Networking nutrients: How nutrition determines the structure of ecological networks.

Nutrients can shape ecological interactions but remain poorly integrated into ecological networks. Concepts such as nutrient-specific foraging nevertheless have the potential to expose the mechanisms structuring complex ecological systems. Nutrients also present an opportunity to predict dynamic processes, such as interaction rewiring and extinction cascades, and increase the accuracy of network analyses. Here, we propose the concept of nutritional networks. By integrating nutritional data into ecological networks, we envisage significant advances to our understanding of ecological processes from individual to ecosystem scales. We show that networks can be constructed with nutritional data to illuminate how nutrients structure ecological interactions in natural systems through an empirical example. Throughout, we identify fundamental ecological hypotheses that can be explored in a nutritional network context, alongside methods for resolving those networks. Nutrients influence the structure and complexity of ecological networks through mechanistic processes and concepts including nutritional niche differentiation, functional responses, landscape diversity, ecological invasions and ecosystem robustness. Future research on ecological networks should consider nutrients when investigating the drivers of network structure and function.

The complex epistemological challenge of data curation in dietary metabarcoding: Comment on "The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation" by Littleford-Colquhoun et al. (2022).

In their article, Littleford-Colquhoun et al. (2022) advise against using arbitrary relative read abundance (RRA) thresholds (i.e., minimum sequence copy thresholds) for removing low-abundance sequences since they can increase false negative rates in dietary DNA metabarcoding data sets. The main criticisms presented against these widespread methods are that they (i) are arbitrary, often existing as standard values or defined based on researcher-selected delineations, (ii) are subjective, varying between studies and contexts, and, most problematically, (iii) result in the exclusion of true positives, particularly rarely consumed taxa, to the detriment of ecological insight. We commend the authors for presenting a refreshing and timely perspective on this often neglected topic, which is certainly in need of greater discussion following over a decade of significant advances in dietary metabarcoding. In this complex epistemological problem of false positives versus false negatives, we feel that several of the points raised deserve additional discussion. We address these aspects below, including measured approaches to data filtration and consistent representation of RRAs, and we welcome any further discourse to solidify or refute the concepts therein.

The problem of omnivory: A synthesis on omnivory and DNA metabarcoding.

Dietary analysis using DNA metabarcoding is a powerful tool that is increasingly being used to further our knowledge of trophic interactions in highly complex food webs but is not without limitations. Omnivores, the most generalist of consumers, pose unique challenges when using such methods. Here, we provide the rationale to understand the problems associated with analysing the complex diets of omnivores. By reviewing existing metabarcoding studies of omnivorous diet, and constructing hypothetical scenarios arising from each, we outline that great caution is required when interpreting sequencing data in such cases. In essence, the problems of accidental consumption and secondary ingestion are significant sources of error when investigating omnivorous diets. The integration of multiple high throughput sequencing markers increases the taxonomic breadth of taxa detected but we reveal how some detections may be misleading. Disentangling which taxa have been deliberately or accidentally consumed by the focal omnivore is challenging and can falsely emphasise those that were not intentionally consumed, obscuring biologically meaningful interactions. Although we suggest ways to disentangle these issues, we urge that the results of such analyses should be interpreted with caution and all possible scenarios for the presence of biota within omnivores given due consideration.

Influence of European Beech (Fagales: Fagaceae) Rot Hole Habitat Characteristics on Invertebrate Community Structure and Diversity.

Hollows of veteran trees (i.e., rot holes) provide habitat for many rare and threatened saproxylic invertebrates. Rot holes are highly heterogeneous, particularly in terms of substrate and microclimate conditions. There is, however, a dearth of information regarding the differences in biological communities inhabiting rot holes with different environmental conditions. Invertebrates were sampled from European beech (Fagus sylvatica) rot holes in Windsor, Savernake, and Epping Forests (United Kingdom). For each rot hole, physical and environmental conditions were measured, including tree diameter, rot hole dimensions, rot hole height, substrate density, water content, and water potential. These parameters were used to assess the influence of environmental conditions and habitat characteristics on invertebrate communities. Rot hole invertebrate communities were extremely diverse, containing both woodland generalist and saproxylic specialist taxa. Large variation in community structure was observed between rot holes and across woodlands; all sites supported threatened and endangered taxa. Environmental conditions in rot holes were highly variable within and between woodland sites, and communities were predominantly structured by these environmental conditions. In particular, turnover between invertebrate communities was linked to high ß-diversity. The linked heterogeneity of environmental conditions and invertebrate communities in rot holes suggests that management of deadwood habitats in woodlands should strive to generate environmental heterogeneity to promote invertebrate diversity. Additional research is required to define how management and conservation activities can further promote enhanced biodiversity across rot holes.

Understanding trophic interactions in a warming world by bridging foraging ecology and biomechanics with network science.

