Life goes on: Spatial heterogeneity promotes biodiversity in an urbanized coastal marine ecosystem.

Both human populations and marine biodiversity are concentrated along coastlines, with growing conservation interest in how these ecosystems can survive intense anthropogenic impacts. Tropical urban centres provide valuable research opportunities because these megacities are often adjacent to mega-diverse coral reef systems. The Pearl River Delta is a prime exemplar, as it encompasses one of the most densely populated and impacted regions in the world and is located just northwest of the Coral Triangle. However, the spatial and taxonomic complexity of this biodiversity, most of which is small, cryptic in habitat and poorly known, make comparative analyses challenging. We deployed standardized settlement structures at seven sites differing in the intensity of human impacts and used COI metabarcoding to characterize benthic biodiversity, with a focus on metazoans. We found a total of 7184 OTUs, with an average of 665 OTUs per sampling unit; these numbers exceed those observed in many previous studies using comparable methods, despite the location of our study in an urbanized environment. Beta diversity was also high, with 52% of the OTUs found at just one site. As expected, we found that the sites close to point sources of pollution had substantially lower diversity (44% less) relative to sites bathed in less polluted oceanic waters. However, the polluted sites contributed substantially to the total animal diversity of the region, with 25% of all OTUs occurring only within polluted sites. Further analysis of Arthropoda, Annelida and Mollusca showed that phylogenetic clustering within a site was common, suggesting that environmental filtering reduced biodiversity to a subset of lineages present within the region, a pattern that was most pronounced in polluted sites and for the Arthropoda. The water quality gradients surrounding the PRD highlight the unique role of in situ studies for understanding the impacts of complex urbanization pressures on biodiversity.

Vegetation structure and climate shape mountain arthropod distributions across trophic levels.

Arthropods play a vital role in ecosystems; yet, their distributions remain poorly understood, particularly in mountainous regions. This study delves into the modelling of the distribution of 31 foliar arthropod genera in the French Alps, using a comprehensive approach encompassing multi-trophic sampling, community DNA metabarcoding and random forest models. The results underscore the significant importance of vegetation structure, such as herbaceous vegetation density, and forest density and heterogeneity, along with climate, in shaping the distributions of most arthropods. These responses to environmental gradients are consistent across trophic groups, with the exception of nectarivores, whose distributions are more sensitive to landscape structure and water availability. By leveraging community DNA metabarcoding, this study sheds light on the understudied drivers of arthropod distributions, emphasizing the importance of modelling across diverse trophic groups to anticipate arthropod responses to global change.

Feeding en route: Prey availability and traits influence prey selection by an avian predator on migration.

During animal migration, ephemeral communities of taxa at all trophic levels co-occur over space and time. The interactions between predators and prey along migration corridors are ecologically and evolutionarily significant. However, these interactions remain understudied in terrestrial systems and warrant further investigations using novel approaches. We investigated the predator-prey interactions between a migrating avivorous predator and ephemeral avian prey community in the fall migration season. We tested for associations between avian traits and prey selection and hypothesized that prey traits (i.e. relative size, flocking behaviour, habitat, migration tendency and availability) would influence prey selection by a sexually dimorphic raptor on migration. To document prey consumption, we sampled trace prey DNA from beaks and talons of migrating sharp-shinned hawks Accipiter striatus (n = 588). We determined prey availability in the ephemeral avian community by extracting weekly abundance indices from eBird Status and Trends data. We used discrete choice models to assess prey selection and visualized the frequency of prey in diet and availability on the landscape over the fall migration season. Using eDNA metabarcoding, we detected prey species on 94.1% of the hawks sampled (n = 525/588) comprising 1396 prey species detections from 65 prey species. Prey frequency in diet and eBird relative abundance of prey species were correlated over the migration season for top-selected prey species, suggesting prey availability is an important component of raptor-songbird interactions during fall. Prey size, flocking behaviour and non-breeding habitat association were prey traits that significantly influenced predator choice. We found differences between female and male hawk prey selection, suggesting that sexual size dimorphism has led to distinct foraging strategies on migration. This research integrated field data collected by a volunteer-powered raptor migration monitoring station and public-generated data from eBird to reveal elusive predator-prey dynamics occurring in an ephemeral raptor-songbird community during fall migration. Understanding dynamic raptor-songbird interactions along migration routes remains a relatively unexplored frontier in animal ecology and is necessary for the conservation and management efforts of migratory and resident communities.

