New approaches narrow global species estimates for beetles, insects, and terrestrial arthropods

Experimental evolution reveals that males evolving within warmer thermal regimes improve reproductive performance under heatwave conditions in a model insect

Climate change is increasing mean temperatures, and intensifying heatwaves. Natural populations may respond to stress through shorter-term acclimation via plasticity and/or longer-term inter-generational evolution. However, if the pace and/or extent of thermal change is too great, local extinctions occur; one potential cause in ectotherms is identified to be the heat-liability of male reproductive biology. Recent data from several species, including the beetle Tribolium castaneum, confirmed that male reproductive biology is vulnerable to heatwaves, which may constrain populations. However, such reproductive-damage may be overestimated, if there is potential to adapt to elevated mean temperatures associated with climate change via evolution and/or acclimation. Here, we tested this to evaluate whether pre-exposures could improve heatwave tolerance (adaptation or acclimation), by experimentally evolving Tribolium castaneum populations to divergent thermal regimes (30 °C vs. 38 °C). Findings across assays revealed that relative to 30 °C-regime males, males from the 38 °C regime, maintained constantly at 8 °C warmer for 25 generations, displayed an increase; (i) in post heatwave (42 °C) reproductive fitness by 55%, (ii) survival by 33%, and (iii) 32% larger testes volumes. Unexpectedly, in the acclimation assay, warm-adapted males' post-heatwave survival and reproduction were best if they experienced cool developmental acclimation beforehand, suggesting a cost to adapting to 38 °C. These results help progress knowledge of the potential for survival and reproduction to adapt to climate change; trait specific adaptation to divergent thermal regimes can occur over relatively few generations, but this capacity depended on the interaction of evolutionary and thermal acclimatory processes.

Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity

For two decades, DNA barcoding and, more recently, DNA metabarcoding have been used for molecular species identification and estimating biodiversity. Despite their growing use, few studies have systematically evaluated these methods. This study aims to evaluate the efficacy of barcoding methods in identifying species and estimating biodiversity, by assessing their consistency with traditional morphological identification and evaluating how assignment consistency is influenced by taxonomic group, sequence similarity thresholds and geographic distance. We first analysed 951 insect specimens across three taxonomic groups: butterflies, bumblebees and parasitic wasps, using both morphological taxonomy and single-specimen COI DNA barcoding. An additional 25,047 butterfly specimens were identified by COI DNA metabarcoding. Finally, we performed a systematic review of 99 studies to assess average consistency between insect species identity assigned via morphology and COI barcoding and to examine the distribution of research effort. Species assignment consistency was influenced by taxonomic group, sequence similarity thresholds and geographic distance. An average assignment consistency of 49% was found across taxonomic groups, with parasitic wasps displaying lower consistency due to taxonomic impediment. The number of missing matches doubled with a 100% sequence similarity threshold and COI intraspecific variation increased with geographic distance. Metabarcoding results aligned well with morphological biodiversity estimates and a strong positive correlation between sequence reads and species abundance was found. The systematic review revealed an 89% average consistency and also indicated taxonomic and geographic biases in research effort. Together, our findings demonstrate that while problems persist, barcoding approaches offer robust alternatives to traditional taxonomy for biodiversity assessment.

Barcode 100K Specimens: In a Single Nanopore Run

It is a global priority to better manage the biosphere, but action must be informed by comprehensive data on the abundance and distribution of species. The acquisition of such information is currently constrained by high costs. DNA barcoding can speed the registration of unknown animal species, the most diverse kingdom of eukaryotes, as the BIN system automates their recognition. However, inexpensive sequencing protocols are critical as the census of all animal species is likely to require the analysis of a billion or more specimens. Barcoding involves DNA extraction followed by PCR and sequencing with the last step dominating costs until 2017. By enabling the sequencing of highly multiplexed samples, the Sequel platforms from Pacific BioSciences slashed costs by 90%, but these instruments are only deployed in core facilities because of their expense. Sequencers from Oxford Nanopore Technologies provide an escape from high capital and service costs, but their low sequence fidelity has, until recently, constrained adoption. However, the improved performance of its latest flow cells (R10.4.1) erases this barrier. This study demonstrates that a MinION flow cell can characterise an amplicon pool derived from 100,000 specimens while a Flongle flow cell can process one derived from several thousand. At $0.01 per specimen, DNA sequencing is now the least expensive step in the barcode workflow.

