Toward a standardized quantitative and qualitative insect monitoring scheme

Synchronised monitoring of plant and insect diversity: a case study using automated Malaise traps and DNA-based methods

The occurrence and distribution of insects and their possible associations with plant species are largely unknown in Germany and baseline data to monitor future trends are urgently needed. Using newly-designed automated Malaise trap multi-samplers, the occurrence of insect species and their potential associations with plants was monitored synchronously at two contrasting field sites in Germany: an urban botanical garden and a forest research station. Taxa were identified by metabarcoding of the insects and the plant traces present in the preservative ethanol of the Malaise trap samples. For comparison, a botanical survey was conducted in the vicinity of the traps. Across both sites, we identified a total of 1290 exact sequence variants (ESVs) assigned to Insecta, of which 205 are known to be pollinators. In the botanical garden, we detected the occurrence of 128 plant taxa, of which 41 also had one of their known insect pollinator species detected. Insect species richness was highest in May, mainly attributed to an increase in Diptera. These results present a case study of the applicability of automated sampling and DNA-based methods to monitor the timings of flowering and corresponding activity of plant-visiting insects.

Collective and harmonized high throughput barcoding of insular arthropod biodiversity: Toward a Genomic Observatories Network for islands

Current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species, and as such can provide key insights into processes governing biodiversity. Novel high throughput sequencing (HTS) approaches are now emerging as powerful tools to overcome limitations in the availability of arthropod biodiversity data, and hence provide insights into these processes. Here, we explored how these tools might be most effectively exploited for comprehensive and comparable inventory and monitoring of insular arthropod biodiversity. We first reviewed the strengths, limitations and potential synergies among existing approaches of high throughput barcode sequencing. We considered how this could be complemented with deep learning approaches applied to image analysis to study arthropod biodiversity. We then explored how these approaches could be implemented within the framework of an island Genomic Observatories Network (iGON) for the advancement of fundamental and applied understanding of island biodiversity. To this end, we identified seven island biology themes at the interface of ecology, evolution and conservation biology, within which collective and harmonized efforts in HTS arthropod inventory could yield significant advances in island biodiversity research.

Earlier and more uniform spring green-up linked to lower insect richness and biomass in temperate forests

Urbanization and agricultural intensification are considered the main causes of recent insect decline in temperate Europe, while direct climate warming effects are still ambiguous. Nonetheless, higher temperatures advance spring leaf emergence, which in turn may directly or indirectly affect insects. We therefore investigated how Sentinel-2-derived start of season (SOS) and its spatial variability (SV-SOS) are affected by spring temperature and whether these green-up variables can explain insect biomass and richness across a climate and land-use gradient in southern Germany. We found that the effects of both spring green-up variables on insect biomass and richness differed between land-use types, but were strongest in forests. Here, insect richness and biomass were higher with later green-up (SOS) and higher SV-SOS. In turn, higher spring temperatures advanced SOS, while SV-SOS was lower at warmer sites. We conclude that with a warming climate, insect biomass and richness in forests may be affected negatively due to earlier and more uniform green-up. Promising adaptation strategies should therefore focus on spatial variability in green-up in forests, thus plant species and structural diversity.

Soundscapes and deep learning enable tracking biodiversity recovery in tropical forests

Tropical forest recovery is fundamental to addressing the intertwined climate and biodiversity loss crises. While regenerating trees sequester carbon relatively quickly, the pace of biodiversity recovery remains contentious. Here, we use bioacoustics and metabarcoding to measure forest recovery post-agriculture in a global biodiversity hotspot in Ecuador. We show that the community composition, and not species richness, of vocalizing vertebrates identified by experts reflects the restoration gradient. Two automated measures - an acoustic index model and a bird community composition derived from an independently developed Convolutional Neural Network - correlated well with restoration (adj-R² = 0.62 and 0.69, respectively). Importantly, both measures reflected composition of non-vocalizing nocturnal insects identified via metabarcoding. We show that such automated monitoring tools, based on new technologies, can effectively monitor the success of forest recovery, using robust and reproducible data.

