Biology subjects

Lurgi, M.

Publications and source records attributed to Lurgi, M..

14 recordsLinked to original sources

bioRxiv2026

Ocean depth modifies host-microbiome ecology and evolution

A major unsolved question in ecology and evolution is how similar free-living and symbiotic microbial communities are. In marine systems, depth homogenises free-living communities due to stronger dispersal and weaker environmental filtering compared to surface waters. We show that symbiotic communities of marine sponges follow a different pattern, with a subset of sponge species mirroring the increased similarity with depth seen in their free-living counterparts, while others remain highly host-specific both in shallow and deep waters. Moreover, in deep waters, more phylogenetically similar hosts harbor more similar microbiomes, yet host-symbiont cophylogeny nearly vanishes. This reveals two contrasting eco-evolutionary assembly rules: in more constant environments like the deep sea, community assembly is driven by host and environmental filtering with minimal signature of coevolution, whereas in variable environments, like shallow waters, host-symbiont coevolution is strong and key to maintain host-specific microbiomes.

microbiology↗

bioRxiv2026

SPARK-ID: Dynamic DSB-sensor interactomes reveal modular nuclear repair networks coordinated by connector proteins

DNA double-strand breaks (DSBs) activate repair pathways that must be coordinated with other cellular functions. Although DSB sensors SIRT6, Ku80, and MRE11 initiate repair, how they organize these nuclear processes remains unknown. SPARK-ID is a proximity-labeling strategy mapping DDR interactome dynamics. Using these sensors as baits, we resolved chromatin-associated interactomes from damage formation to recovery. The sensors shared an enriched repair core while capturing distinct interactors, allowing temporal specialization: SIRT6ID was biased toward RNA and chromatin regulation, Ku80ID toward telomere-associated and translational programs, and MRE11ID toward recombination and DNA synthesis. Modularity analysis showed these functions are organized into modules linked by "connectors". Among them, Nucleolin linked DNA repair, RNA-metabolism, and nucleolar modules. Nucleolin depletion rewired DSB-sensor interactomes, altered repair-associated complex composition, expanded {gamma}H2AX domains, and reduced BRCA1, 53BP1, and phospho-ATM foci. Altogether, SPARK-ID reveals modular DSB-sensor interactomes whose robustness depends on connectors that integrate and constrain the DNA damage response. Graphical AbstractThree DSB sensors (MRE11, Ku80, SIRT6) orchestrate DNA repair through dynamic protein-protein interaction networks that expand upon DSB induction. Proximity labeling reveals distinct sensor interactomes that share a functional core of nuclear processes while incorporating sensor-specific interactors for pathway specialization. These networks contain connector nodes that coordinate multiple parallel nuclear functions, enabling functional diversification and conferring robustness to the DNA damage response. The sensors reshape their interactome structure and composition to integrate and constrain cellular responses through organized macromolecular complexes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/740882v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1bb112dorg.highwire.dtl.DTLVardef@64cc4dorg.highwire.dtl.DTLVardef@1a0e2d1org.highwire.dtl.DTLVardef@18b3e8b_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2026

Habitat restoration promotes recolonisation by extirpated species in model meta food webs

Successful ecosystem restoration is intimately linked to the persistence of species in local communities and across landscapes. As such quantitative approaches to ecological restoration require the integration of community and metapopulation ecology. Together these disciplines demonstrate that local colonisation, via habitat connectivity and size, and species interactions, both modulate the process of community assembly. However, thus far restoration ecology still remains disconnected from network ecology this preventing a holistic, community-wide perspective to restoration. We aim to inform ecological restoration using a multi-layer modelling framework integrating ecological interactions and species dispersal dynamics. We explore the drivers that modulate recolonisation dynamics of species across restored landscapes. We further investigate how restoration improves the structural properties of food webs, the number of successful recolonisations and the role of configuration of restored patches in restoration outcomes. We find that recolonisation is the result of a trade-off between dispersal ability and energy requirements. 97% of plant recolonisation and 88% of herbivore recolonisations happened within close proximity to the source patches. Better dispersers - intermediate and top species in the food webs - were able to recolonise habitat by benefitting from the increased biomass influx from restoration. When only a small proportion of the landscape could be restored, the location and connectivity of restored areas strongly influenced the outcome of restoration: more connected patches enabled on average the recolonisation of about 1 additional intermediate species compared to that of isolated patches. However, this difference faded as soon as more patches were restored, and improving larger portions of the landscape always resulted in better outcomes. Restoring 1/3 of the landscape enabled on average the recolonisation of ~4 additional species. Our findings suggest that quantitative models can inform restoration efforts necessary to bring native species back to restored areas. They also suggest that attention should be given to the requirements of the recolonisers, the distance of their introduction from restored areas and their trophic and ecological niche. These aspects are crucial to assess their energy and habitat requirements for successful establishment.