Discovery of a new gall-inducing species, Aciurinaluminaria (Insecta, Diptera, Tephritidae) via multi-trait integrative taxonomy

Integrative taxonomic practices that combine multiple lines of evidence for species delimitation greatly improve our understanding of intra- and inter-species variation and biodiversity. However, extended phenotypes remain underutilized despite their potential as a species-specific set of extracorporeal morphological and life history traits. Primarily relying on variations in wing patterns has caused taxonomic confusion in the genus Aciurina, which are gall-inducing flies on Asteraceae plants in western North America. However, species display distinct gall morphologies that can be crucial for species identification. Here we investigate a unique gall morphotype in New Mexico and Colorado that was previously described as a variant of that induced by Aciurinabigeloviae (Cockerell, 1890). Our analysis has discovered several consistent features that distinguish it from galls of A.bigeloviae. A comprehensive description of Aciurinaluminaria Baine, sp. nov. and its gall is provided through integrative taxonomic study of gall morphology, host plant ecology, wing morphometrics, and reduced-representation genome sequencing.

A reproducible workflow for assembling the mitochondrial genome of Acheta domesticus (Orthoptera: Gryllidae)

In this study, we report the assembly and annotation of the mitochondrial genome (mitogenome) of Acheta domesticus from breeding facility, a species commonly known as the house cricket. This species is considered to be an important edible cricket. The mitogenome was assembled using a reproducible protocol implemented on the Galaxy Europe Server, which involved uploading paired-end fastq reads for bioinformatic analysis. The resulting mitogenome is 15,784 base pairs in length and has a GC content of 29.05%. The nucleotide composition of this mitogenome is similar to that of other insect mitogenomes, with A, T, C, and G nucleotides comprising 39.2%, 31.7%, 19.6%, and 9.5% of the mitogenome, respectively. The gene organization of the A. domesticus mitogenome is identical to that of other cricket species. The mitogenome consists of 37 genes, including 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The congruence between PCA and Bayesian evolutionary tree analysis in clustering the divergent A. domesticus sequences highlights these genomes as candidates for further study to elucidate their distinct features and evolutionary history.

Newly Woody Artificial Diet Reveals Antibacterial Activity of Hemolymph in Larvae of Zophobas atratus (Fabricius, 1775) (Coleoptera: Tenebrionidae)

The rearing of saproxylic insects in laboratory conditions is an important task for studying the biology of insects. Through understanding nutritional needs, it is possible to optimize beetle rearing in laboratory conditions. In this study, an artificial fungi-based diet (FD) was developed for the cultivation of the darkling beetle Zophobas atratus (Fabricius, 1775) (Coleoptera: Tenebrionidae) in laboratory conditions as a model object for studying the biology of saproxylophagous beetles. To assess the influence of the diet, a number of physiological parameters were measured, including development time, body size, and weight of all stages of the beetle's life cycle, as well as its immune status. The immune status of Z. atratus was assessed on the basis of larval hemolymph antibacterial activity against six different bacterial strains assessed using disk-diffusion and photometric tests. Our findings show that the FD reduces development time and boosts the immune status as compared to beetles reared on a standard diet (SD). Samples from FD-reared larvae had pronounced antibacterial activity as compared to samples from SD-reared larvae. This work is of fundamental importance for understanding the correlations between nutrition and development of saproxylic Coleoptera and is the first report on immune status regulation in this group of insects.