Durante la migración animal, las comunidades efímeras de taxones de todos los niveles tróficos coexisten en el espacio y el tiempo. Las interacciones entre depredadores y presas a lo largo de los corredores migratorios son significativas desde el punto de vista ecológica y evolutivo. Sin embargo, estas interacciones siguen siendo poco estudiadas en los sistemas terrestres y justifican más investigaciones utilizando enfoques novedosos. Investigamos las interacciones depredador­presa entre un depredador avívoro migratorio y una comunidad de presas aviares efímeras en la temporada migratoria otoñal. Probamos las asociaciones entre los rasgos de las aves y la selección de presas y planteamos la hipótesis de que los rasgos de las presas (tamaño relativo, comportamiento de bandada, hábitat, tendencia migratoria y disponibilidad) influirían en la selección de presas por parte de una rapaz sexualmente dimórfica durante la migración. Para documentar el consumo de presas, recogimos rastros de ADN de presas de picos y garras de Gavilán Americano Accipiter striatus (n = 588) migratorios. Determinamos la disponibilidad de presas en la comunidad de aves efímeras extrayendo índices de abundancia semanales de los datos de eBird Estado y Tendencias. Utilizamos modelos de elección discreta para evaluar la selección de presas y visualizamos la frecuencia de las presas en la dieta y la disponibilidad en el paisaje durante la temporada migratoria otoñal. Utilizando el metacódigo de barras del ADN ambiental, detectamos especies de presas en el 94,1% de los halcones muestreados (n = 525/588), comprendiendo 1396 detecciones de 65 especies de presas. La frecuencia de presas en la dieta y la abundancia relativa de especies de presas en eBird se correlacionaron a lo largo de la temporada de migración para las principales especies de presas seleccionadas, lo que sugiere que la disponibilidad de presas es un componente importante de las interacciones entre aves rapaces y aves canoras durante el otoño. El tamaño de las presas, el comportamiento de las bandadas y la asociación con el hábitat no reproductivo fueron rasgos de presa que influyeron significativamente en la elección de los depredadores. Encontramos diferencias entre la selección de presas de gavilán hembra y macho, lo que sugiere que el dimorfismo sexual de tamaño ha conducido a distintas estrategias de alimentación durante la migración. Esta investigación integró datos de campo recopilados por una estación de monitoreo de migración de rapaces impulsada por voluntarios y datos generados públicamente por eBird para revelar la esquiva dinámica depredador­presa que ocurre en una comunidad efímera de rapaces y aves canoras durante la migración otoñal. Comprender las interacciones dinámicas entre rapaces y aves canoras a lo largo de las rutas migratorias sigue siendo una frontera relativamente inexplorada en la ecología animal y es necesaria para los esfuerzos de conservación y gestión de las comunidades migratorias y residentes.

Resource partitioning in a novel herbivore assemblage in South America.

Human-induced species declines and extinctions have led to the downsizing of large-herbivore assemblages, with implications for many ecosystem processes. Active reintroduction of extirpated large herbivores or their functional equivalents may help to reverse this trend and restore diverse ecosystems and their processes. However, it is unclear whether resource competition between native and non-native herbivores could threaten restoration initiatives, or to what extent (re)introduced species may influence local vegetation dynamics. To answer these questions, we investigated the diets of a novel South American herbivore assemblage that includes resident native species, reintroduced native species and introduced non-native species. We examined plant composition, diet breadth and the overlap between species to describe the local herbivory profile and the potential for resource competition. Using DNA metabarcoding on faecal samples (n = 465), we analysed the diets of the herbivore assemblage in the Rincón del Socorro rewilding area of Iberá National Park, Argentina. We compared the species richness of faecal samples, the occurrence of plant families/growth forms and the compositional similarity of samples (inter- and intraspecifically). Our results indicate species-level taxonomic partitioning of plant resources by herbivores in this system. Differences in sample richness, composition and diet breadth reflected a diverse range of herbivory strategies, from grazers (capybara) to mixed feeders/browsers (brocket deer, lowland tapir). Differences in diet compositional similarity (Jaccard) revealed strong taxonomic resource partitioning. The two herbivores with the most similar diets (Pampas deer and brocket deer) still differed by more than 80%. Furthermore, all but one species (axis deer) had more similar diet composition intraspecifically than compared to the others. Overall, we found little evidence for resource competition between herbivore species. Instead, recently reintroduced native species and historically introduced non-natives are likely expanding the range of herbivory dynamics in the ecosystem. Further research will be needed to determine the full ecological impacts of these (re)introduced herbivores. In conclusion, we show clear differences in diet breadth and composition among native, reintroduced and non-native herbivore species that may be key to promoting resource partitioning, species coexistence and the restoration of ecological function.