ecology↗

bioRxiv2026

An eco-evolutionary theory of host-associated microbiomes

Host-associated microbiomes often display host specificity and heritability, yet the evolutionary processes under which such structured communities first emerge are still unclear. In particular, the conditions by which intergenerational (i.e. vertical) transmission of microbes can evolve and generate host-specific microbiomes are still unresolved. Here, we present an eco-evolutionary theory of microbiome assembly under minimal assumptions of microbial dynamics (i.e. neutrally driven by environmental fluctuations) and host control. We consider the adaptive evolution of microbial and host traits, including microbiome size and vertical transmission. We show that environmental fluctuations can generate enough among-host microbial variation to enable host-level selection favouring beneficial microbiome configurations. Vertical transmission can then evolve and, even when weak, allow microbiome specificity to be inherited and amplified across generations despite continuous influx from the external environment. Selection is most effective at intermediate levels of environmental fluctuation and host lifespan, revealing fundamental trade-offs between stochastic assembly, inheritance, and dispersal of microbes. The resulting microbiomes are dense, host-specific, and heritable, yet retain high intraspecific variability and lack strict phylosymbiosis. Simulated patterns of microbial dominance, diversity, and host-microbiome dissimilarity closely match those observed in nature, as evidenced using marine sponge microbiomes. Our results provide a mechanistic theory for the early evolution of host-associated microbiomes, showing that beneficial and species-specific communities can arise through selection and inheritance prior to the evolution of dedicated host-control mechanisms.

evolutionary biology↗

bioRxiv2025

The eco-evolutionary assembly of complex communities with multiple interaction types

Identifying the mechanisms that generate structure in complex ecological communities is fundamental to understand their assembly. A comprehensive picture of how ecology and evolution act together to generate these patterns is in its infancy. We developed an eco-evolutionary model of community assembly that incorporates interaction-driven population dynamics and evolutionary processes, including speciation and the inheritance of interactions, to unveil the mechanisms of generation and maintenance of biodiversity in complex species interaction networks. Importantly, our model unpicks the effects of selection of interaction types from those of inheritance by comparing evolutionary assembly with assembly by invasion under different combinations of interaction types. We found that a cost-benefit balance of accumulating interactions separates communities into two distinct types. Interactions with weak benefits for the partners involved produce communities with sparse species interaction networks dominated by competition. Strongly beneficial interactions, on the other hand, give rise to highly mutualistic, more connected communities. Mutualism, driven by both selection and inheritance, facilitates the emergence of large yet stable communities with increased complexity. By contrasting the model results with empirical patterns from microbial communities, we identify potential drivers of the assembly of these complex ecosystems and their likely patterns of interaction. Our results provide a classification system of complex ecosystems based on their composition of ecological interactions, thus generating testable hypotheses on the conditions under which different community types (mutualistic vs. competitive) might emerge.

