Linking differences in microbial network structure with changes in coral larval settlement.

Coral cover and recruitment have decreased on reefs worldwide due to climate change-related disturbances. Achieving reliable coral larval settlement under aquaculture conditions is critical for reef restoration programmes; however, this can be challenging due to the lack of reliable and universal larval settlement cues. To investigate the role of microorganisms in coral larval settlement, we undertook a settlement choice experiment with larvae of the coral Acropora tenuis and microbial biofilms grown for different periods on the reef and in aquaria. Biofilm community composition across conditioning types and time was profiled using 16S and 18S rRNA gene sequencing. Co-occurrence networks revealed that strong larval settlement correlated with diverse biofilm communities, with specific nodes in the network facilitating connections between modules comprised of low- vs high-settlement communities. Taxa associated with high-settlement communities were identified as Myxoccales sp., Granulosicoccus sp., Alcanivoraceae sp., unassigned JTB23 sp. (Gammaproteobacteria), and Pseudovibrio denitrificans. Meanwhile, taxa closely related to Reichenbachiella agariperforans, Pleurocapsa sp., Alcanivorax sp., Sneathiella limmimaris, as well as several diatom and brown algae were associated with low settlement. Our results characterise high-settlement biofilm communities and identify transitionary taxa that may develop settlement-inducing biofilms to improve coral larval settlement in aquaculture.

Ecological network complexity scales with area.

Larger geographical areas contain more species-an observation raised to a law in ecology. Less explored is whether biodiversity changes are accompanied by a modification of interaction networks. We use data from 32 spatial interaction networks from different ecosystems to analyse how network structure changes with area. We find that basic community structure descriptors (number of species, links and links per species) increase with area following a power law. Yet, the distribution of links per species varies little with area, indicating that the fundamental organization of interactions within networks is conserved. Our null model analyses suggest that the spatial scaling of network structure is determined by factors beyond species richness and the number of links. We demonstrate that biodiversity-area relationships can be extended from species counts to higher levels of network complexity. Therefore, the consequences of anthropogenic habitat destruction may extend from species loss to wider simplification of natural communities.

Disruption of Metapopulation Structure Reduces Tasmanian Devil Facial Tumour Disease Spread at the Expense of Abundance and Genetic Diversity.

Metapopulation structure plays a fundamental role in the persistence of wildlife populations. It can also drive the spread of infectious diseases and transmissible cancers such as the Tasmanian devil facial tumour disease (DFTD). While disrupting this structure can reduce disease spread, it can also impair host resilience by disrupting gene flow and colonisation dynamics. Using an individual-based metapopulation model we investigated the synergistic effects of host dispersal, disease transmission rate and inter-individual contact distance for transmission, on the spread and persistence of DFTD from local to regional scales. Disease spread, and the ensuing population declines, are synergistically determined by individuals' dispersal, disease transmission rate and within-population mixing. Transmission rates can be magnified by high dispersal and inter-individual transmission distance. The 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) local populations had a significant effect on disease prevalence, highlighting the importance of considering metapopulation structure when implementing metapopulation-scale disease control measures. Our findings suggest 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.

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 temperature on invasion success, and their synergistic effects on community structure and dynamics. Using size-structured food web models, we found that higher temperatures increased invasion success. The direct physiological effects of temperature on invasions were minimal in comparison with indirect effects mediated by changes on food web structure and stability. Warmer 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 temperature regimes. When invaded, warmer communities became smaller, more connected and with more predator species 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 along temperature gradients.

The spatial scaling of food web structure across European biogeographical regions.

The species-area relationship (SAR) is one of the most well-established scaling patterns in ecology. Its implications for understanding how communities change across spatial gradients are numerous, including the effects of habitat loss on biodiversity. However, ecological communities are not mere collections of species. They are the result of interactions between these species forming complex networks that tie them together. Should we aim to grasp the spatial scaling of biodiversity as a whole, it is fundamental to understand the changes in the structure of interaction networks with area. In spite of a few empirical and theoretical studies that address this challenge, we still do not know much about how network structure changes with area, or what are the main environmental drivers of these changes. Here, using the meta-network of potential interactions between all terrestrial vertebrates in Europe (1140 species and 67 201 feeding interactions), we analysed network-area relationships (NARs) that summarize how network properties scale with area. We do this across ten biogeographical regions, which differ in environmental characteristics. We found that the spatial scaling of network complexity strongly varied across biogeographical regions. However, once the variation in SARs was accounted for, differences in the shape of NARs vanished. On the other hand, the proportion of species across trophic levels remained remarkably constant across biogeographical regions and spatial scales, despite the great variation in species richness. Spatial variation in mean annual temperature and habitat clustering were the main environmental determinants of the shape of both SARs and NARs across Europe. Our results suggest new avenues in the exploration of the effects of environmental factors on the spatial scaling of biodiversity. We argue that NARs can provide new insights to analyse and understand ecological communities.