La disminución y extinción de especies ocasionada por el hombre ha llevado a la reducción de tamaño de las comunidades de grandes herbívoros, con implicaciones para muchos procesos ecosistémicos. La reintroducción activa de grandes herbívoros extirpados, o sus equivalentes funcionales, puede ayudar a revertir esta tendencia y restaurar diversos ecosistemas y sus procesos. Sin embargo, no está claro si la competencia por recursos entre herbívoros nativos y no nativos podría amenazar las iniciativas de restauración, o en qué medida las especies (re)introducidas pueden influir la dinámica de la vegetación local. Para responder a estas preguntas, investigamos las dietas de una comunidad de herbívoros sudamericanos que incluye especies nativas, especies nativas reintroducidas y especies no nativas introducidas. Examinamos la composición de plantas, la amplitud de la dieta y la superposición entre especies para describir el perfil herbívoro local y el potencial de competencia por los recursos. Utilizando metabarcoding de ADN en muestras fecales (n = 465), analizamos las dietas de la comunidad de herbívoros en el sitio de rewilding Rincón del Socorro dentro del Parque Nacional Iberá, Argentina. Comparamos la riqueza de especies en las muestras fecales, la ocurrencia de familias de plantas/formas de crecimiento y la similitud en la composición de las muestras (interespecíficamente e intraespecíficamente). Nuestros resultados indican la partición taxonómica a nivel de especie de los recursos vegetales por parte de los herbívoros en este sistema. Las diferencias en la riqueza de las muestras, la composición y la amplitud de las dietas reflejaron una amplia gama de estrategias de herbivoría, desde pastoreadores (capibara) hasta herbívoros mixtos/ramoneadores (corzuela, tapir amazónico). Las diferencias en la similitud de la composición de la dieta (Jaccard) revelaron una fuerte partición taxonómica de los recursos. Los dos herbívoros con las dietas más similares (venado de las pampas y corzuela), aún así diferían en más del 80%. Además, todas las especies menos una (ciervo axis) tenían una composición dietética más similar intraespecíficamente que en comparación con las demás. En general, encontramos poca evidencia de competencia por recursos entre las especies de herbívoros. En cambio, las especies nativas reintroducidas recientemente y las no nativas introducidas históricamente probablemente estén ampliando el rango de dinámica de herbivoría en el ecosistema. Se necesitarán más investigaciones para determinar todos los impactos ecológicos de estos herbívoros (re)introducidos. En conclusión, mostramos diferencias claras en la amplitud y composición de la dieta entre especies de herbívoros nativas, reintroducidas y no nativas que pueden ser clave para promover la partición de recursos, la coexistencia de especies y la restauración de las funciones ecológicas.

Distinct Communities and Differing Dispersal Routes in Bacteria and Fungi of Honey Bees, Honey, and Flowers.

Microbiota, the communities of microbes on and in organisms or organic matter, are essential for the functioning of ecosystems. How microbes are shared and transmitted delineates the formation of a microbiota. As pollinators forage, they offer a route to transfer microbes among the flowering plants, themselves, and their nests. To assess how the two components of the microbiota, bacteria and fungi, in pollination communities are shared and transferred, we focused on the honey bee Apis mellifera and collected honey bee, honey (representing the hive microbiota), and flower samples three times during the summer in Finland. We identified the bacteria and fungi by DNA metabarcoding. To determine the impact of honey bees' flower choices on the honey bee and hive microbiota, we identified also plant DNA in honey. The bacterial communities of honey bees, honey, and flowers all differ greatly from each other, while the fungal communities of honey bees and honey are very similar, yet different from flowers. The time of the summer and the sampling area influence all these microbiota. For flowers, the plant identity impacts both bacterial and fungal communities' composition the most. For the dispersal pathways of bacteria to honey bees, they are acquired directly from the honey and indirectly from flowers through the honey, while fungi are directly transmitted to honey bees from flowers. Overall, the distinctiveness of the microbiota of honey bees, honey, and the surrounding flowers suggests the sharing of microbes among them occurs but plays a minor role for the established microbiota.