ecology↗

bioRxiv2025

Towards key principles of host-associated microbiome assembly

Symbiotic relationships between microbes and host organisms frequently involve the assembly of complex microbial communities (microbiomes) within hosts. Patterns at the community level influence life-history traits, the evolutionary trajectories of both microbes and their hosts, and are often critical for maintaining host health. These community-level patterns are dynamically driven by eco-evolutionary mechanisms acting at the individual level, such as microbial dispersal, host selection, and microbe-resource interactions. Critically, we still lack a clear picture of the ways in which these mechanisms interact to shape microbiome assembly. Here, we present a model of assembly to describe how distinct community structures can be characterised by underlying mechanisms. To illustrate the approach, we analyse microbiome data from marine sponges and simulate different structures of host-microbe associations, thereby bridging mechanistic models and empirical patterns. We further apply the model to human microbiome data to explore its relevance across biological systems, proposing that the combined effect of a small set of general mechanisms may govern diverse patterns of microbial diversity and abundance. Our findings advance ecological theory by linking individual-level processes to community-scale patterns, illuminating the key drivers underlying microbiome assembly.

microbiology↗

bioRxiv2025

Optimising biodiversity offsetting to account for habitat succession and species colonisation dynamics

Biodiversity offsetting schemes aim to balance habitat loss from development through conservation and restoration, yet their long-term ecological outcomes under repeated impact-offset cycles remain uncertain. Using a conceptual modelling framework based on forest succession, we show that offsetting success hinges on two critical factors: the scale of habitat compensation and the duration of conservation commitments. We show that effective offsetting requires not only restoring areas larger than those impacted, but also sustaining conservation over timeframes that align with the ecological timescales of habitat development. Rapid habitat conversion consistently undermines offset success, particularly since the persistence and recovery of habitat-dependent, colonising species are highly sensitive to how quickly habitats are lost, how long restoration sites are protected, and how much time they need to reach sufficient habitat quality. Moreover, we show that short-term improvements do not necessarily meet long-term biodiversity targets. Given that habitat succession unfolds over decades or more, offset policies must move beyond short-term metrics. We emphasise that offsetting schemes must be scrutinized to ensure sufficient spatial compensation and time for habitat succession. Offsetting schemes should also account for different ecological indicators to avoid the ecological fallacy of short-term restoration success resulting in long-term biodiversity and ecosystem integrity loss.

systems biology↗

bioRxiv2025

More dominant baboons have less and lower quality sleep

The amount and quality of sleep individuals get can impact various aspects of human and non-human animal health, ultimately affecting fitness. For wild animals that sleep in groups, individuals may disturb one another, influencing sleep quality and quantity, but this aspect of social sleep has been understudied due to methodological challenges. Here, using nighttime rest (absence of bodily movements) as a proxy for sleep, we test the hypothesis that individuals social dominance can affect sleep opportunities by studying a troop of wild chacma baboons (Papio ursinus), a species with a strong hierarchical social structure. First, we show that the troops night-time rest (determined by 40Hz acceleration data) is highly synchronised. Next, we link night-time rest dynamics to daytime spatial networks and dominance hierarchy (from 1Hz GPS data and direct observations). We show that baboon rest synchrony is higher between similarly ranked individuals, and unexpectedly, more dominant baboons experience less and lower-quality rest. We propose that this hierarchy effect is explained by higher-ranked baboons resting closer to more group members, which also leads them exerting greater influence on each others night-time behaviour compared to lower-ranked individuals. Our study provides the first empirical evidence for the impact of social hierarchies on sleep in a wild primate, suggesting that dominance status may impose trade-offs between social rank and the quality and quantity of sleep.

animal behavior and cognition↗

bioRxiv2024

Structural stability determines evolutionary stability in mutualistic model ecosystems

