Food-web structure and ecosystem services: insights from the Serengeti

Co-occurrence patterns between Chlorophyta and nucleocytoplasmic large DNA virus in coastal ecosystem, South Korea

Nucleocytoplasmic large DNA viruses (NCLDVs) are known to infect phytoplankton and play a significant role in regulating their population dynamics. In this study, we aimed to investigate the co-occurrence patterns between phytoplankton and NCLDVs in the southern coastal ecosystem of South Korea. We collected seawater every month from March 2018 to December 2020 and analyzed the samples using Cytochrome c Oxidase subunit I metabarcoding and metagenomic analyses. Chlorophyta (36.08%) was the most abundant eukaryotic taxon, with Bathycoccaceae (58.25%) and Mamiellaceae (41.51%) being the most dominant families within Chlorophyta. Bathycoccaceae was dominant in winter, whereas Mamiellaceae was dominant in summer. In the NCLDV community, Phycodnaviridae (75.12%) was found to be the major family. The co-occurrence pattern of Phycodnaviridae showed a high correlation with Bathycoccaceae and Mamiellaceae, which is explained by the "boom-and-bust" concept. In particular, we predicted co-occurrence patterns between Bathycoccus prasinos and Prasnovirus, with known infectious relationships, and confirmed co-occurrence patterns between B. prasinos and Coccolithovirus and Micromonas pusilla and Prymnesiovirus, with unknown infectious relationships. These co-occurrence patterns between Chlorophyta and Phycodnaviridae provide valuable insights into the control of pico-sized primary production and the microbial loop of the coastal ecosystem.

Quantifying co-extinctions and ecosystem service vulnerability in coastal ecosystems experiencing climate warming

Climate change is negatively impacting ecosystems and their contributions to human well-being, known as ecosystem services. Previous research has mainly focused on the direct effects of climate change on species and ecosystem services, leaving a gap in understanding the indirect impacts resulting from changes in species interactions within complex ecosystems. This knowledge gap is significant because the loss of a species in a food web can lead to additional species losses or "co-extinctions," particularly when the species most impacted by climate change are also the species that play critical roles in food web persistence or provide ecosystem services. Here, we present a framework to investigate the relationships among species vulnerability to climate change, their roles within the food web, their contributions to ecosystem services, and the overall persistence of these systems and services in the face of climate-induced species losses. To do this, we assess the robustness of food webs and their associated ecosystem services to climate-driven species extinctions in eight empirical rocky intertidal food webs. Across food webs, we find that highly connected species are not the most vulnerable to climate change. However, we find species that directly provide ecosystem services are more vulnerable to climate change and more connected than species that do not directly provide services, which results in ecosystem service provision collapsing before food webs. Overall, we find that food webs are more robust to climate change than the ecosystem services they provide and show that combining species roles in food webs and services with their vulnerability to climate change offer predictions about the impacts of co-extinctions for future food web and ecosystem service persistence. However, these conclusions are limited by data availability and quality, underscoring the need for more comprehensive data collection on linking species roles in interaction networks and their vulnerabilities to climate change.

Species motif participation provides unique information about species risk of extinction

Loss of species in food webs can set in motion a cascade of additional (secondary) extinctions. A species' position in a food web (e.g. its trophic level or number of interactions) is known to affect its ability to persist following disturbance. These simple measures, however, offer only a coarse description of how species fit into their community. One would therefore expect that more detailed structural measures such as participation in three-species motifs (meso-scale structures which provide information on a species' direct and indirect interactions) will also be related to probability of persistence. Disturbances affecting the basal resources have particularly strong effects on the rest of the food web. However, how disturbances branch out and affect consumer persistence depends on the structural pattern of species interactions in several steps. The magnitude, for example, the proportion of basal resources lost, will likely also affect the outcome. Here, we analyse whether a consumer's risk of secondary extinction after the removal of basal resources depends on the consumer's motif participation and how this relationship varies with the severity of disturbance. We show that consumer species which participate more frequently in the direct competition motif and less frequently in the omnivory motif generally have higher probability of persistence following disturbance to basal resources. However, both the strength of the disturbance and the overall network structure (i.e. connectance) affect the strength and direction of relationships between motif participation and persistence. Motif participation therefore captures important trends in species persistence and provides a rich description of species' structural roles in their communities, but must be considered in the context of network structure as a whole and of the specific disturbance applied.