Microbial Symbiont-Based Detoxification of Different Phytotoxins and Synthetic Toxic Chemicals in Insect Pests and Pollinators

Insects are the most diverse form of life, and as such, they interact closely with humans, impacting our health, economy, and agriculture. Beneficial insect species contribute to pollination, biological control of pests, decomposition, and nutrient cycling. Pest species can cause damage to agricultural crops and vector diseases to humans and livestock. Insects are often exposed to toxic xenobiotics in the environment, both naturally occurring toxins like plant secondary metabolites and synthetic chemicals like herbicides, fungicides, and insecticides. Because of this, insects have evolved several mechanisms of resistance to toxic xenobiotics, including sequestration, behavioral avoidance, and enzymatic degradation, and in many cases had developed symbiotic relationships with microbes that can aid in this detoxification. As research progresses, the important roles of these microbes in insect health and function have become more apparent. Bacterial symbionts that degrade plant phytotoxins allow host insects to feed on otherwise chemically defended plants. They can also confer pesticide resistance to their hosts, especially in frequently treated agricultural fields. It is important to study these interactions between insects and the toxic chemicals they are exposed to in order to further the understanding of pest insect resistance and to mitigate the negative effect of pesticides on nontarget insect species like Hymenopteran pollinators.

Odd-Paired is Involved in Morphological Divergence of Snail-Feeding Beetles

Body shape and size diversity and their evolutionary rates correlate with species richness at the macroevolutionary scale. However, the molecular genetic mechanisms underlying the morphological diversification across related species are poorly understood. In beetles, which account for one-fourth of the known species, adaptation to different trophic niches through morphological diversification appears to have contributed to species radiation. Here, we explored the key genes for the morphological divergence of the slender to stout body shape related to divergent feeding methods on large to small snails within the genus Carabus. We show that the zinc-finger transcription factor encoded by odd-paired (opa) controls morphological variation in the snail-feeding ground beetle Carabus blaptoides. Specifically, opa was identified as the gene underlying the slender to stout morphological difference between subspecies through genetic mapping and functional analysis via gene knockdown. Further analyses revealed that changes in opa cis-regulatory sequences likely contributed to the differences in body shape and size between C. blaptoides subspecies. Among opa cis-regulatory sequences, single nucleotide polymorphisms on the transcription factor binding sites may be associated with the morphological differences between C. blaptoides subspecies. opa was highly conserved in a wide range of taxa, especially in beetles. Therefore, opa may play an important role in adaptive morphological divergence in beetles.

Ultrastructural Organization and Metal Elemental Composition of the Mandibles in Two Ladybird Species

The mandibles are among the most important appendages of insects' mouthparts. Their morpho-functional organization is correlated with the variation in dietary preferences. In this study, we investigated the ultrastructural organization and metal composition of the mandibles of two ladybird species with different dietary habits: Harmonia axyridis (an entomophagous species) and Subcoccinella vigintiquatuorpunctata (a phytophagous species). The ultrastructural organization was studied using Scanning and Transmission Electron Microscopy, whereas the metal composition was investigated using Energy-Dispersive X-ray spectroscopy (EDX). Significant differences were observed in the general organization and metal enrichment pattern between the two species. The mandibles of H. axyridis are large and present a molar part with two teeth, with the apical one showing a bifid apex. In contrast, S. vigintiquatuorpunctata exhibited a molar region with several teeth on its apical part. The study revealed significant differences in metal content between the teeth and the prostheca of H. axyridis. Mn was the most abundant element in teeth, whereas Cl was more abundant in the prostheca. In the case of S. vigintiquatuorpunctata, Si was the most abundant element in the prostheca, while Mn was more present in the teeth. A comparison between the two species revealed that both teeth and prostheca showed significant variation in the elemental composition. These findings underscore the role of dietary preferences in shaping the structural and metal composition variations in the mandibles of these two ladybird species.