Understanding the factors that influence the persistence and stability of complex ecological networks is a central focus of ecological research. Recent research into these factors has predominantly attempted to unveil the ecological processes and structural constraints that influence network stability. Comparatively little attention has been given to the consequences of evolutionary events, despite the fact that the interplay between ecology and evolution has been recognised as fundamental to understand the formation of ecological communities and predict their reaction to change. In light of current environmental challenges, there is a compelling need for a quantitative framework to predict biodiversity loss under environmental perturbations while accounting for evolutionary processes. We extend existing mutualistic population dynamical models by incorporating evolutionary adaptation events to address this critical gap. We relate ecological aspects of mutualistic community stability to the stability of persistent evolutionary pathways. Our findings highlight the significance of the structural stability of ecological systems in predicting biodiversity loss under both evolutionary and environmental changes, particularly in relation to species-level selection. Notably, our simulations reveal that the evolution of mutualistic networks tends to increase a network-dependent parameter termed critical competition, which places systems in a regime in which mutualistic interactions enhance structural stability and, consequently, biodiversity. This research emphasizes the pivotal role of natural selection in shaping ecological networks, steering them towards reduced effective competition below a critical threshold where mutualistic interactions foster stability. The outcomes of our study contribute to the development of a predictive framework for eco-evolutionary dynamics, offering insights into the interplay between ecological and evolutionary processes in the face of environmental change.

ecology↗

bioRxiv2024

Mutualism provides the basis for biodivesity in eco-evolutionary community assembly

Unveiling the ecological and evolutionary mechanisms underpinning the assembly of stable and complex ecosystems is a main focus of community ecology. Ecological theory predicts the necessity of structural constraints on the network of species interactions to allow for growth of complexity in assembling multispecies communities. A promising research avenue is the search for an understanding of how the coexistence of diverse species interaction types could influence the development of complexity and how an ideal composition could arise in nature. We propose an ecological model with mixed interaction types incorporating evolutionary assembly by speciation. This framework allows to investigate the eco-evolutionary assembly on complex species interaction networks with multiple interaction types and its consequences for ecosystem stability. Our results show that highly mutualistic communities are conducive of complexity and promote the emergence of consumer-resource interactions. Furthermore, we show that an evolutionary process is required to produce such condition. Moreover, this evolutionary assembly generates a diversity of outcomes and promotes two distinct types of complexity depending on speciation constraints. Assembled communities are thus either larger (more species) or more connected, in agreement with patterns previously observed in microbial communities. Our results produce invaluable theoretical insight into the mechanisms behind the emergence of ecological complexity and into the roles of mutualism and speciation on community formation.

ecology↗

bioRxiv2024

Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean

Sponges (phylum Porifera) harbour specific microbial communities that drive the ecology and evolution of the host. Understanding the structure and dynamics of these communities is emerging as a primary focus in marine microbial ecology research. Much of the work to date has focused on sponges from warm and shallow coastal waters, while sponges from the deep ocean remain less well-studied. Here, we present a metataxonomic analysis of the microbial consortia associated with 23 deep-sea sponges. We identify a high abundance of archaea relative to bacteria across these communities, with certain sponge microbiomes comprising more than 90% archaea. Specifically, the archaeal family Nitrosopumilaceae are prolific, comprising over 99% of all archaeal reads. Our analysis revealed sponge microbial communities mirror the host sponge phylogeny, indicating a key role for host taxonomy in defining microbiome composition. Our work confirms the contribution of both evolutionary and environmental processes to the composition of microbial communities in deep-sea sponges. ImportanceThe deep ocean is the largest biome on Earth, accounting for >90% of the planets marine environment. Despite this it remains a largely unexplored ecosystem, with less than 0.01% of the deep seafloor having been quantitatively sampled. Deep-sea sponges are ancient metazoans which harbour complex microbial communities and much still remains to be learned about the composition and diversity of these unique microbiomes. In an effort to address this, here we report a metataxonomic analysis of the microbial consortia associated with 23 deep-sea sponges from the equatorial Atlantic Ocean. Our findings reveal intricate, species-specific microbial communities dominated by ammonia-oxidizing archaea. This study highlights the significant role sponges play in shaping microbial consortia, providing new insights into deep-sea ecosystem dynamics. Importantly, our findings provide a scientific basis for understanding the evolutionary relationships between sponges and their symbiotic microorganisms.