Marine Fungal Diversity and Dynamics in the Gulf of Trieste (Northern Adriatic Sea).

Fungi contribute to different important ecological processes, including decomposition of organic matter and nutrient cycling, but in the marine environment the main factors influencing their diversity and dynamics at the spatial and temporal levels are still largely unclear. In this study, we performed DNA metabarcoding on seawater sampled monthly over a year and a half in the Gulf of Trieste (northern Adriatic Sea), targeting the internal transcribed spacer (ITS) and the 18S rRNA gene regions. The fungal communities were diverse, very dynamic, and belonged predominantly to marine taxa. Samples could be clustered in two groups, mainly based on the high (> 30%) or low relative proportion of the ascomycetes Parengyodontium album, which emerged as a key taxon in this area. Dissolved and particulate organic C:N ratio played important roles in shaping the mycoplankton assemblages, suggesting that differently bioavailable organic matter pools may be utilized by different consortia. The proportion of fungal over total reads was 31% for ITS and 0.7% for 18S. ITS had the highest taxonomic resolution but low power to detect early divergent fungal lineages. Our results on composition, distribution, and environmental drivers extended our knowledge of the structure and function of the mycobiome of coastal waters.

Investigating seed bank potential of crustose coralline algae using DNA metabarcoding.

To examine the potential for the autogenic ecosystem engineers, crustose coralline algae (CCA), to serve as seed banks or refugia for life stages of other species, it is critical to develop sampling protocols that reflect the diversity of life present. In this pilot study on two shallow water species of CCA collected from Raoul Island (Kermadec Islands; Rangitahua) New Zealand, we investigated two preservation methods (ethanol vs. silica gel), sampled inner and outer regions of the crusts, and used DNA metabarcoding and seven genes/gene regions (16S rRNA, 18S rRNA, 23S rRNA, cox1, rbcL, and tufA genes and the ITS rRNA region) to develop a protocol for taxa identification. The results revealed immense diversity, with typically more taxa identified within the inner layers than the outer layers. As highlighted in other metabarcoding studies and in earlier work on rhodoliths (nodose coralline algae), reference databases are incomplete, and to some extent, the use of multiple markers mitigates this issue. Specifically, the 23S rRNA and rbcL genes are currently more suitable for identifying algae, while the cox1 gene fares better at capturing the diversity present inclusive of algae. Further investigation of these autogenic ecosystem engineers that likely act as marine seed banks is needed.

Microbiome stability and structure is governed by host phylogeny over diet and geography in woodrats (Neotoma spp.).

The microbiome is critical for host survival and fitness, but gaps remain in our understanding of how this symbiotic community is structured. Despite evidence that related hosts often harbor similar bacterial communities, it is unclear whether this pattern is due to genetic similarities between hosts or to common ecological selection pressures. Here, using herbivorous rodents in the genus Neotoma, we quantify how geography, diet, and host genetics, alongside neutral processes, influence microbiome structure and stability under natural and captive conditions. Using bacterial and plant metabarcoding, we first characterized dietary and microbiome compositions for animals from 25 populations, representing seven species from 19 sites across the southwestern United States. We then brought wild animals into captivity, reducing the influence of environmental variation. In nature, geography, diet, and phylogeny collectively explained ∼50% of observed microbiome variation. Diet and microbiome diversity were correlated, with different toxin-enriched diets selecting for distinct microbial symbionts. Although diet and geography influenced natural microbiome structure, the effects of host phylogeny were stronger for both wild and captive animals. In captivity, gut microbiomes were altered; however, responses were species specific, indicating again that host genetic background is the most significant predictor of microbiome composition and stability. In captivity, diet effects declined and the effects of host genetic similarity increased. By bridging a critical divide between studies in wild and captive animals, this work underscores the extent to which genetics shape microbiome structure and stability in closely related hosts.