Experimental heatwaves reduce the effectiveness of ejaculates at occupying female reproductive tracts in a model insect

Globally, heatwaves have become more common with hazardous consequences on biological processes. Research using a model insect (Tribolium castaneum) found that 5-day experimental heatwave conditions damaged several aspects of male reproductive biology, while females remained unaffected. However, females' reproductive fitness may still be impacted, as insects typically store sperm from multiple males in specialized organs for prolonged periods. Consequently, using males which produce sperm with green fluorescent protein (GFP)-tagged sperm nuclei, we visualized in vivo whether thermal stress affects the ejaculate occupancy across female storage sites under two scenarios; (i) increasing time since insemination and (ii) in the presence of defending competitor sperm. We reconfirmed that sperm from heatwave-exposed males sired fewer offspring with previously mated females and provided new scenarios for in vivo distributions of heat-stress-exposed males' sperm. Sperm from heatwave-exposed males occupied a smaller area and were at lower densities across the females' storage sites. Generally, sperm occupancy decreased with time since insemination, and sperm from the first male to mate dominated the long-term storage site. Reassuringly, although heated males' ejaculate was less successful in occupying female tracts, they were not lost from female storage at a faster rate and were no worse than control males in their offensive ability to enter storage sites occupied by competitor sperm. Future work should consider the potential site-specificity of factors influencing sperm storage where amenable.

Structural basis of ligand specificity and channel activation in an insect gustatory receptor

Gustatory receptors (GRs) are critical for insect chemosensation and are potential targets for controlling pests and disease vectors, making their structural investigation a vital step toward such applications. We present structures of Bombyx mori Gr9 (BmGr9), a fructose-gated cation channel, in agonist-free and fructose-bound states. BmGr9 forms a tetramer similar to distantly related insect odorant receptors (ORs). Upon fructose binding, BmGr9's channel gate opens through helix S7b movements. In contrast to ORs, BmGr9's ligand-binding pocket, shaped by a kinked helix S4 and a shorter extracellular S3-S4 loop, is larger and solvent accessible in both agonist-free and fructose-bound states. Also, unlike ORs, fructose binding by BmGr9 involves helix S5 and a pocket lined with aromatic and polar residues. Structure-based sequence alignments reveal distinct patterns of ligand-binding pocket residue conservation in GR subfamilies associated with different ligand classes. These data provide insight into the molecular basis of GR ligand specificity and function.

Diverse material properties and morphology of moth proboscises relates to the feeding habits of some macromoth and other lepidopteran lineages

Insects have evolved unique structures that host a diversity of material and mechanical properties, and the mouthparts (proboscis) of butterflies and moths (Lepidoptera) are no exception. Here, we examined proboscis morphology and material properties from several previously unstudied moth lineages to determine if they relate to flower visiting and non-flower visiting feeding habits. Scanning electron microscopy and three-dimensional imaging were used to study proboscis morphology and assess surface roughness patterns on the galeal surface, respectively. Confocal laser scanning microscopy was used to study patterns of cuticular autofluorescence, which was quantified with colour analysis software. We found that moth proboscises display similar autofluorescent signals and morphological patterns in relation to feeding habits to those previously described for flower and non-flower visiting butterflies. The distal region of proboscises of non-flower visitors is brush-like for augmented capillarity and exhibited blue autofluorescence, indicating the possible presence of resilin and increased flexibility. Flower visitors have smoother proboscises and show red autofluorescence, an indicator of high sclerotization, which is adaptive for floral tube entry. We propose the lepidopteran proboscis as a model structure for understanding how insects have evolved a suite of morphological and material adaptations to overcome the challenges of acquiring fluids from diverse sources.

Could insects be an alternative food source? A comprehensive review

According to the United Nations, more than 800 million people are exposed to starvation. It is predicted that the world population will face much more serious starvation for reasons such as global warming, diseases, economic problems, rapid urbanization, and destruction of agricultural areas and water resources. Thus, there are significant hesitations about the sustainability of food resources, and the search for alternative food sources has increased. One of the leading alternative food sources is insects. Although the use of edible insects has been accepted in some areas of the world, entomophagy is not preferred in some countries due to sociocultural conditions, health concerns, neophobia, and entomophobia. Many people do not accept the direct consumption of raw insects, but insects can be transformed into more preferred forms by using different cooking techniques. Some ground edible insects are satisfactory in terms of nutritional value and have a reasonable level of acceptability when added to products such as bread, tortilla, and pasta in varying percentages. The world market value of edible insects was estimated to be US$3.2 million in 2021 and US$17.6 billion in 2032. In this review, the current and future situation of insects as an alternative food source is comprehensively discussed.