Mismatch between IUCN range maps and species interactions data illustrated using the Serengeti food web

Background

Range maps are a useful tool to describe the spatial distribution of species. However, they need to be used with caution, as they essentially represent a rough approximation of a species' suitable habitats. When stacked together, the resulting communities in each grid cell may not always be realistic, especially when species interactions are taken into account. Here we show the extent of the mismatch between range maps, provided by the International Union for Conservation of Nature (IUCN), and species interactions data. More precisely, we show that local networks built from those stacked range maps often yield unrealistic communities, where species of higher trophic levels are completely disconnected from primary producers.

Methodology

We used the well-described Serengeti food web of mammals and plants as our case study, and identify areas of data mismatch within predators' range maps by taking into account food web structure. We then used occurrence data from the Global Biodiversity Information Facility (GBIF) to investigate where data is most lacking.

Results

We found that most predator ranges comprised large areas without any overlapping distribution of their prey. However, many of these areas contained GBIF occurrences of the predator.

Conclusions

Our results suggest that the mismatch between both data sources could be due either to the lack of information about ecological interactions or the geographical occurrence of prey. We finally discuss general guidelines to help identify defective data among distributions and interactions data, and we recommend this method as a valuable way to assess whether the occurrence data that are being used, even if incomplete, are ecologically accurate.

Novel Virus Identification through Metagenomics: A Systematic Review

Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.

Grouping behaviour and activity patterns of impala (Aepyceros melampus) in a nutrient –rich and a nutrient-poor savanna in Tanzania

African savannas are broadly categorised into nutrient-rich and nutrient-poor according to soil nutrient availability and precipitation. Soil nutrients limit plant growth in the nutrient-rich savannas, leading to little plant biomass of high nutrient concentrations. In the nutrient-poor savannas soil nutrients are depleted before plant growth ceases, resulting in large production of nutrient-poor plant biomass. Impala (Aepyceros melampus), are medium-sized antelopes occurring in both savannas, but they face feeding challenges in the nutrient-poor savannas because of high energy requirements. Activity patterns of impala are well studied, but few studies compared savannas with differing soil nutrients and animal communities. I used the scanning methods to study impala activities in a nutrient-rich savanna, the Serengeti National Park, and a nutrient-poor savanna, the Mikumi National Park in Tanzania, during the wet and dry seasons. Impala are gregarious and mixed feeders, utilising grasses during the wet season, switching to browsing during the dry season, making them good candidates for comparing savannas and seasons. The impala formed bigger groups in Mikumi during the wet season splitting during the dry season. Grazing time was higher in the wet season than in the dry season in Serengeti, but did not differ between the seasons in Mikumi. Browsing time was longer in Mikumi than Serengeti during the dry season, and longer in Serengeti than Mikumi during the wet season. Resting time was longer in Serengeti than Mikumi during the wet season, while walking time was longer in Mikumi than Serengeti during the dry season. Family groups spent longer time resting than bachelor groups in both sites. The study shows obvious differences in grouping and activity patterns of impala between the sites and the seasons. Further studies are recommended to explore the influence of savanna and season on grouping behaviour and activity patterns of herbivores.

Causes, Consequences, and Conservation of Ungulate Migration

Our understanding of ungulate migration is advancing rapidly due to innovations in modern animal tracking. Herein, we review and synthesize nearly seven decades of work on migration and other long-distance movements of wild ungulates. Although it has long been appreciated that ungulates migrate to enhance access to forage, recent contributions demonstrate that their movements are fine tuned to dynamic landscapes where forage, snow, and drought change seasonally. Researchers are beginning to understand how ungulates navigate migrations, with the emerging view that animals blend gradient tracking with spatial memory, some of which is socially learned. Although migration often promotes abundant populations—with broad effects on ecosystems—many migrations around the world have been lost or are currently threatened by habitat fragmentation, climate change, and barriers to movement. Fortunately, new efforts that use empirical tracking data to map migrations in detail are facilitating effective conservation measures to maintain ungulate migration.

An ecological network approach to predict ecosystem service vulnerability to species losses

Human-driven threats are changing biodiversity, impacting ecosystem services. The loss of one species can trigger secondary extinctions of additional species, because species interact-yet the consequences of these secondary extinctions for services remain underexplored. Herein, we compare robustness of food webs and the ecosystem services (hereafter 'services') they provide; and investigate factors determining service responses to secondary extinctions. Simulating twelve extinction scenarios for estuarine food webs with seven services, we find that food web and service robustness are highly correlated, but that robustness varies across services depending on their trophic level and redundancy. Further, we find that species providing services do not play a critical role in stabilizing food webs - whereas species playing supporting roles in services through interactions are critical to the robustness of both food webs and services. Together, our results reveal indirect risks to services through secondary species losses and predictable differences in vulnerability across services.