A multitaxa assessment of the effectiveness of agri-environmental schemes for biodiversity management.

Agri-environmental schemes (AES) aim to restore biodiversity and biodiversity-mediated ecosystem services in landscapes impoverished by modern agriculture. However, a systematic, empirical evaluation of different AES types across multiple taxa and functional groups is missing. Within one orthogonal design, we studied sown flowering AES types with different temporal continuity, size, and landscape context and used calcareous grasslands as seminatural reference habitat. We measured species richness of 12 taxonomic groups (vascular plants, cicadas, orthopterans, bees, butterflies, moths, hoverflies, flower visiting beetles, parasitoid wasps, carabid beetles, staphylinid beetles, and birds) representing 5 trophic levels. A total of 54,955 specimens were identified using traditional taxonomic methods, and bulk arthropod samples were identified through DNA metabarcoding, resulting in a total of 1,077 and 2,110 taxa, respectively. Species richness of most taxonomic groups, as well as multidiversity and richness of pollinators, increased with temporal continuity of AES types. Some groups responded to size and landscape context, but multidiversity and richness of pollinators and natural enemies were not affected. AES flowering fields supported different species assemblages than calcareous grasslands, but assemblages became more similar to those in seminatural grasslands with increasing temporal continuity. Our results indicate that AES flowering fields and seminatural grasslands function synergistically. Flowering fields support biodiversity even when they are relatively small and in landscapes with few remaining seminatural habitats. We therefore recommend a network of smaller, temporally continuous AES flowering fields of different ages, combined with permanent seminatural grasslands, to maximize benefits for biodiversity conservation and ecosystem service delivery in agricultural landscapes.

Large herbivores suppress liana infestation in an African savanna.

African savannas are the last stronghold of diverse large-mammal communities, and a major focus of savanna ecology is to understand how these animals affect the relative abundance of trees and grasses. However, savannas support diverse plant life-forms, and human-induced changes in large-herbivore assemblages-declining wildlife populations and their displacement by livestock-may cause unexpected shifts in plant community composition. We investigated how herbivory affects the prevalence of lianas (woody vines) and their impact on trees in an East African savanna. Although scarce (<2% of tree canopy area) and defended by toxic latex, the dominant liana, Cynanchum viminale (Apocynaceae), was eaten by 15 wild large-herbivore species and was consumed in bulk by native browsers during experimental cafeteria trials. In contrast, domesticated ungulates rarely ate lianas. When we experimentally excluded all large herbivores for periods of 8 to 17 y (simulating extirpation), liana abundance increased dramatically, with up to 75% of trees infested. Piecewise exclusion of different-sized herbivores revealed functional complementarity among size classes in suppressing lianas. Liana infestation reduced tree growth and reproduction, but herbivores quickly cleared lianas from trees after the removal of 18-y-old exclosure fences (simulating rewilding). A simple model of liana contagion showed that, without herbivores, the long-term equilibrium could be either endemic (liana-tree coexistence) or an all-liana alternative stable state. We conclude that ongoing declines of wild large-herbivore populations will disrupt the structure and functioning of many African savannas in ways that have received little attention and that may not be mitigated by replacing wildlife with livestock.

Increasing marine trophic web knowledge through DNA analyses of fish stomach content: a step towards an ecosystem-based approach to fisheries research.

Multispecies and ecosystem models, which are key for the implementation of ecosystem-based approaches to fisheries management, require extensive data on the trophic interactions between marine organisms, including changes over time. DNA metabarcoding, by allowing the simultaneous taxonomic identification of the community present in hundreds of samples, could be used for speeding up large-scale stomach content data collection. Yet, for DNA metabarcoding to be routinely implemented, technical challenges should be addressed, such as the potentially complicated sampling logistics, the detection of a high proportion of predator DNA, and the inability to provide reliable abundance estimations. Here, we present a DNA metabarcoding assay developed to examine the diet of five commercially important fish, which can be feasibly incorporated into routinary samplings. The method is devised to speed up the analysis process by avoiding the stomach dissection and content extraction steps, while preventing the amplification of predator DNA by using blocking primers. Tested in mock samples and in real stomach samples, the method has proven effective and shows great effectiveness discerning diet variations due to predator ecology or prey availability. Additionally, by applying our protocol to mackerel stomachs previously analyzed by visual inspection, we showcase how DNA metabarcoding could complement visually based data by detecting overlooked prey by the visual approach. We finally discuss how DNA metabarcoding-based data can contribute to trophic data collection. Our work reinforces the potential of DNA metabarcoding for the study and monitoring of fish trophic interactions and provides a basis for its incorporation into routine monitoring programs, which will be critical for the implementation of ecosystem-based approaches to fisheries management.