Climate change will disrupt biological processes at every scale. Ecosystem functions and services vital to ecological resilience are set to shift, with consequences for how we manage land, natural resources, and food systems. Increasing temperatures cause morphological shifts, with concomitant implications for biomechanical performance metrics crucial to trophic interactions. Biomechanical performance, such as maximum bite force or running speed, determines the breadth of resources accessible to consumers, the outcome of interspecific interactions, and thus the structure of ecological networks. Climate change-induced impacts to ecosystem services and resilience are therefore on the horizon, mediated by disruption of biomechanical performance and, consequently, trophic interactions across whole ecosystems. Here, we argue that there is an urgent need to investigate the complex interactions between climate change, biomechanical traits and foraging ecology to help predict changes to ecological networks and ecosystem functioning. We discuss how these seemingly disparate disciplines can be connected through network science. Using an ant-plant network as an example, we illustrate how different data types could be integrated to investigate the interaction between warming, bite force and trophic interactions, and discuss what such an integration will achieve. It is our hope that this integrative framework will help to identify a viable means to elucidate previously intractable impacts of climate change, with effective predictive potential to guide management and mitigation.

Non-native ants drive dramatic declines in animal community diversity: A meta-analysis.

Non-native ants can cause ecosystem-wide ecological change, and these changes are generally assumed to be negative. Despite this, the evidence base has never been holistically synthesised to quantify whether and to what degree non-native ants impact native species diversity.In this study, we performed a meta-analysis of the effects of ant invasion on animal communities. We extracted data from 46 published articles investigating abundance (156 effect sizes) and richness (53 effect sizes) responses of animal taxa to ant invasion in locations relatively unimpacted by other stressors (e.g. human disturbance, other non-native species) to help isolate the effects of invasion.Overall, local animal diversity declined severely, with species abundance and richness lower by 42.79% and 53.56%, respectively, in areas with non-native ants compared with intact uninvaded sites. We then combined responses of individual animal taxa extracted from an article into a single response to represent the 'community' abundance (40 effect sizes) or richness (28 effect sizes) response to non-native ants represented in each article. Local communities decreased substantially in total abundance (52.67%) and species richness (53.47%) in invaded sites.These results highlight non-native ants as the drivers, rather than passengers, of large net-negative reductions to animal community diversity in relatively undisturbed systems around the world, approximately halving local species abundance and richness in invaded areas. Improved international prevention processes, early detection systems harnessing emerging technologies, and well-designed control measures deployable by conservation practitioners are urgently needed if these effects are to be mitigated, prevented or reversed.

The predator problem and PCR primers in molecular dietary analysis: Swamped or silenced; depth or breadth?

Dietary metabarcoding has vastly improved our ability to analyse the diets of animals, but it is hampered by a plethora of technical limitations including potentially reduced data output due to the disproportionate amplification of the DNA of the focal predator, here termed "the predator problem". We review the various methods commonly used to overcome this problem, from deeper sequencing to exclusion of predator DNA during PCR, and how they may interfere with increasingly common multipredator-taxon studies. We suggest that multiprimer approaches with an emphasis on achieving both depth and breadth of prey detections may overcome the issue to some extent, although multitaxon studies require further consideration, as highlighted by an empirical example. We also review several alternative methods for reducing the prevalence of predator DNA that are conceptually promising but require additional empirical examination. The predator problem is a key constraint on molecular dietary analyses but, through this synthesis, we hope to guide researchers in overcoming this in an effective and pragmatic way.

Otterly delicious: Spatiotemporal variation in the diet of a recovering population of Eurasian otters (Lutra lutra) revealed through DNA metabarcoding and morphological analysis of prey remains.

Eurasian otters are apex predators of freshwater ecosystems and a recovering species across much of their European range; investigating the dietary variation of this predator over time and space, therefore, provides opportunities to identify changes in freshwater trophic interactions and factors influencing the conservation of otter populations. Here we sampled feces from 300 dead otters across England and Wales between 2007 and 2016, conducting both morphological analyses of prey remains and dietary DNA metabarcoding. Comparison of these methods showed that greater taxonomic resolution and breadth could be achieved using DNA metabarcoding but combining data from both methodologies gave the most comprehensive dietary description. All otter demographics exploited a broad range of taxa and variation likely reflected changes in prey distributions and availability across the landscape. This study provides novel insights into the trophic generalism and adaptability of otters across Britain, which is likely to have aided their recent population recovery, and may increase their resilience to future environmental changes.

Monitoring SARS-CoV-2 Using Infoveillance, National Reporting Data, and Wastewater in Wales, United Kingdom: Mixed Methods Study.

