely unexplored. In this study, we systematically map metaproteomic responses of ex vivo human gut microbiota to 312 compounds, generating 4.6 million microbial protein responses, available as an interactive resource (https://shiny.imetalab.ca/MPR_Viz/). Protein-level analyses identify significant metaproteomic shifts induced by 47 compounds, with neuropharmaceuticals as the sole drug class significantly enriched among these hits. Further analyses on the community level reveal a tri-stability pattern in microbial composition and the emergence of three distinct functional states, based on a functional beta-diversity metric. Notably, neuropharmaceuticals cause particularly strong effects on the microbiomes, lowering the proteome-level functional redundancy and raising the level of antimicrobial resistance proteins, ultimately pushing the microbiome into an alternative functional state. Preliminary validation suggests that enhancing functional redundancy may contribute to maintaining microbiota resilience against neuropharmaceutical-induced antimicrobial resistance. Overall, this work establishes a comprehensive view of how drugs influence gut microbiome function and ecology at the protein level, proposes a landscape-based framework for interpreting community resilience, and highlights the need to consider protein-level and ecological responses in the evaluation of therapeutic interventions.

microbiology↗

bioRxiv2025

Likelihood of social-ecological genetic model

The genetic structure of populations depends on two parallel processes - genetic and social-ecological - providing mutual information. Models that describe species responses within social-ecological systems are increasingly important in the context of modern environmental crises. Advances in genetic data collection now provide access to vast numbers of markers, enabling a more comprehensive understanding of species dynamics. However, current statistical inference methods do not fully integrate these processes into a single cohesive model, and rely on summary statistics derived from separate inferences and simulations. In this work, I propose a probabilistic framework based on a coalescent model to compute the likelihood of a demogenetic model represented as connected graphs. The population graph, linking population nodes, is characterized by a backward gene adjacency matrix, which describes the probability of gene origins and is influenced by niche and dispersal functions. The genetic graph, linking allele nodes, captures mutation probabilities. A third graph represents the coalescence process of genes within the demographic and genetic graphs. Coalescence is simulated within the demographic model, and its probability is estimated based on the genetic model, or vice versa. Likelihood estimation is performed using a Monte Carlo algorithm. This framework allow likelihood-based sampling and Bayesian inference, offering a robust approach for environmental niche and meta-population modeling. I also discuss the practical applications of this model. By combining environmental niche functions with a coalescent framework, this approach enables probabilistic reconstructions of past species distributions based on present and historical occurrence data. It can incorporate various data sources, including historical records, absence data, and genetic information. By integrating niche and dispersal processes into a unified model, this framework provides a powerful tool for improving species distribution forecasting and deepening our understanding of species responses to environmental change as interconnected systems. Author summaryInferring biodiversity responses to social-ecosystem history using population genetic and environmental history data is crucial in the context of modern environmental crises. However, existing models do not fully integrate key processes such as niche modeling, coalescent modeling, and genetic modeling, often relying on approximate Bayesian computation for inference. In this work, I propose a method to estimate the likelihood of a fully integrated demo-genetic model that links population genetic data with socio-ecosystem history. The proposed method is based on a hidden coalescent process simulated within a social-ecosystem graph, along with a sampling process represented in a genetic mutation graph. In the social-ecosystem graph, nodes represent populations, and their effective sizes are estimated using niche models that account for environmental variables. The edges of the graph represent effective migration, which is estimated through connectivity models. The resulting likelihood function can be used for Bayesian or maximum likelihood inference of genetic changes within socio-ecosystems. This approach offers a flexible framework for inferring demo-genetic models across various fields, including phylogeography, agrobiodiversity evolution, ecology, and epidemiology. It can be applied for forecasting or hypothesis testing, providing a comprehensive tool for understanding genetic dynamics in relation to socio-ecosystem processes.

bioinformatics↗

bioRxiv2025

MNetClass: A Control-Free Microbial Network Clustering Framework for Identifying Central Subcommunities Across Ecological Niches

Investigating microbiome subnetworks and identifying central microbes in specific ecological niches is a critical issue in human microbiome studies. Traditional methods typically require control samples, limiting the ability to study microbiomes at distinct body sites without matched controls. Moreover, some clustering methods are not well-suited for microbial data and fail to identify central subcommunities across ecological niches after clustering. In this study, we present MNetClass, a novel microbial network clustering analysis framework. It utilizes a random walk algorithm and a rank-sum ratio-entropy weight evaluation model to classify key subnetworks and identify central microbes at any body site without the need for control samples. By applying MNetClass to microbiome data from five distinct oral sites, we successfully uncovered site-specific microbial subgroups and their central microbes. Additionally, simulations and Autism Spectrum Disorder (ASD) cohort datasets demonstrated that MNetClass outperforms existing unsupervised microbial clustering methods in terms of both accuracy and predictive power. In case studies, MNetClass identified age-related microbial communities across different oral sites, highlighting its broad applicability in microbiome research. IMPORTANCEMNetClass provides a valuable tool for microbiome network analysis, enabling the identification of key microbial subcommunities across diverse ecological niches. Implemented as an R package (https://github.com/YihuaWWW/MNetClass), it offers broad accessibility for researchers. Here, we systematically benchmarked MNetClass against existing microbial clustering methods across multiple datasets using various performance metrics, demonstrating its superior efficacy. Notably, MNetClass operates without the need for control groups and effectively identifies central microbes, highlighting its potential as a robust framework for advancing microbiome research.

bioinformatics↗

bioRxiv2025

EcoFoldDB: Protein structure-guided functional profiling of ecologically relevant microbial traits at the metagenome scale