How many species of algae are there? A reprise. Four kingdoms, 14 phyla, 63 classes and still growing

To date (1 November 2023), the online database AlgaeBase has documented 50,589 species of living algae and 10,556 fossil species here referred to four kingdoms (Eubacteria, Chromista, Plantae, and Protozoa), 14 phyla, and 63 classes. The algae are the third most speciose grouping of plant-like organisms after the flowering plants (≈382,000 species) and fungi (≈170,000 species, including lichens) but are the least well defined of all the botanical groupings. Priority is given to phyla and class names that are familiar to phycologists and that are nomenclaturally valid. The most species-rich phylum is the Heterokontophyta to which 18 classes are referred with 21,052 living species and which is dominated by the diatoms in three classes with 18,673 species (16,427 living; 2239 fossil). The next most species-rich phyla are the red algae (7276 living), the green algae (6851 living), the blue-green algae (Cyanobacteria, 5723 living), the charophytes (4950 living, including the Charophyceae, 511 species living, and the Zygnematophyceae, 4335 living species), Dinoflagellata (2956 living, including the Dinophyceae, 2828 extant), and haptophytes (Haptophyta 1722 species, 517 living).

Understanding the ant's unique biting system can improve surgical needle holders

Mechanical grasping and holding devices depend upon a firm and controlled grip. The possibility to improve this gripping performance is severely limited by the need for miniaturization in many applications, such as robotics, microassembly, or surgery. In this paper, we show how this gripping can be improved in one application (the endoscopic needle holder) by understanding and imitating the design principles that evolution has selected to make the mandibles of an ant a powerful natural gripping device. State-of-the-art kinematic, morphological, and engineering approaches show that the ant, in contrast to other insects, has considerable movement within the articulation and the jaw´s rotational axis. We derived three major evolutionary design principles from the ant's biting apparatus: 1) a mobile joint axis, 2) a tilted orientation of the mandibular axis, and 3) force transmission of the adductor muscle to the tip of the mandible. Application of these three principles to a commercially available endoscopic needle holder resulted in calculated force amplification up to 296% and an experimentally measured one up to 433%. This reduced the amount of translations and rotations of the needle, compared to the needle's original design, while retaining its size or outer shape. This study serves as just one example showing how bioengineers might find elegant solutions to their design problems by closely observing the natural world.

The polyketide to fatty acid transition in the evolution of animal lipid metabolism

Animals synthesize simple lipids using a distinct fatty acid synthase (FAS) related to the type I polyketide synthase (PKS) enzymes that produce complex specialized metabolites. The evolutionary origin of the animal FAS and its relationship to the diversity of PKSs remain unclear despite the critical role of lipid synthesis in cellular metabolism. Recently, an animal FAS-like PKS (AFPK) was identified in sacoglossan molluscs. Here, we explore the phylogenetic distribution of AFPKs and other PKS and FAS enzymes across the tree of life. We found AFPKs widely distributed in arthropods and molluscs (>6300 newly described AFPK sequences). The AFPKs form a clade with the animal FAS, providing an evolutionary link bridging the type I PKSs and the animal FAS. We found molluscan AFPK diversification correlated with shell loss, suggesting AFPKs provide a chemical defense. Arthropods have few or no PKSs, but our results indicate AFPKs contributed to their ecological and evolutionary success by facilitating branched hydrocarbon and pheromone biosynthesis. Although animal metabolism is well studied, surprising new metabolic enzyme classes such as AFPKs await discovery.

How many species will Earth lose to climate change?