Robber flies and hover flies (Insecta, Diptera, Asilidae and Syrphidae) in beech forests of the central Apennines: a contribution to the inventory of insect biodiversity in Italian State Nature Reserves

Background

The present paper describes a sampling-event dataset on species belonging to two families of Diptera (Syrphidae and Asilidae) collected between 2012 and 2019 in two Italian beech forests located in the central Apennines. The reference dataset consists of an annotated checklist and has been published on Zenodo. Syrphidae and Asilidae are two widespread and key ecological groups, including predator, pollinator and saproxylic species. Despite their pivotal role in both natural and man-made ecosystems, these families are still poorly known in terms of local distribution and open-access sampling-event data are rare in Italy.

New information

This open-access dataset includes 2,295 specimens for a total of 21 Asilidae and 65 Syrphidae species. Information about the collection (e.g. place, date, methods applied, collector) and the identification (e.g. species name, author, taxon ID) of the species is provided. Given the current biodiversity crisis, the publication of checklists, sampling-event data and datasets on insect communities in open-access repositories is highly recommended, as it represents the opportunity to share biodiversity information amongst different stakeholders. Moreover, such data are also a valuable source of information for nature reserve managers responsible for monitoring the conservation status of protected and endangered species and habitats and for evaluating the effects of conservation actions over time.

Monitoring insect biodiversity and comparison of sampling strategies using metabarcoding: A case study in the Yanshan Mountains, China

Insects are the richest and most diverse group of animals and yet there remains a lack, not only of systematic research into their distribution across some key regions of the planet, but of standardized sampling strategies for their study. The Yanshan Mountains, being the boundary range between the Inner Mongolian Plateau and the North China Plain, present an indispensable piece of the insect biodiversity puzzle: both requiring systematic study and offering opportunities for the development of standardized methodologies. This is the first use of DNA metabarcoding to survey the insect biodiversity of the Yanshan Mountains. The study focuses on differences of community composition among samples collected via different methods and from different habitat types. In total, 74 bulk samples were collected from five habitat types (scrubland, woodland, wetland, farmland and grassland) using three collection methods (sweep netting, Malaise traps and light traps). After DNA extraction, PCR amplification, sequencing and diversity analysis were performed, a total of 7427 Operational Taxonomic Units (OTUs) at ≥97% sequence similarity level were delimited, of which 7083 OTUs were identified as belonging to Insecta. Orthoptera, Diptera, Coleoptera and Hemiptera were found to be the dominant orders according to community composition analysis. Nonmetric multidimensional scaling (NMDS) analysis based on Bray-Curtis distances revealed highly divergent estimates of insect community composition among samples differentiated by the collection method (R = .524802, p = .001), but nonsignificant difference among samples differentiated according to habitat (R = .051102, p = .078). The study therefore appears to indicate that the concurrent use of varied collection methods is essential to the accurate monitoring of insect biodiversity.

Plant species composition and local habitat conditions as primary determinants of terrestrial arthropod assemblages

Arthropods respond to vegetation in multiple ways since plants provide habitat and food resources and indicate local abiotic conditions. However, the relative importance of these factors for arthropod assemblages is less well understood. We aimed to disentangle the effects of plant species composition and environmental drivers on arthropod taxonomic composition and to assess which aspects of vegetation contribute to the relationships between plant and arthropod assemblages. In a multi-scale field study in Southern Germany, we sampled vascular plants and terrestrial arthropods in typical habitats of temperate landscapes. We compared independent and shared effects of vegetation and abiotic predictors on arthropod composition distinguishing between four large orders (Lepidoptera, Coleoptera, Hymenoptera, Diptera), and five functional groups (herbivores, pollinators, predators, parasitoids, detritivores). Across all investigated groups, plant species composition explained the major fraction of variation in arthropod composition, while land-cover composition was another important predictor. Moreover, the local habitat conditions depicted by the indicator values of the plant communities were more important for arthropod composition than trophic relationships between certain plant and arthropod species. Among trophic groups, predators showed the strongest response to plant species composition, while responses of herbivores and pollinators were stronger than those of parasitoids and detritivores. Our results highlight the relevance of plant community composition for terrestrial arthropod assemblages across multiple taxa and trophic levels and emphasize the value of plants as a proxy for characterizing habitat conditions that are hardly accessible to direct environmental measurements.