Disease control across urban-rural gradients.

Controlling the regional re-emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) after its initial spread in ever-changing personal contact networks and disease landscapes is a challenging task. In a landscape context, contact opportunities within and between populations are changing rapidly as lockdown measures are relaxed and a number of social activities re-activated. Using an individual-based metapopulation model, we explored the efficacy of different control strategies across an urban-rural gradient in Wales, UK. Our model shows that isolation of symptomatic cases or regional lockdowns in response to local outbreaks have limited efficacy unless the overall transmission rate is kept persistently low. Additional isolation of non-symptomatic infected individuals, who may be detected by effective test-and-trace strategies, is pivotal to reducing the overall epidemic size over a wider range of transmission scenarios. We define an 'urban-rural gradient in epidemic size' as a correlation between regional epidemic size and connectivity within the region, with more highly connected urban populations experiencing relatively larger outbreaks. For interventions focused on regional lockdowns, the strength of such gradients in epidemic size increased with higher travel frequencies, indicating a reduced efficacy of the control measure in the urban regions under these conditions. When both non-symptomatic and symptomatic individuals are isolated or regional lockdown strategies are enforced, we further found the strongest urban-rural epidemic gradients at high transmission rates. This effect was reversed for strategies targeted at symptomatic individuals only. Our results emphasize the importance of test-and-trace strategies and maintaining low transmission rates for efficiently controlling SARS-CoV-2 spread, both at landscape scale and in urban areas.

Viral ecogenomics across the Porifera.

BACKGROUND: Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide diversity of microorganisms and this high symbiont complexity makes them an ideal model for studying viral ecology. Here, we used morphological and molecular approaches to illuminate the diversity and function of viruses inhabiting nine sponge species from the Great Barrier Reef and seven from the Red Sea. RESULTS: Viromic sequencing revealed host-specific and site-specific patterns in the viral assemblages, with all sponge species dominated by the bacteriophage order Caudovirales but also containing variable representation from the nucleocytoplasmic large DNA virus families Mimiviridae, Marseilleviridae, Phycodnaviridae, Ascoviridae, Iridoviridae, Asfarviridae and Poxviridae. Whilst core viral functions related to replication, infection and structure were largely consistent across the sponge viromes, functional profiles varied significantly between species and sites largely due to differential representation of putative auxiliary metabolic genes (AMGs) and accessory genes, including those associated with herbicide resistance, heavy metal resistance and nylon degradation. Furthermore, putative AMGs varied with the composition and abundance of the sponge-associated microbiome. For instance, genes associated with antimicrobial activity were enriched in low microbial abundance sponges, genes associated with nitrogen metabolism were enriched in high microbial abundance sponges and genes related to cellulose biosynthesis were enriched in species that host photosynthetic symbionts. CONCLUSIONS: Our results highlight the diverse functional roles that viruses can play in marine sponges and are consistent with our current understanding of sponge ecology. Differential representation of putative viral AMGs and accessory genes across sponge species illustrate the diverse suite of beneficial roles viruses can play in the functional ecology of these complex reef holobionts. Video Abstract.

Geographical variation of multiplex ecological networks in marine intertidal communities.

Understanding the drivers of geographical variation in species distributions, and the resulting community structure, constitutes one of the grandest challenges in ecology. Geographical patterns of species richness and composition have been relatively well studied. Less is known about how the entire set of trophic and non-trophic ecological interactions, and the complex networks that they create by gluing species together in complex communities, change across geographical extents. Here, we compiled data of species composition and three types of ecological interactions occurring between species in rocky intertidal communities across a large spatial extent (~970 km of shoreline) of central Chile, and analyzed the geographical variability in these multiplex networks (i.e., comprising several interaction types) of ecological interactions. We calculated nine network summary statistics common across interaction types, and additional network attributes specific to each of the different types of interactions. We then investigated potential environmental drivers of this multivariate network organization. These included variation in sea surface temperature and coastal upwelling, the main drivers of productivity in nearshore waters. Our results suggest that structural properties of multiplex ecological networks are affected by local species richness and modulated by factors influencing productivity and environmental predictability. Our results show that non-trophic negative interactions are more sensitive to spatially structured temporal environmental variation than feeding relationships, with non-trophic positive interactions being the least labile to it. We also show that environmental effects are partly mediated through changes in species richness and partly through direct influences on species interactions, probably associated to changes in environmental predictability and to bottom-up nutrient availability. Our findings highlight the need for a comprehensive picture of ecological interactions and their geographical variability if we are to predict potential effects of environmental changes on ecological communities.