Marine conservation: towards a multi-layered network approach

Valuing, managing and conserving marine biodiversity and a full range of ecosystem services is at the forefront of research and policy agendas. However, biodiversity is being lost at up to a thousand times the average background rate. Traditional disciplinary and siloed conservation approaches are not able to tackle this massive loss of biodiversity because they generally ignore or overlook the interactive and dynamic nature of ecosystems processes, limiting their predictability. To conserve marine biodiversity, we must assess the interactions and impacts among biodiversity and ecosystem services (BD-ES). The scaling up in complexity from single species to entire communities is necessary, albeit challenging, for a deeper understanding of how ecosystem services relate to biodiversity and the roles species have in ecosystem service provision. These interactions are challenging to map, let alone fully assess, but network and system-based approaches provide a powerful way to progress beyond those limitations. Here, we introduce a conceptual multi-layered network approach to understanding how ecosystem services supported by biodiversity drive the total service provision, how different stressors impact BD-ES and where conservation efforts should be placed to optimize the delivery of ecosystem services and protection of biodiversity. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.

The Structure of Ecological Networks Across Levels of Organization

Interactions connect the units of ecological systems, forming networks. Individual-based networks characterize variation in niches among individuals within populations. These individual-based networks merge with each other, forming species-based networks and food webs that describe the architecture of ecological communities. Networks at broader spatiotemporal scales portray the structure of ecological interactions across landscapes and over macroevolutionary time. Here, I review the patterns observed in ecological networks across multiple levels of biological organization. A fundamental challenge is to understand the amount of interdependence as we move from individual-based networks to species-based networks and beyond. Despite the uneven distribution of studies, regularities in network structure emerge across scales due to the fundamental architectural patterns shared by complex networks and the interplay between traits and numerical effects. I illustrate the integration of these organizational scales by exploring the consequences of the emergence of highly connected species for network structures across scales.

Resolving Food-Web Structure

Food webs are a major focus and organizing theme of ecology, but the data used to assemble them are deficient. Early debates over food-web data focused on taxonomic resolution and completeness, lack of which had produced spurious inferences. Recent data are widely believed to be much better and are used extensively in theoretical and meta-analytic research on network ecology. Confidence in these data rests on the assumptions ( a) that empiricists correctly identified consumers and their foods and ( b) that sampling methods were adequate to detect a near-comprehensive fraction of the trophic interactions between species. Abundant evidence indicates that these assumptions are often invalid, suggesting that most topological food-web data may remain unreliable for inferences about network structure and underlying ecological and evolutionary processes. Morphologically cryptic species are ubiquitous across taxa and regions, and many trophic interactions routinely evade detection by conventional methods. Molecular methods have diagnosed the severity of these problems and are a necessary part of the cure.

An Ecosystems Perspective on Virus Evolution and Emergence

Understanding the emergence of pathogenic viruses has dominated studies of virus evolution. However, new metagenomic studies imply that relatively few of an immense number of viruses may lead to overt disease. This suggests a change in emphasis, from viruses as habitual pathogens to integral components of ecosystems. Here we show how viruses alter interactions between host individuals, populations, and ecosystems, impacting ecosystem health, resilience, and function, and how host ecology in turn impacts viral abundance and diversity. Moving to an ecosystems perspective will put virus evolution and disease emergence in its true context, and enhance our understanding of ecological processes.

Climate-driven ecological stability as a globally shared cause of Late Quaternary megafaunal extinctions: the Plaids and Stripes Hypothesis