Repeated subsamples during DNA extraction reveal increased diversity estimates in DNA metabarcoding of Malaise traps

With increased application of DNA metabarcoding in biodiversity assessment, various laboratory protocols have been optimized, and their further evaluation is subject of current research. Homogenization of bulk samples and subsequent DNA extraction from a subsample of destructed tissue is a common first stage of the metabarcoding process. This can either be conducted using sample material soaked in a storage fixative, e.g., ethanol (here referred to as "wet" treatment) or from dried individuals ("dry"). However, it remains uncertain if perfect mixing and equal distribution of DNA within the tube is ensured during homogenization and to what extent incomplete mixing and resulting variations in tissue composition affect diversity assessments if only a fraction of the destructed sample is processed in the downstream metabarcoding workflow. Here we investigated the efficiency of homogenization under wet and dry conditions and tested how variations in destructed tissue composition might affect diversity assessments of complex arthropod samples. We considered five time intervals of Malaise trap bulk samples and process nine different subsamples of homogenized tissue (20 mg each) in both treatments. Results indicate a more consistent diversity assessment from dried material, but at the cost of a higher processing time. Both approaches detected comparable OTU diversity and revealed similar taxa compositions in a single tissue extraction. With an increased number of tissue subsamples during DNA extraction, OTU diversity increased for both approaches, especially for highly diverse samples obtained during the summer. Here, particularly the detection of small and low-biomass taxa increased. The processing of multiple subsamples in the metabarcoding protocol can therefore be a helpful procedure to enhance diversity estimates and counteract taxonomic bias in biodiversity assessments. However, the process induces higher costs and time effort and the application in large-scale biodiversity assessment, e.g., in monitoring schemes needs to be considered on project-specific prospects.

Fluctuating insect diversity, abundance and biomass across agricultural landscapes

Habitat destruction and deterioration of habitat quality caused a severe decline of biodiversity, such as insect diversity. In this study, we analyze insect diversity and biomass across agro-environments. We collected flying insects with 20 malaise traps across a landscape mosaic consisting of organic (eight traps) and conventional (four traps) farmland, as well as across agricultural land that has been recently converted from conventional to organic farming (eight traps). Sampling was conducted over 2 years, in 2019 and 2020, with in total 340 sampling events. We measured the dry weight of the captured organisms and identified species diversity by analyzing Operational Taxonomic Units (OTUs) and Barcode Index Numbers (BINs) via metabarcoding. The results obtained show temporal dynamics. The number of OTUs were always higher than the number of BINs. OTUs and BINs were moderately to highly correlated, while the number of OTUs and BINs were only moderately positively correlated with dry biomass. OTUs and BINs as well as biomass were highest in the recently transformed farmland if compared with pure organic and conventional farmland sites, which showed no significant differences in respect of insect diversity. OTU and BIN numbers but not the OTU/BIN ratio significantly decreased with increasing distance from the nearest forest fringe. The numbers of OTUs, BINs and the OTU/BIN proportion, as well as OTU and BIN/biomass proportions varied strongly over seasons, irrespective of agricultural practice. Based on our findings, we suggest to combine data on insect species richness and biomass measured over a period of time, to derive a largely complete and meaningful assessment of biodiversity for a specific region.

Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods

Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale syntheses may be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners, method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options. We advocate the adoption and further development of the terrestrial arthropod module. We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization.

Using Malaise Traps and Metabarcoding for Biodiversity Assessment in Vineyards: Effects of Weather and Trapping Effort

Metabarcoding is a powerful tool for ecological studies and monitoring that might provide a solution to the time-consuming taxonomic identification of the vast diversity of insects. Here, we assess how ambient weather conditions during Malaise trap exposure and the effort of trapping affect biomass and taxa richness in vineyards. Biomass varied by more than twofold with weather conditions. It increased with warmer and drier weather but was not significantly related with wind or precipitation. Taxa richness showed a saturating relationship with increasing trapping duration and was influenced by environmental and seasonal effects. Taxa accumulation was high, increasing fourfold from three days of monthly trap exposure compared to continuous trapping and nearly sixfold from sampling at a single site compared to 32 sites. The limited saturation was mainly due to a large number of singletons, such as rare species, in the metabarcoding dataset. Metabarcoding can be key for long-term insect monitoring. We conclude that single traps operated for up to ten days per month are suitable to monitor the presence of common species. However, more intensive trapping is necessary for a good representation of rare species in biodiversity monitoring. The data collected here can potentially guide the design of monitoring studies.