Evaluating the effects of landscape structure on the recovery of an invasive vertebrate after population control.

CONTEXT: Effective landscape control of invasive species is context-dependent due to the interplay between the landscape structure, local population dynamics, and metapopulation processes. We use a modelling approach incorporating these three elements to explore the drivers of recovery of populations of invasive species after control. OBJECTIVES: We aim to improve our understanding of the factors influencing the landscape-level control of invasive species. METHODS: We focus on the case study of invasive brushtail possum (Trichosurus vulpecula) control in New Zealand. We assess how 13 covariates describing the landscape, patch, and population features influence the time of population recovery to a management density threshold of two possums/ha. We demonstrate the effects of those covariates on population recovery under three scenarios of population growth: logistic growth, strong Allee effects, and weak Allee effects. RESULTS: Recovery times were rapid regardless of the simulated population dynamics (average recovery time < 2 years), although populations experiencing Allee effects took longer to recover than those growing logistically. Our results indicate that habitat availability and patch area play a key role in reducing times to recovery after control, and this relationship is consistent across the three simulated scenarios. CONCLUSIONS: The control of invasive possum populations in patchy landscapes would benefit from a patch-level management approach (considering each patch as an independent management unit), whereas simple landscapes would be better controlled by taking a landscape-level view (the landscape as the management unit). Future research should test the predictions of our models with empirical data to refine control operations.

The stability of multitrophic communities under habitat loss.

Habitat loss (HL) affects species and their interactions, ultimately altering community dynamics. Yet, a challenge for community ecology is to understand how communities with multiple interaction types-hybrid communities-respond to HL prior to species extinctions. To this end, we develop a model to investigate the response of hybrid terrestrial communities to two types of HL: random and contiguous. Our model reveals changes in stability-temporal variability in population abundances-that are dependent on the spatial configuration of HL. Our findings highlight that habitat area determines the variability of populations via changes in the distribution of species interaction strengths. The divergent responses of communities to random and contiguous HL result from different constraints imposed on individuals' mobility, impacting diversity and network structure in the random case, and destabilising communities by increasing interaction strength in the contiguous case. Analysis of intermediate HL suggests a gradual transition between the two extreme cases.

The Australian National Rabbit Database: 50 yr of population monitoring of an invasive species.

With ongoing introductions into Australia since the 1700s, the European rabbit (Oryctolagus cuniculus) has become one of the most widely distributed and abundant vertebrate pests, adversely impacting Australia's biodiversity and agroeconomy. To understand the population and range dynamics of the species and its impacts better, occurrence and abundance data have been collected by researchers and citizens from sites covering a broad spectrum of climatic and environmental conditions in Australia. The lack of a common and accessible repository for these data has, however, limited their use in determining important spatiotemporal drivers of the structure and dynamics of the geographical range of rabbits in Australia. To meet this need, we created the Australian National Rabbit Database, which combines more than 50 yr of historical and contemporary survey data collected from throughout the range of the species in Australia. The survey data, obtained from a suite of complementary monitoring methods, were combined with high-resolution weather, climate, and environmental information, and an assessment of data quality. The database provides records of rabbit occurrence (689,265 records) and abundance (51,241 records, >120 distinct sites) suitable for identifying the spatiotemporal drivers of the rabbit's distribution and for determining spatial patterns of variation in its key life-history traits, including maximum rates of population growth. Because all data are georeferenced and date stamped, they can be coupled with information from other databases and spatial layers to explore the potential effects of rabbit occurrence and abundance on Australia's native wildlife and agricultural production. The Australian National Rabbit Database is an important tool for understanding and managing the European rabbit in its invasive range and its effects on native biodiversity and agricultural production. It also provides a valuable resource for addressing questions related to the biology, success, and impacts of invasive species more generally. No copyright or proprietary restrictions are associated with the use of this data set other than citation of this Data Paper.