BACKGROUND: The COVID-19 pandemic necessitated rapid real-time surveillance of epidemiological data to advise governments and the public, but the accuracy of these data depends on myriad auxiliary assumptions, not least accurate reporting of cases by the public. Wastewater monitoring has emerged internationally as an accurate and objective means for assessing disease prevalence with reduced latency and less dependence on public vigilance, reliability, and engagement. How public interest aligns with COVID-19 personal testing data and wastewater monitoring is, however, very poorly characterized. OBJECTIVE: This study aims to assess the associations between internet search volume data relevant to COVID-19, public health care statistics, and national-scale wastewater monitoring of SARS-CoV-2 across South Wales, United Kingdom, over time to investigate how interest in the pandemic may reflect the prevalence of SARS-CoV-2, as detected by national testing and wastewater monitoring, and how these data could be used to predict case numbers. METHODS: Relative search volume data from Google Trends for search terms linked to the COVID-19 pandemic were extracted and compared against government-reported COVID-19 statistics and quantitative reverse transcription polymerase chain reaction (RT-qPCR) SARS-CoV-2 data generated from wastewater in South Wales, United Kingdom, using multivariate linear models, correlation analysis, and predictions from linear models. RESULTS: Wastewater monitoring, most infoveillance terms, and nationally reported cases significantly correlated, but these relationships changed over time. Wastewater surveillance data and some infoveillance search terms generated predictions of case numbers that correlated with reported case numbers, but the accuracy of these predictions was inconsistent and many of the relationships changed over time. CONCLUSIONS: Wastewater monitoring presents a valuable means for assessing population-level prevalence of SARS-CoV-2 and could be integrated with other data types such as infoveillance for increasingly accurate inference of virus prevalence. The importance of such monitoring is increasingly clear as a means of objectively assessing the prevalence of SARS-CoV-2 to circumvent the dynamic interest and participation of the public. Increased accessibility of wastewater monitoring data to the public, as is the case for other national data, may enhance public engagement with these forms of monitoring.

DNA metabarcoding reveals introduced species predominate in the diet of a threatened endemic omnivore, Telfair's skink (Leiolopisma telfairii).

Introduced species can exert disproportionately negative effects on island ecosystems, but their potential role as food for native consumers is poorly studied. Telfair's skinks are endemic omnivores living on Round Island, Mauritius, a globally significant site of biodiversity conservation. We aimed to determine the dietary diversity and key trophic interactions of Telfair's skinks, whether introduced species are frequently consumed, and if diet composition changes seasonally between male and female skinks. We used DNA metabarcoding of skink fecal samples to identify animals (COI) and plants (ITS2) consumed by skinks. There were 389 dietary presence counts belonging to 77 dietary taxa found across the 73 Telfair's skink fecal samples. Introduced taxa were cumulatively consumed more frequently than other categories, accounting for 49.4% of all detections, compared to cryptogenic (20.6%), native (20.6%), and endemic taxa (9.5%). The most frequently consumed introduced species was the ant, Pheidole megacephala, present in 40% of samples. Blue latan palm, Latania loddigesii, was the most frequently consumed endemic species, present in 33% of samples but was only detected in the dry season, when fruits are produced. We found a strong seasonal difference in diet composition explained by the presence of certain plant species solely or primarily in one season and a marked increase in the consumption of animal prey in the dry season. Male and female skinks consumed several taxa at different frequencies. These results present a valuable perspective on the role of introduced species in the trophic network of their invaded ecosystem. Both native and introduced species provide nutritional resources for skinks, and this may have management implications in the context of species conservation and island restoration.

MEDI: Macronutrient Extraction and Determination from invertebrates, a rapid, cheap and streamlined protocol.

Macronutrients, comprising carbohydrates, proteins and lipids, underpin many ecological processes, but their quantification in ecological studies is often inaccurate and laborious, requiring large investments of time and bulk samples, which make individual-level studies impossible. This study presents Macronutrient Extraction and Determination from Invertebrates (MEDI), a protocol for the direct, rapid and relatively low-cost determination of macronutrient content from single small macroinvertebrates.Macronutrients were extracted by a sequential process of soaking in 1:12 chloroform:methanol solution to remove lipid and then solubilising tissue in 0.1 M NaOH. Proteins, carbohydrates and lipids were determined by colorimetric assays from the same individual specimens.The limits of detection of MEDI with the equipment and conditions used were 0.067, 0.065 and 0.006 mg/ml for proteins, carbohydrates and lipids respectively. Adjusting the volume of reagents used for extraction and determination can broaden the range of concentrations that can be detected. MEDI successfully identified taxonomic differences in macronutrient content between five insect species.Macronutrient Extraction and Determination from Invertebrates can directly and rapidly determine macronutrient content in tiny (dry mass ~3 mg) and much larger individual invertebrates. Using MEDI, the total macronutrient content of over 50 macroinvertebrates can be determined within around 3 days of collection at a cost of ~$1.35 per sample.