Interactive effects of climate and land use on pollinator diversity differ among taxa and scales

Changes in climate and land use are major threats to pollinating insects, an essential functional group. Here, we unravel the largely unknown interactive effects of both threats on seven pollinator taxa using a multiscale space-for-time approach across large climate and land-use gradients in a temperate region. Pollinator community composition, regional gamma diversity, and community dissimilarity (beta diversity) of pollinator taxa were shaped by climate-land-use interactions, while local alpha diversity was solely explained by their additive effects. Pollinator diversity increased with reduced land-use intensity (forest < grassland < arable land < urban) and high flowering-plant diversity at different spatial scales, and higher temperatures homogenized pollinator communities across regions. Our study reveals declines in pollinator diversity with land-use intensity at multiple spatial scales and regional community homogenization in warmer and drier climates. Management options at several scales are highlighted to mitigate impacts of climate change on pollinators and their ecosystem services.

A novel approach for reliable qualitative and quantitative prey spectra identification of carnivorous plants combining DNA metabarcoding and macro photography

Prey spectra (the number and composition of captured arthropods) represent a crucial aspect of carnivorous plant ecology, yet remain poorly studied. Traditional morphology-based approaches for prey identification are time-intensive, require specialists with considerable knowledge of arthropod taxonomy, and are hampered by high numbers of unidentifiable (i.e., heavily digested) prey items. We examined prey spectra of three species of closely-related annual Drosera (Droseraceae, sundews) from tropical northern Australia using a novel DNA metabarcoding approach with in-situ macro photography as a plausibility control and to facilitate prey quantity estimations. This new method facilitated accurate analyses of carnivorous plant prey spectra (even of heavily digested prey lacking characteristic morphological features) at a taxonomic resolution and level of completeness far exceeding morphology-based methods and approaching the 100% mark at arthropod order level. Although the three studied species exhibited significant differences in detected prey spectra, little prey specialisation was observed and habitat or plant population density variations were likely the main drivers of prey spectra dissimilarity.

Arthropod dark taxa provide new insights into diversity responses to bark beetle infestations

Natural disturbances are increasing around the globe, also impacting protected areas. Although previous studies have indicated that natural disturbances result in mainly positive effects on biodiversity, these analyses mostly focused on a few well established taxonomic groups, and thus uncertainty remains regarding the comprehensive impact of natural disturbances on biodiversity. Using Malaise traps and meta-barcoding, we studied a broad range of arthropod taxa, including dark and cryptic taxa, along a gradient of bark beetle disturbance severities in five European national parks. We identified order-level community thresholds of disturbance severity and classified barcode index numbers (BINs; a cluster system for DNA sequences, where each cluster corresponds to a species) as negative or positive disturbance indicators. Negative indicator BINs decreased above thresholds of low to medium disturbance severity (20%-30% of trees killed), whereas positive indicator BINs benefited from high disturbance severity (76%-98%). BINs allocated to a species name contained nearly as many positive as negative disturbance indicators, but dark and cryptic taxa, particularly Diptera and Hymenoptera in our data, contained higher numbers of negative disturbance indicator BINs. Analyses of changes in the richness of BINs showed variable responses of arthropods to disturbance severity at lower taxonomic levels, whereas no significant signal was detected at the order level due to the compensatory responses of the underlying taxa. We conclude that the analyses of dark taxa can offer new insights into biodiversity responses to disturbances. Our results suggest considerable potential for forest management to foster arthropod diversity, for example by maintaining both closed-canopy forests (>70% cover) and open forests (<30% cover) on the landscape.

Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea)

DNA barcoding has become the most popular approach for species identification in recent years. As part of the German Barcode of Life project, the first DNA barcode library for terrestrial and freshwater isopods from Germany is presented. The analyzed barcode library included 38 terrestrial (78% of the documented species of Germany) and five freshwater (63%) species. A total of 513 new barcodes was generated and 518 DNA barcodes were analyzed. This analysis revealed surprisingly high intraspecific genetic distances for numerous species, with a maximum of 29.4% for Platyarthrus hoffmannseggii Brandt, 1833. The number of BINs per species ranged from one (32 species, 68%) to a maximum of six for Trachelipus rathkii (Brandt, 1833). In spite of such high intraspecific variability, interspecific distances with values between 12.6% and 29.8% allowed a valid species assignment of all analyzed isopods. The observed high intraspecific distances presumably result from phylogeographic events, Wolbachia infections, atypical mitochondrial DNAs, heteroplasmy, or various combinations of these factors. Our study represents the first step in generating an extensive reference library of DNA barcodes for terrestrial and freshwater isopods for future molecular biodiversity assessment studies.