Climate change may be an important threat to global biodiversity, potentially leading to the extinction of numerous species. But how many? There have been various attempts to answer this question, sometimes yielding strikingly different estimates. Here, we review these estimates, assess their disagreements and methodology, and explore how we might reach better estimates. Large-scale studies have estimated the extinction of ~1% of sampled species up to ~70%, even when using the same approach (species distribution models; SDMs). Nevertheless, worst-case estimates often converge near 20%-30% species loss, and many differences shrink when using similar assumptions. We perform a new review of recent SDM studies, which show ~17% loss of species to climate change under worst-case scenarios. However, this review shows that many SDM studies are biased by excluding the most vulnerable species (those known from few localities), which may lead to underestimating global species loss. Conversely, our analyses of recent climate change responses show that a fundamental assumption of SDM studies, that species' climatic niches do not change over time, may be frequently violated. For example, we find mean rates of positive thermal niche change across species of ~0.02°C/year. Yet, these rates may still be slower than projected climate change by ~3-4 fold. Finally, we explore how global extinction levels can be estimated by combining group-specific estimates of species loss with recent group-specific projections of global species richness (including cryptic insect species). These preliminary estimates tentatively forecast climate-related extinction of 14%-32% of macroscopic species in the next ~50 years, potentially including 3-6 million (or more) animal and plant species, even under intermediate climate change scenarios.

Structure of an insect gustatory receptor

Gustatory Receptors (GRs) are critical for insect chemosensation and are potential targets for controlling pests and disease vectors. However, GR structures have not been experimentally determined. We present structures of Bombyx mori Gr9 (BmGr9), a fructose-gated cation channel, in agonist-free and fructose-bound states. BmGr9 forms a tetramer similar to distantly related insect Olfactory Receptors (ORs). Upon fructose binding, BmGr9's ion channel gate opens through helix S7b movements. In contrast to ORs, BmGR9's ligand-binding pocket, shaped by a kinked helix S4 and a shorter extracellular S3-S4 loop, is larger and solvent accessible in both agonist-free and fructose-bound states. Also unlike ORs, fructose binding by BmGr9 involves helix S5 and a binding pocket lined with aromatic and polar residues. Structure-based sequence alignments reveal distinct patterns of ligand-binding pocket residue conservation in GR subfamilies associated with distinct ligand classes. These data provide insight into the molecular basis of GR ligand specificity and function.

Genetic architecture of dispersal behaviour in the post-harvest pest and model organism Tribolium castaneum

Dispersal behaviour is an important aspect of the life-history of animals. However, the genetic architecture of dispersal-related traits is often obscure or unknown, even in well studied species. Tribolium castaneum is a globally significant post-harvest pest and established model organism, yet studies of its dispersal have shown ambiguous results and the genetic basis of this behaviour remains unresolved. We combine experimental evolution and agent-based modelling to investigate the number of loci underlying dispersal in T. castaneum, and whether the trait is sex-linked. Our findings demonstrate rapid evolution of dispersal behaviour under selection. We find no evidence of sex-biases in the dispersal behaviour of the offspring of crosses, supporting an autosomal genetic basis of the trait. Moreover, simulated data approximates experimental data under simulated scenarios where the dispersal trait is controlled by one or few loci, but not many loci. Levels of dispersal in experimentally inbred lines, compared with simulations, indicate that a single locus model is not well supported. Taken together, these lines of evidence support an oligogenic architecture underlying dispersal in Tribolium castaneum. These results have implications for applied pest management and for our understanding of the evolution of dispersal in the coleoptera, the world's most species-rich order.

Enumerating soil biodiversity

Soil is an immense habitat for diverse organisms across the tree of life, but just how many organisms live in soil is surprisingly unknown. Previous efforts to enumerate soil biodiversity consider only certain types of organisms (e.g., animals) or report values for diverse groups without partitioning species that live in soil versus other habitats. Here, we reviewed the biodiversity literature to show that soil is likely home to 59 ± 15% of the species on Earth. We therefore estimate an approximately two times greater soil biodiversity than previous estimates, and we include representatives from the simplest (microbial) to most complex (mammals) organisms. Enchytraeidae have the greatest percentage of species in soil (98.6%), followed by fungi (90%), Plantae (85.5%), and Isoptera (84.2%). Our results demonstrate that soil is the most biodiverse singular habitat. By using this estimate of soil biodiversity, we can more accurately and quantitatively advocate for soil organismal conservation and restoration as a central goal of the Anthropocene.