Controversy persists about why so many large-bodied mammal species went extinct around the end of the last ice age. Resolving this is important for understanding extinction processes in general, for assessing the ecological roles of humans, and for conserving remaining megafaunal species, many of which are endangered today. Here we explore an integrative hypothesis that asserts that an underlying cause of Late Quaternary megafaunal extinctions was a fundamental shift in the spatio-temporal fabric of ecosystems worldwide. This shift was triggered by the loss of the millennial-scale climate fluctuations that were characteristic of the ice age but ceased approximately 11700 years ago on most continents. Under ice-age conditions, which prevailed for much of the preceding 2.6 Ma, these radical and rapid climate changes prevented many ecosystems from fully equilibrating with their contemporary climates. Instead of today's 'striped' world in which species' ranges have equilibrated with gradients of temperature, moisture, and seasonality, the ice-age world was a disequilibrial 'plaid' in which species' ranges shifted rapidly and repeatedly over time and space, rarely catching up with contemporary climate. In the transient ecosystems that resulted, certain physiological, anatomical, and ecological attributes shared by megafaunal species pre-adapted them for success. These traits included greater metabolic and locomotory efficiency, increased resistance to starvation, longer life spans, greater sensory ranges, and the ability to be nomadic or migratory. When the plaid world of the ice age ended, many of the advantages of being large were either lost or became disadvantages. For instance in a striped world, the low population densities and slow reproductive rates associated with large body size reduced the resiliency of megafaunal species to population bottlenecks. As the ice age ended, the downsides of being large in striped environments lowered the extinction thresholds of megafauna worldwide, which then increased the vulnerability of individual species to a variety of proximate threats they had previously tolerated, such as human predation, competition with other species, and habitat loss. For many megafaunal species, the plaid-to-stripes transition may have been near the base of a hierarchy of extinction causes whose relative importances varied geographically, temporally, and taxonomically.

Towards a multi-trophic extension of metacommunity ecology

Metacommunity theory provides an understanding of how spatial processes determine the structure and function of communities at local and regional scales. Although metacommunity theory has considered trophic dynamics in the past, it has been performed idiosyncratically with a wide selection of possible dynamics. Trophic metacommunity theory needs a synthesis of a few influential axis to simplify future predictions and tests. We propose an extension of metacommunity ecology that addresses these shortcomings by incorporating variability among trophic levels in 'spatial use properties'. We define 'spatial use properties' as a set of traits (dispersal, migration, foraging and spatial information processing) that set the spatial and temporal scales of organismal movement, and thus scales of interspecific interactions. Progress towards a synthetic predictive framework can be made by (1) documenting patterns of spatial use properties in natural food webs and (2) using theory and experiments to test how trophic structure in spatial use properties affects metacommunity dynamics.

Male rutting calls synchronize reproduction in Serengeti wildebeest

Tightly synchronized reproduction in vast wildebeest herds underpins the keystone role this iconic species plays in the Serengeti. However, despite decades of study, the proximate synchronizing mechanism remains unknown. Combining a season-long field experiment with simple stochastic process models, we show that females exposed to playback of male rutting vocalizations are over three times more synchronous in their expected time to mating than a control group isolated from all male stimuli. Additionally, predictions of both mating and calving synchrony based on the playback group were highly consistent with independent data on wildebeest mating and calving synchrony, while control-based predictions were inconsistent with the data. Taken together, our results provide the first experimental evidence that male rutting vocalizations alone could account for the highly synchronized reproduction observed in Serengeti wildebeest. Given anthropogenically driven losses in many areas, a mechanistic understanding of synchrony can highlight additional risks declining wildebeest populations may face.

The spatial distribution of African savannah herbivores: species associations and habitat occupancy in a landscape context

Herbivores play an important role in determining the structure and function of tropical savannahs. Here, we (i) outline a framework for how interactions among large mammalian herbivores, carnivores and environmental variation influence herbivore habitat occupancy in tropical savannahs. We then (ii) use a Bayesian hierarchical model to analyse camera trap data to quantify spatial patterns of habitat occupancy for lions and eight common ungulates of varying body size across an approximately 1100 km(2) landscape in the Serengeti ecosystem. Our results reveal strong positive associations among herbivores at the scale of the entire landscape. Lions were positively associated with migratory ungulates but negatively associated with residents. Herbivore habitat occupancy differed with body size and migratory strategy: large-bodied migrants, at less risk of predation and able to tolerate lower quality food, were associated with high NDVI, while smaller residents, constrained to higher quality forage, avoided these areas. Small herbivores were strongly associated with fires, likely due to the subsequent high-quality regrowth, while larger herbivores avoided burned areas. Body mass was strongly related to herbivore habitat use, with larger species more strongly associated with riverine and woodlands than smaller species. Large-bodied migrants displayed diffuse habitat occupancy, whereas smaller species demonstrated fine-scale occupancy reflecting use of smaller patches of high-quality habitat. Our results demonstrate the emergence of strong positive spatial associations among a diverse group of savannah herbivores, while highlighting species-specific habitat selection strongly determined by herbivore body size.This article is part of the themed issue 'Tropical grassy biomes: linking ecology, human use and conservation'.