Pooling size sorted Malaise trap fractions to maximize taxon recovery with metabarcoding

Background

Small and rare specimens can remain undetected when metabarcoding is applied on bulk samples with a high specimen size heterogeneity. This is especially critical for Malaise trap samples, where most of the biodiversity is contributed by small taxa with low biomass. The separation of samples in different size fractions for downstream analysis is one possibility to increase detection of small and rare taxa. However, experiments systematically testing different size sorting approaches and subsequent proportional pooling of fractions are lacking, but would provide important information for the optimization of metabarcoding protocols. We set out to find a size sorting strategy for Malaise trap samples that maximizes taxonomic recovery but remains scalable and time efficient.

Methods

Three Malaise trap samples were sorted into four size classes using dry sieving. Each fraction was homogenized and lysed. The corresponding lysates were pooled to simulate unsorted samples. Pooling was additionally conducted in equal proportions and in four different proportions enriching the small size fraction of samples. DNA from the individual size classes as well as the pooled fractions was extracted and metabarcoded using the FwhF2 and Fol-degen-rev primer set. Additionally, alternative wet sieving strategies were explored.

Results

The small size fractions harboured the highest diversity and were best represented when pooling in favour of small specimens. Metabarcoding of unsorted samples decreases taxon recovery compared to size sorted samples. A size separation into only two fractions (below 4 mm and above) can double taxon recovery compared to not size sorting. However, increasing the sequencing depth 3- to 4-fold can also increase taxon recovery to levels comparable with size sorting, but remains biased towards biomass rich taxa in the sample.

Conclusion

We demonstrate that size fractionation of Malaise trap bulk samples can increase taxon recovery. While results show distinct patterns, the lack of statistical support due to the limited number of samples processed is a limitation. Due to increased speed and lower risk of cross-contamination as well as specimen damage we recommend wet sieving and proportional pooling of the lysates in favour of the small size fraction (80–90% volume). However, for large-scale projects with time constraints, increasing sequencing depth is an alternative solution.

Relationship of insect biomass and richness with land use along a climate gradient

Recently reported insect declines have raised both political and social concern. Although the declines have been attributed to land use and climate change, supporting evidence suffers from low taxonomic resolution, short time series, a focus on local scales, and the collinearity of the identified drivers. In this study, we conducted a systematic assessment of insect populations in southern Germany, which showed that differences in insect biomass and richness are highly context dependent. We found the largest difference in biomass between semi-natural and urban environments (-42%), whereas differences in total richness (-29%) and the richness of threatened species (-56%) were largest from semi-natural to agricultural environments. These results point to urbanization and agriculture as major drivers of decline. We also found that richness and biomass increase monotonously with increasing temperature, independent of habitat. The contrasting patterns of insect biomass and richness question the use of these indicators as mutual surrogates. Our study provides support for the implementation of more comprehensive measures aimed at habitat restoration in order to halt insect declines.

Standards and Best Practices for Monitoring and Benchmarking Insects

Benchmark studies of insect populations are increasingly relevant and needed amid accelerating concern about insect trends in the Anthropocene. The growing recognition that insect populations may be in decline has given rise to a renewed call for insect population monitoring by scientists, and a desire from the broader public to participate in insect surveys. However, due to the immense diversity of insects and a vast assortment of data collection methods, there is a general lack of standardization in insect monitoring methods, such that a sudden and unplanned expansion of data collection may fail to meet its ecological potential or conservation needs without a coordinated focus on standards and best practices. To begin to address this problem, we provide simple guidelines for maximizing return on proven inventory methods that will provide insect benchmarking data suitable for a variety of ecological responses, including occurrence and distribution, phenology, abundance and biomass, and diversity and species composition. To track these responses, we present seven primary insect sampling methods—malaise trapping, light trapping, pan trapping, pitfall trappings, beating sheets, acoustic monitoring, and active visual surveys—and recommend standards while highlighting examples of model programs. For each method, we discuss key topics such as recommended spatial and temporal scales of sampling, important metadata to track, and degree of replication needed to produce rigorous estimates of ecological responses. We additionally suggest protocols for scalable insect monitoring, from backyards to national parks. Overall, we aim to compile a resource that can be used by diverse individuals and organizations seeking to initiate or improve insect monitoring programs in this era of rapid change.