Modularity and predicted functions of the global sponge-microbiome network.

Defining the organisation of species interaction networks and unveiling the processes behind their assembly is fundamental to understanding patterns of biodiversity, community stability and ecosystem functioning. Marine sponges host complex communities of microorganisms that contribute to their health and survival, yet the mechanisms behind microbiome assembly are largely unknown. We present the global marine sponge-microbiome network and reveal a modular organisation in both community structure and function. Modules are linked by a few sponge species that share microbes with other species around the world. Further, we provide evidence that abiotic factors influence the structuring of the sponge microbiome when considering all microbes present, but biotic interactions drive the assembly of more intimately associated 'core' microorganisms. These findings suggest that both ecological and evolutionary processes are at play in host-microbe network assembly. We expect mechanisms behind microbiome assembly to be consistent across multicellular hosts throughout the tree of life.

Different effects of alpine woody plant expansion on domestic and wild ungulates.

Changes in land-use and climate affect the distribution and diversity of plant and animal species at different spatiotemporal scales. The extent to which species-specific phenotypic plasticity and biotic interactions mediate organismal adaptation to changing environments, however, remains poorly understood. Woody plant expansion is threatening the extent of alpine grasslands worldwide, and evaluating and predicting its effects on herbivores is of crucial importance. Here, we explore the impact of shrubification on the feeding efficiency of Pyrenean chamois (Rupicapra p. pyrenaica), as well as on the three most abundant coexisting domestic ungulate species: cattle, sheep and horses. We use observational diet composition from May to October and model different scenarios of vegetation availability where shrubland and woodland proliferate at the expense of grassland. We then predicted if the four ungulate species could efficiently utilize their food landscapes with their current dietary specificities measuring their niche breath in each scenario. We observed that the wild counterpart, due to a higher trophic plasticity, is less disturbed by shrubification compared to livestock, which rely primarily on herbaceous plants and will be affected 3.6 times more. Our results suggest that mixed feeders, such as chamois, could benefit from fallow landscapes, and that mountain farmers are at a growing economic risk worldwide due to changing land-use practices and climate conditions.

A concise guide to developing and using quantitative models in conservation management.

Quantitative models are powerful tools for informing conservation management and decision-making. As applied modeling is increasingly used to address conservation problems, guidelines are required to clarify the scope of modeling applications and to facilitate the impact and acceptance of models by practitioners. We identify three key roles for quantitative models in conservation management: (a) to assess the extent of a conservation problem; (b) to provide insights into the dynamics of complex social and ecological systems; and, (c) to evaluate the efficacy of proposed conservation interventions. We describe 10 recommendations to facilitate the acceptance of quantitative models in conservation management, providing a basis for good practice to guide their development and evaluation in conservation applications. We structure these recommendations within four established phases of model construction, enabling their integration within existing workflows: (a) design (two recommendations); (b) specification (two); (c) evaluation (one); and (d) inference (five). Quantitative modeling can support effective conservation management provided that both managers and modelers understand and agree on the place for models in conservation. Our concise review and recommendations will assist conservation managers and modelers to collaborate in the development of quantitative models that are fit-for-purpose, and to trust and use these models appropriately while understanding key drivers of uncertainty.

The spatial scaling of species interaction networks.

Species-area relationships (SARs) are pivotal to understand the distribution of biodiversity across spatial scales. We know little, however, about how the network of biotic interactions in which biodiversity is embedded changes with spatial extent. Here we develop a new theoretical framework that enables us to explore how different assembly mechanisms and theoretical models affect multiple properties of ecological networks across space. We present a number of testable predictions on network-area relationships (NARs) for multi-trophic communities. Network structure changes as area increases because of the existence of different SARs across trophic levels, the preferential selection of generalist species at small spatial extents and the effect of dispersal limitation promoting beta-diversity. Developing an understanding of NARs will complement the growing body of knowledge on SARs with potential applications in conservation ecology. Specifically, combined with further empirical evidence, NARs can generate predictions of potential effects on ecological communities of habitat loss and fragmentation in a changing world.

Navigating the complexity of ecological stability.