Disease-mediated bottom-up regulation: An emergent virus affects a keystone prey, and alters the dynamics of trophic webs

Emergent diseases may alter the structure and functioning of ecosystems by creating new biotic interactions and modifying existing ones, producing cascading processes along trophic webs. Recently, a new variant of the rabbit haemorrhagic disease virus (RHDV2 or RHDVb) arguably caused widespread declines in a keystone prey in Mediterranean ecosystems - the European rabbit (Oryctolagus cuniculus). We quantitatively assess the impact of RHDV2 on natural rabbit populations and in two endangered apex predator populations: the Iberian lynx (Lynx pardinus) and the Spanish Imperial eagle (Aquila adalberti). We found 60–70% declines in rabbit populations, followed by decreases of 65.7% in Iberian lynx and 45.5% in Spanish Imperial eagle fecundities. A revision of the web of trophic interactions among rabbits and their dependent predators suggests that RHDV2 acts as a keystone species, and may steer Mediterranean ecosystems to management-dependent alternative states, dominated by simplified mesopredator communities. This model system stresses the importance of diseases as functional players in the dynamics of trophic webs.

Marine ecosystem connectivity mediated by migrant-resident interactions and the concomitant cross-system flux of lipids

Accumulating research argues that migrants influence the functioning and productivity of local habitats and ecosystems along migration routes and potentially drive cross-system energy fluxes of considerable magnitude, yet empirical documentation of local ecological effects and descriptions of the underlying mechanisms are surprisingly rare. In this study, we discovered migrant-resident interactions and substantial cross-system lipid transportation in the transition zone between the Baltic Sea and the North Sea where a resident cod population (predators) was found to interact with a herring population (prey) on a seasonal basis. We traced the lipids, using fatty acid trophic markers (FATM), from the herring feeding grounds in the North Sea to the cod livers in the Western Baltic Sea. Time series analysis of population dynamics indicated that population-level production of cod is positively affected by the herring subsidies. However, the underlying mechanisms were more complicated than anticipated. During the herring season, large cod received most of its dietary lipids from the herring, whereas smaller cod were prevented from accessing the lipid pool due to a mismatch in predator-prey size ratio. Furthermore, while the herring were extremely rich in bulk energy, they were surprisingly poor in a specific functional fatty acid. Hence, our study was the first to illustrate how the magnitude cross-system fluxes of subsidies in migrant-resident systems are potentially constrained by the size structure of the resident predator population and the nutritional quality of the migrants.

Ecosystem Service Valuation Assessments for Protected Area Management: A Case Study Comparing Methods Using Different Land Cover Classification and Valuation Approaches

Accurate and spatially-appropriate ecosystem service valuations are vital for decision-makers and land managers. Many approaches for estimating ecosystem service value (ESV) exist, but their appropriateness under specific conditions or logistical limitations is not uniform. The most accurate techniques are therefore not always adopted. Six different assessment approaches were used to estimate ESV for a National Nature Reserve in southwest China, across different management zones. These approaches incorporated two different land-use land cover (LULC) maps and development of three economic valuation techniques, using globally or locally-derived data. The differences in ESV across management zones for the six approaches were largely influenced by the classifications of forest and farmland and how they corresponded with valuation coefficients. With realistic limits on access to time, data, skills and resources, and using acquired estimates from globally-relevant sources, the Buffer zone was estimated as the most valuable (2.494 million ± 1.371 million CNY yr(-1) km(-2)) and the Non-protected zone as the least valuable (770,000 ± 4,600 CNY yr(-1) km(-2)). However, for both LULC maps, when using the locally-based and more time and skill-intensive valuation approaches, this pattern was generally reversed. This paper provides a detailed practical example of how ESV can differ widely depending on the availability and appropriateness of LULC maps and valuation approaches used, highlighting pitfalls for the managers of protected areas.

Migratory animals couple biodiversity and ecosystem functioning worldwide

Animal migrations span the globe, involving immense numbers of individuals from a wide range of taxa. Migrants transport nutrients, energy, and other organisms as they forage and are preyed upon throughout their journeys. These highly predictable, pulsed movements across large spatial scales render migration a potentially powerful yet underappreciated dimension of biodiversity that is intimately embedded within resident communities. We review examples from across the animal kingdom to distill fundamental processes by which migratory animals influence communities and ecosystems, demonstrating that they can uniquely alter energy flow, food-web topology and stability, trophic cascades, and the structure of metacommunities. Given the potential for migration to alter ecological networks worldwide, we suggest an integrative framework through which community dynamics and ecosystem functioning may explicitly consider animal migrations.