Long-term Consequences on Soil Fungal Community Structure: Monoculture Planting and Natural Regeneration.

Understanding the regeneration and succession of belowground communities, particularly in forests, is vital for maintaining ecosystem health. Despite its importance, there is limited knowledge regarding how fungal communities change over time during ecosystem development, especially under different forest restoration strategies. In this study, we focused on two restoration methods used in northern Japan: monoculture planting and natural regeneration. We examined the responses of the fungal community to monoculture plantations (active tree planting) and naturally regenerated (passive regeneration) forests over a 50-year chronosequence, using natural forests as a reference. Based on DNA metabarcoding, we assessed the richness of fungal Operational Taxonomic Units (OTUs) and their dissimilarity. Our findings revealed that soil fungal richness remained stable after natural regeneration but declined in monoculture plantations, from 354 to 247 OTUs. While the compositional dissimilarity of fungal assemblages between monoculture plantations and natural forests remained consistent regardless of the time since tree planting, it significantly decreased after natural regeneration, suggesting recovery to a state close to the reference level. Notably, the composition of key functional fungal groups-saprotrophic and ectomycorrhizal- has increasingly mirrored that of natural forests over time following passive natural regeneration. In summary, our study suggests that monoculture plantations may not be effective for long-term ecosystem function and service recovery because of their limited support for soil fungal diversity. These results underscore the importance of natural regeneration in forest restoration and management strategies.

Insights into trophic interactions: DNA metabarcoding reveals species composition in black-tailed gull fecal samples in coastal environments of South Korea.

This study explored the algae, zooplankton, macroinvertebrate, fish, and parasitic single-celled organism communities in Larus crassirostris (black-tailed gull) fecal samples from Baengnyeongdo, Hongdo, and Ulleungdo in South Korea. The fecal samples can identify key species consumed by black-tailed gull, providing insights into their, trophic interactions, and habitat dependencies. Using DNA metabarcoding, we identified algae, zooplankton, macroinvertebrate, fish, and intestinal and single-celled parasite species in the fecal samples. Parasitic single-celled organisms, such as Rhogostoma sp., Rhogostoma schuessleri, Eimeria furonis, and Aggregata eberthi, showed differing relative abundances at each sampling location, indicating variability in parasite diversity in the fecal DNA analysis of birds at each site. Intestinal parasites showed similar site-specific variability, though Clistobothrium sp. and Tetrabothrius sp. were common at all locations. Algae species, including Heterocapsa steinii, Heterocapsa niei, and Sargassum cristaefolium, also displayed habitat-specific patterns, as did zooplankton, with Calanus sp., Corycaeus speciosus, and Caprella californica being dominant on Baengnyeongdo, Hongdo, and Ulleungdo, respectively. In the macroinvertebrate communities, Octopus sinensis was prevalent at all locations but at varying abundances. Site-specific dominant fish species were also identified, with Ammodytes personatus, Decapterus maruadsi, and Arctoscopus japonicus highly predominant on Baengnyeongdo, Hongdo, and Ulleungdo, respectively. Other fish species, such as Ammodytes hexapterus, were detected in lower frequencies, suggesting a diverse diet for the seabirds. These results offer insights into the species composition and ecological dynamics in black-tailed gull populations across disparate Korean islands.

Negative effects of urbanisation on diurnal and nocturnal pollen-transport networks.