Microbial communities are fundamental to planetary health and ecosystem processes. High-throughput metagenomic sequencing has provided unprecedented insights into the structure and function of these communities. However, functionally profiling metagenomes remains constrained due to the limited sensitivity of existing sequence homology-based methods to annotate evolutionarily divergent genes. Protein structure, more conserved than sequence, and intrinsically tied to molecular function, offers a solution. Capitalising on recent breakthroughs in structural bioinformatics, we present EcoFoldDB, a database of protein structures curated for ecologically relevant microbial traits, and its companion pipeline, EcoFoldDB-annotate, which leverages Foldseek with the ProstT5 protein language model for rapid structural homology searching directly from sequence data. EcoFoldDB-annotate outperforms state-of-the-art sequence-based methods in annotating metagenomic proteins, in terms of sensitivity and precision. To demonstrate its utility and scalability, we performed structure-guided functional profiling of 32 million proteins encoded by 8,000 high-quality metagenome-assembled genomes from the global soil microbiome. EcoFoldDB-annotate could resolve the phylogenetic partitioning of important nitrogen cycling pathways, from taxonomically restricted nitrifiers to more widespread denitrifiers, as well as identifying novel, uncultivated bacterial taxa enriched in plant growth-promoting traits. We anticipate that EcoFoldDB will enable researchers to extract ecological insights from environmental genomes and metagenomes, and accelerate discoveries in microbial ecology.

microbiology↗

bioRxiv2025

In Silico Evaluation and Therapeutic Targeting of LVDD9B Protein for WSSV Inhibition: Molecular and Ecological Insights for Aquaculture Solutions

BackgroundThis study aimed to investigate structural dynamics, binding interactions, stability, pharmacokinetics, ecological risks, and bioactivity of shrimp receptor protein LVDD9B to identify potential therapeutic candidates against White Spot Syndrome Virus (WSSV). MethodsLVDD9B proteins 3D structure was predicted using SWISS-MODEL and validated with ProSA and Ramachandran plots. Protein-protein docking between LVDD9B and VP26 (WSSV protein) was performed using HADDOCK 2.4 server. Molecular docking, dynamics simulations, binding-free energy calculations, principal component analysis (PCA), electrostatic, and vibrational frequency analyses evaluated binding affinity, stability and polarity of complexes. Results128-amino-acids of LVDD9B protein was predicted as predominantly cytoplasmic with stable, and hydrophilic, with structural analysis identified key secondary structures and conserved chitin-binding site. Docking studies revealed strong interactions between LVDD9B and VP26, supported by hydrogen-bonds and salt bridges. Molecular dynamics simulations demonstrated stable complexes with fluctuating RMSD values, and MM/GBSA calculations indicated favorable binding free energies. Pharmacokinetic analysis highlighted promising bioavailability and drug-like properties for Luteolin and Quercetin from Cuscuta reflexa, while ecological assessment identified Cosmosiin as least hazardous, with Quercetin and Luteolin showing higher toxicity. PCA revealed stable protein-ligand complexes with flexibility in Apo form. Isorhoifolin exhibited the lowest internal energy (-2099.4722 Hartree) and highest dipole moment (8.1833 Debye). Frontier orbital analysis showed HOMO-LUMO gaps (4.05-4.34 eV) influencing reactivity, while MEP and vibrational frequency analyses supported compound stability and bioactivity. ConclusionsThis study explores LVDD9Bs structural and interaction dynamics for developing antiviral therapy against WSSV, highlighting therapeutic potential of Cosmosiin, Isorhoifolin, Quercetin and Luteolin based on their pharmacokinetic and ecological profiles.

bioinformatics↗

bioRxiv2025

Wild raccoons are more innovative but not bolder than another ecological generalist, the Virginia opossum, on a pull-string task

Humans are altering natural environments at unprecedented rates. Ecological generalism is one of the strongest predictors of survival in light of these changes which, in animals, may be shaped by bold and innovative behaviours. Species with greater habitat generalism are proposed to behave more boldly (e.g., touching and ingesting novel food). Species with greater dietary generalism are proposed to behave more innovatively (e.g., novel problem-solving to access food). Support for both hypotheses exists but remains largely restricted to broad comparisons between generalists and specialists. Further comparative data are needed to understand the extent to which these behavioural patterns might shape more nuanced ecological variation between species, such as species with finer-scale niche differences. We compared bold and innovative behaviour in two wild sympatric generalists, the Northern raccoon (Procyon lotor) and Virginia opossum (Didelphis virginiana), using a pull-string task with strings and wires attached to vertical cups containing high-value food. Although both species are broadly classified as generalists, raccoons show relatively greater habitat and dietary flexibility than opossums. Because they live sympatrically, it offers a unique opportunity to test - at the same time and locations - whether these finer-scale niche differences are reflective of differences in their bold and innovative behaviour. We predicted that raccoons would display bolder behaviour (in terms of touching our novel task) and more innovative behaviour (in terms of solving it). We found that both species were equally likely to acknowledge and touch the task, but raccoons were more likely to display innovation to access the food. Raccoons propensity for using innovation to solve novel foraging challenges may contribute to their greater ecological flexibility compared to opossums. More broadly, our findings may help explain differences in how each species adapts to environmental changes. HighlightsO_LIBold and innovative behaviour may help some species adapt to environmental changes C_LIO_LIWe administered a novel pull-string task to wild raccoons and opossums C_LIO_LIRaccoons displayed more innovative, not bolder, behaviour than opossums C_LIO_LIBoth species are generalists, but raccoons are more flexible than opossums C_LIO_LIDifferences in innovation may shape their finer-scale niche differences C_LI

animal behavior and cognition↗