microbiology↗

bioRxiv2023

Protected areas enhance avian food webs

Restoring and conserving habitat and the species they shelter has become a primary focus to mitigate the current extinction crisis. Setting aside land designated as protected areas (PAs) is an efficient way of achieving these aims. This strategy has been proven to enhance different aspects of species richness and abundance across ecosystems1-4. However, to truly understand the effects of global environmental change on biodiversity, and the efficiency of our mitigation measures, we must account for one of its fundamental dimensions: species interactions. Here we show that PAs enhance avian food webs across Europe by protecting key network and species traits. Using 376,556 observational records of 509 bird species from citizen science databases distributed across 45 networks of PAs, we found beneficial effects of protection on 10 out of 13 food web properties on an average of 25.9% of sites. PAs enhance food webs by harbouring large top predators, in turn increasing the length of biomass flow paths from basal to top species. Furthermore, we link these beneficial effects to environmental drivers and PA designations. PA benefits were augmented by specific protection goals such as European Directives for conservation. This study provides evidence for the effectiveness of PAs as a strategy to preserve fundamental aspects of biodiversity beyond species richness. We anticipate our study to be a starting point for the development of comprehensive frameworks to assess the critical role of PAs in safeguarding biodiversity worldwide. Improving the mapping of species occurrences and ecological interactions across the globe will is fundamental to develop optimal strategies for establishing networks of PAs aimed at protecting all aspects of ecosystem diversity.

ecology↗

bioRxiv2021

Disruption of metapopulation structure effectively reduces Tasmanian devil facial tumour disease spread at the expense of abundance and genetic diversity

Metapopulation structure (i.e. the spatial arrangement of local populations and corridors between them) plays a fundamental role in the persistence of wildlife populations, but can also drive the spread of infectious diseases. While the disruption of metapopulation connectivity can reduce disease spread, it can also impair host resilience by disrupting gene flow and colonisation dynamics. Thus, a pressing challenge for many wildlife populations is to elucidate whether the benefits of disease management methods that reduce metapopulation connectivity outweigh the associated risks. Directly transmissible cancers are clonal malignant cell lines capable to spread through host populations without immune recognition, when susceptible and infected hosts become in close contact. Using an individual-based metapopulation model we investigate the effects of the interplay between host dispersal, disease transmission rate and inter-individual contact distance for transmission (determining within-population mixing) on the spread and persistence of a transmissible cancer, Tasmanian devil facial tumour disease (DFTD), from local to regional scales. Further, we explore population isolation scenarios to devise management strategies to mitigate disease spread. Disease spread, and the ensuing population declines, are synergistically determined by individuals dispersal, disease transmission rate and within-population mixing. Low to intermediate transmission rates can be magnified by high dispersal and inter-individual transmission distance. Once disease transmission rate is high, dispersal and inter-individual contact distance do not impact the outcome of the disease transmission dynamics. Isolation of local populations effectively reduced metapopulation-level disease prevalence but caused severe declines in metapopulation size and genetic diversity. The relative position of managed (i.e. isolated) populations within the metapopulation had a significant effect on disease prevalence, highlighting the importance of considering metapopulation structure when implementing metapopulation-scale disease control measures. Our findings suggests that population isolation is not an ideal management method for preventing disease spread in species inhabiting already fragmented landscapes, where genetic diversity and extinction risk are already a concern, such as the Tasmanian devil.

ecology↗

bioRxiv2020

Warming indirectly increases invasion success in food webs

Climate warming and biological invasions are key drivers of biodiversity change. Their combined effects on ecological communities remain largely unexplored. We investigated the direct and indirect influences of warming on invasion success, and their synergistic effects on community structure and dynamics. Using size-structured food web models, we found that warming increased invasion success. The direct physiological effects of warming on invasions were minimal in comparison to indirect effects mediated by changes on food web structure and stability. Warmed communities with less connectivity, shortened food chains and reduced temporal variability were more susceptible to invasions. The directionality and magnitude of invasions effects on food webs varied across warming regimes. Warmer communities became smaller, more connected, and with more predator species when invaded than their colder counterparts. They were also less stable and their species more abundant. Considering food web structure is crucial to predict invasion success and its impacts under warming.

ecology↗