Clinical description and treatment outcomes of Paederus dermatitis in Phuentsholing, Bhutan in 2021: A cross-sectional study

An increasing number of beetle population and outbreaks of irritant contact dermatitis are reported from newer geographic locations. Bhutan is one such country that witnessed an outbreak of Paederus dermatitis (PD) in Phuentsholing sub-district in 2021. This study describes the clinical symptoms, skin lesions and treatment outcomes of PD in Bhutan. This was a descriptive cross-sectional study of an outbreak of Paederus-related contact dermatitis in Phuentsholing, Bhutan. Clinical symptoms, skin lesions, duration of illness, recovery time and response to treatment were recorded. Of the 81 patients with PD, the males constituted 54% (44) and the mean age was 22 years (range: 1-51 years). The commonly affected groups were those aged 11-20 years (40.7%) and school or college students (50.6%). The common symptoms were pain, itching, redness, tenderness and blister formation. The lesions were erythematovesicular (70%), linear (54.3%) and kissing lesions (28.4%). All patients received some form of topical or oral steroid therapy and recovery was 100%. The mean duration from the onset till the recovery of the skin rash was 13 days (SD ± 8.3 days). PD outbreak is a self-limiting form of contact dermatitis. This is the first report of PD in the sub-Himalayan region and may be linked to climate change. There is a need for active surveillance and monitoring of such emerging weather/climate-related agents for appropriate health system response in disease prevention and treatment.

FAVIS: Fast and versatile protocol for non-destructive metabarcoding of bulk insect samples

Insects are diverse and sustain essential ecosystem functions, yet remain understudied. Recent reports about declines in insect abundance and diversity have highlighted a pressing need for comprehensive large-scale monitoring. Metabarcoding (high-throughput bulk sequencing of marker gene amplicons) offers a cost-effective and relatively fast method for characterizing insect community samples. However, the methodology applied varies greatly among studies, thus complicating the design of large-scale and repeatable monitoring schemes. Here we describe a non-destructive metabarcoding protocol that is optimized for high-throughput processing of Malaise trap samples and other bulk insect samples. The protocol details the process from obtaining bulk samples up to submitting libraries for sequencing. It is divided into four sections: 1) Laboratory workspace preparation; 2) Sample processing-decanting ethanol, measuring the wet-weight biomass and the concentration of the preservative ethanol, performing non-destructive lysis and preserving the insect material for future work; 3) DNA extraction and purification; and 4) Library preparation and sequencing. The protocol relies on readily available reagents and materials. For steps that require expensive infrastructure, such as the DNA purification robots, we suggest alternative low-cost solutions. The use of this protocol yields a comprehensive assessment of the number of species present in a given sample, their relative read abundances and the overall insect biomass. To date, we have successfully applied the protocol to more than 7000 Malaise trap samples obtained from Sweden and Madagascar. We demonstrate the data yield from the protocol using a small subset of these samples.

Changes in Coleopteran assemblages over a successional chronosequence in a Mexican tropical dry forest

Coleopterans are the most diverse animal group on Earth and constitute good indicators of environmental change. However, little information is available about Coleopteran communities' responses to disturbance and land-use change. Tropical dry forests have undergone especially extensive anthropogenic impacts in the past decades. This has led to mosaic landscapes consisting of areas of primary forest surrounded by pastures, agricultural fields and secondary forests, which negatively impacts many taxonomic groups. However, such impacts have not been assessed for most arthropod groups. In this work, we compared the abundance, richness and diversity of Coleopteran morphospecies in four different successional stages in a tropical dry forest in western Mexico, to answer the question: How do Coleopteran assemblages associate with vegetation change over the course of forest succession? In addition, we assessed the family composition and trophic guilds for the four successional stages. We found 971 Coleopterans belonging to 107 morphospecies distributed in 28 families. Coleopteran abundance and richness were greatest for pastures than for latter successional stages, and the most abundant family was Chrysomelidae, with 29% of the individuals. Herbivores were the most abundant guild, accounting for 57% of the individuals, followed by predators (22%) and saprophages (21%) beetles. Given the high diversity and richness found throughout the successional chronosequence of the studied tropical dry forest, in order to have the maximum number of species associated with tropical dry forests, large tracts of forest should be preserved so that successional dynamics are able to occur naturally.