Human actions challenge nature in many ways. Ecological responses are ineluctably complex, demanding measures that describe them succinctly. Collectively, these measures encapsulate the overall 'stability' of the system. Many international bodies, including the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services, broadly aspire to maintain or enhance ecological stability. Such bodies frequently use terms pertaining to stability that lack clear definition. Consequently, we cannot measure them and so they disconnect from a large body of theoretical and empirical understanding. We assess the scientific and policy literature and show that this disconnect is one consequence of an inconsistent and one-dimensional approach that ecologists have taken to both disturbances and stability. This has led to confused communication of the nature of stability and the level of our insight into it. Disturbances and stability are multidimensional. Our understanding of them is not. We have a remarkably poor understanding of the impacts on stability of the characteristics that define many, perhaps all, of the most important elements of global change. We provide recommendations for theoreticians, empiricists and policymakers on how to better integrate the multidimensional nature of ecological stability into their research, policies and actions.

A Landscape Approach to Invasive Species Management.

Biological invasions are not only a major threat to biodiversity, they also have major impacts on local economies and agricultural production systems. Once established, the connection of local populations into metapopulation networks facilitates dispersal at landscape scales, generating spatial dynamics that can impact the outcome of pest-management actions. Much planning goes into landscape-scale invasive species management. However, effective management requires knowledge on the interplay between metapopulation network topology and management actions. We address this knowledge gap using simulation models to explore the effectiveness of two common management strategies, applied across different extents and according to different rules for selecting target localities in metapopulations with different network topologies. These management actions are: (i) general population reduction, and (ii) reduction of an obligate resource. The reduction of an obligate resource was generally more efficient than population reduction for depleting populations at landscape scales. However, the way in which local populations are selected for management is important when the topology of the metapopulation is heterogeneous in terms of the distribution of connections among local populations. We tested these broad findings using real-world scenarios of European rabbits (Oryctolagus cuniculus) infesting agricultural landscapes in Western Australia. Although management strategies targeting central populations were more effective in simulated heterogeneous metapopulation structures, no difference was observed in real-world metapopulation structures that are highly homogeneous. In large metapopulations with high proximity and connectivity of neighbouring populations, different spatial management strategies yield similar outcomes. Directly considering spatial attributes in pest-management actions will be most important for metapopulation networks with heterogeneously distributed links. Our modelling framework provides a simple approach for identifying the best possible management strategy for invasive species based on metapopulation structure and control capacity. This information can be used by managers trying to devise efficient landscape-oriented management strategies for invasive species and can also generate insights for conservation purposes.

Diversity, structure and convergent evolution of the global sponge microbiome.

Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host-microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions.

On the dimensionality of ecological stability.

Ecological stability is touted as a complex and multifaceted concept, including components such as variability, resistance, resilience, persistence and robustness. Even though a complete appreciation of the effects of perturbations on ecosystems requires the simultaneous measurement of these multiple components of stability, most ecological research has focused on one or a few of those components analysed in isolation. Here, we present a new view of ecological stability that recognises explicitly the non-independence of components of stability. This provides an approach for simplifying the concept of stability. We illustrate the concept and approach using results from a field experiment, and show that the effective dimensionality of ecological stability is considerably lower than if the various components of stability were unrelated. However, strong perturbations can modify, and even decouple, relationships among individual components of stability. Thus, perturbations not only increase the dimensionality of stability but they can also alter the relationships among components of stability in different ways. Studies that focus on single forms of stability in isolation therefore risk underestimating significantly the potential of perturbations to destabilise ecosystems. In contrast, application of the multidimensional stability framework that we propose gives a far richer understanding of how communities respond to perturbations.

Strategies for annotation and curation of translational databases: the eTUMOUR project.

The eTUMOUR (eT) multi-centre project gathered in vivo and ex vivo magnetic resonance (MR) data, as well as transcriptomic and clinical information from brain tumour patients, with the purpose of improving the diagnostic and prognostic evaluation of future patients. In order to carry this out, among other work, a database--the eTDB--was developed. In addition to complex permission rules and software and management quality control (QC), it was necessary to develop anonymization, processing and data visualization tools for the data uploaded. It was also necessary to develop sophisticated curation strategies that involved on one hand, dedicated fields for QC-generated meta-data and specialized queries and global permissions for senior curators and on the other, to establish a set of metrics to quantify its contents. The indispensable dataset (ID), completeness and pairedness indices were set. The database contains 1317 cases created as a result of the eT project and 304 from a previous project, INTERPRET. The number of cases fulfilling the ID was 656. Completeness and pairedness were heterogeneous, depending on the data type involved.