Pollinating insects are declining due to habitat loss and climate change, and cities with limited habitat and floral resources may be particularly vulnerable. The effects of urban landscapes on pollination networks remain poorly understood, and comparative studies of taxa with divergent niches are lacking. Here, for the first time, we simultaneously compare nocturnal moth and diurnal bee pollen-transport networks using DNA metabarcoding and ask how pollination networks are affected by increasing urbanisation. Bees and moths exhibited substantial divergence in the communities of plants they interact with. Increasing urbanisation had comparable negative effects on pollen-transport networks of both taxa, with significant declines in pollen species richness. We show that moths are an important, but overlooked, component of urban pollen-transport networks for wild flowering plants, horticultural crops, and trees. Our findings highlight the need to include both bee and non-bee taxa when assessing the status of critical plant-insect interactions in urbanised landscapes.

Ecological network structure in response to community assembly processes over evolutionary time.

The dynamic structure of ecological communities results from interactions among taxa that change with shifts in species composition in space and time. However, our ability to study the interplay of ecological and evolutionary processes on community assembly remains relatively unexplored due to the difficulty of measuring community structure over long temporal scales. Here, we made use of a geological chronosequence across the Hawaiian Islands, representing 50 years to 4.15 million years of ecosystem development, to sample 11 communities of arthropods and their associated plant taxa using semiquantitative DNA metabarcoding. We then examined how ecological communities changed with community age by calculating quantitative network statistics for bipartite networks of arthropod-plant associations. The average number of interactions per species (linkage density), ratio of plant to arthropod species (vulnerability) and uniformity of energy flow (interaction evenness) increased significantly in concert with community age. The index of specialization H 2 ' has a curvilinear relationship with community age. Our analyses suggest that younger communities are characterized by fewer but stronger interactions, while biotic associations become more even and diverse as communities mature. These shifts in structure became especially prominent on East Maui (~0.5 million years old) and older volcanos, after enough time had elapsed for adaptation and specialization to act on populations in situ. Such natural progression of specialization during community assembly is probably impeded by the rapid infiltration of non-native species, with special risk to younger or more recently disturbed communities that are composed of fewer specialized relationships.

DNA-based networks reveal the ecological determinants of plant-herbivore interactions along environmental gradients.

Understanding the ecological rules structuring the organization of species interactions is a prerequisite to predicting how ecosystems respond to environmental changes. While the ecological determinants of single networks have been documented, it remains unclear whether network ecological rules are conserved along spatial and environmental gradients. To address this gap, we reconstructed 48 plant-herbivore interaction networks along six elevation gradients in the Central European Alps in Switzerland, using DNA metabarcoding on orthoptera faeces. We developed hypotheses on the ecological mechanisms expected to structure interaction networks, based on plant phylogeny, plant abundance, leaf toughness, leaf nitrogen content and plant metabolomics. We show that plant phylogenetic relationships and species abundance have the greatest explanatory power regarding the structure of the ecological networks. Moreover, we found that leaf nitrogen content is a key determinant of interactions in warmer environments, while phenolic compounds and tannins are more important in colder environments, suggesting that determinants of species interactions can shift along environmental gradients. With this work, we propose an approach to study the mechanisms that structure the way species interact with each other between bioregions and ecosystems.

DNA metabarcoding unveils the effects of habitat fragmentation on pollinator diversity, plant-pollinator interactions, and pollination efficiency in Maldive islands.

Habitat fragmentation affects biodiversity, but with unclear effects on pollinators and their interactions with plants in anthropized landscapes. Islands could serve as open air laboratories, suitable to disentangle how land-use alteration impacts pollination ecology. In Maldive islands we investigated how pollinator richness, plant-pollinator interactions and pollination efficiency are influenced by the green area fragmentation (i.e., gardens and semi-natural patches). Moreover, we considered the mediating role of pollinator body size and the plant trait of being invasive in shaping interactions. To do this, we surveyed pollinator insects from 11 islands representing a gradient of green area fragmentation. A DNA metabarcoding approach was adopted to identify the pollen transported by pollinators and characterize the plant-pollinator interactions. We found that intermediate levels of green area fragmentation characterized pollinator communities and increased their species richness, while decreasing interaction network complexity. Invasive plants were more frequently found on pollinator bodies than native or exotic noninvasive ones, indicating a concerningly higher potential for pollen dispersal and reproduction of the former ones. Intriguingly, pollinator body size mediated the effect of landscape alteration on interactions, as only the largest bees expanded the foraging diet in terms of plant richness in the transported pollen at increasing fragmentation. In parallel, the pollination efficiency increased with pollinator species richness in two sentinel plants. This study shows that moderate landscape fragmentation of green areas shapes many aspects of the pollination ecosystem service, where despite interactions being less complex and mediated by pollinator body size, pollinator insect biodiversity and potential plant reproduction are supported.

Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding.

Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, and ultimately leading to species declines. To understand the mechanisms behind community shifts and declines, as well as monitoring and managing impacts, a global effort must be made to characterize plant-pollinator communities in detail, across different habitat types, latitudes, elevations, and levels and types of disturbances. Generating data of this scale will only be feasible with rapid, high-throughput methods. Pollen DNA metabarcoding provides advantages in throughput, efficiency and taxonomic resolution over traditional methods, such as microscopic pollen identification and visual observation of plant-pollinator interactions. This makes it ideal for understanding complex ecological networks and their responses to change. Pollen DNA metabarcoding is currently being applied to assess plant-pollinator interactions, survey ecosystem change and model the spatiotemporal distribution of allergenic pollen. Where samples are available from past collections, pollen DNA metabarcoding has been used to compare contemporary and past ecosystems. New avenues of research are possible with the expansion of pollen DNA metabarcoding to intraspecific identification, analysis of DNA in ancient pollen samples, and increased use of museum and herbarium specimens. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for understanding the evolutionary and ecological processes that support biodiversity, and predicting and responding to the impacts of change.

DNA metabarcoding reveals impact of local recruitment, dispersal, and hydroperiod on assembly of a zooplankton metacommunity.

Understanding the environmental impact on the assembly of local communities in relation to their spatial and temporal connectivity is still a challenge in metacommunity ecology. This study aims to unravel underlying metacommunity processes and environmental factors that result in observed zooplankton communities. Unlike most metacommunity studies, we jointly examine active and dormant zooplankton communities using a DNA metabarcoding approach to overcome limitations of morphological species identification. We applied two-fragment (COI and 18S) metabarcoding to monitor communities of 24 kettle holes over a two-year period to unravel (i) spatial and temporal connectivity of the communities, (ii) environmental factors influencing local communities, and (iii) dominant underlying metacommunity processes in this system. We found a strong separation of zooplankton communities from kettle holes of different hydroperiods (degree of permanency) throughout the season, while the community composition within single kettle holes did not differ between years. Species richness was primarily dependent on pH and permanency, while species diversity (Shannon Index) was influenced by kettle hole location. Community composition was impacted by kettle hole size and surrounding field crops. Environmental processes dominated temporal and spatial processes. Sediment communities showed a different composition compared to water samples but did not differ between ephemeral and permanent kettle holes. Our results suggest that communities are mainly structured by environmental filtering based on pH, kettle hole size, surrounding field crops, and permanency. Environmental filtering based on specific conditions in individual kettle holes seems to be the dominant process in community assembly in the studied zooplankton metacommunity.

Contrasting laboratory and field outcomes of bat-moth interactions.

Predator-prey interactions are important but difficult to study in the field. Therefore, laboratory studies are often used to examine the outcomes of predator-prey interactions. Previous laboratory studies have shown that moth hearing and ultrasound production can help prey avoid being eaten by bats. We report here that laboratory behavioural outcomes may not accurately reflect the outcomes of field bat-moth interactions. We tested the success rates of two bat species capturing moths with distinct anti-bat tactics using behavioural experiments. We compared the results with the dietary composition of field bats using next-generation DNA sequencing. Rhinolophus episcopus and Rhinolophus osgoodi had a lower rate of capture success when hunting for moths that produce anti-bat clicks than for silent eared moths and earless moths. Unexpectedly, the success rates of the bats capturing silent eared moths and earless moths did not differ significantly from each other. However, the field bats had a higher proportion of silent eared moths than that of earless moths and that of clicking moths in their diets. The difference between the proportions of silent eared moths and earless moths in the bat diets can be explained by the difference between their abundance in bat foraging habitats. These findings suggest that moth defensive tactics, bat countertactics and moth availability collectively shape the diets of insectivorous bats. This study illustrates the importance of using a combination of behavioural experiments and molecular genetic techniques to reveal the complex interactions between predators and prey in nature.