Convergence of dominance and neglect in flying insect diversity

Most of arthropod biodiversity is unknown to science. Consequently, it has been unclear whether insect communities around the world are dominated by the same or different taxa. This question can be answered through standardized sampling of biodiversity followed by estimation of species diversity and community composition with DNA barcodes. Here this approach is applied to flying insects sampled by 39 Malaise traps placed in five biogeographic regions, eight countries and numerous habitats (>225,000 specimens belonging to >25,000 species in 458 families). We find that 20 insect families (10 belonging to Diptera) account for >50% of local species diversity regardless of clade age, continent, climatic region and habitat type. Consistent differences in family-level dominance explain two-thirds of variation in community composition despite massive levels of species turnover, with most species (>97%) in the top 20 families encountered at a single site only. Alarmingly, the same families that dominate insect diversity are 'dark taxa' in that they suffer from extreme taxonomic neglect, with little signs of increasing activities in recent years. Taxonomic neglect tends to increase with diversity and decrease with body size. Identifying and tackling the diversity of 'dark taxa' with scalable techniques emerge as urgent priorities in biodiversity science.

Whole genome assemblies of Zophobas morio and Tenebrio molitor

Zophobas morio (=Zophobas atratus) and Tenebrio molitor are darkling beetles with industrial importance due to their use as feeder insects and their apparent ability to biodegrade plastics. High quality genome assemblies were recently reported for both species. Here, we report additional independent Z. morio and T. molitor genome assemblies generated from Nanopore and Illumina data. Following scaffolding against the published genomes, haploid assemblies of 462 Mb (scaffold N90 of 16.8 Mb) and 258 Mb (scaffold N90 of 5.9 Mb) were produced for Z. morio and T. molitor, respectively. Gene prediction led to the prediction of 28,544 and 19,830 genes for Z. morio and T. molitor, respectively. Benchmarking Universal Single Copy Orthologs (BUSCO) analyses suggested that both assemblies have a high level of completeness; 91.5 and 89.0% of the BUSCO endopterygota marker genes were complete in the Z. morio assembly and proteome, respectively, while 99.1 and 92.8% were complete in the T. molitor assembly and proteome, respectively. Phylogenomic analyses of four genera from the family Tenebrionidae yielded phylogenies consistent with those previously constructed based on mitochondrial genomes. Synteny analyses revealed large stretches of macrosynteny across the family Tenebrionidae, as well as numerous within-chromosome rearrangements. Finally, orthogroup analysis identified ∼28,000 gene families across the family Tenebrionidae, of which 8,185 were identified in all five of the analyzed species, and 10,837 were conserved between Z. morio and T. molitor. We expect that the availability of multiple whole genome sequences for Z. morio and T. molitor will facilitate population genetics studies to identify genetic variation associated with industrially relevant phenotypes.

Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant

Reliable survey of arthropods is a crucial for their conservation, community ecology, and pest control on terrestrial plants. However, efficient and comprehensive surveys are hindered by challenges in collecting arthropods and identifying especially small species. To address this issue, we developed a non-destructive environmental DNA (eDNA) collection method termed "plant flow collection" to apply eDNA metabarcoding to terrestrial arthropods. This involves spraying distilled or tap water, or using rainfall, which eventually flows over the surface of the plant, and is collected in a container that is set at the plant base. DNA is extracted from collected water and a DNA barcode region of cytochrome c oxidase subunit I (COI) gene is amplified and sequenced using a high-throughput Illumina Miseq platform. We identified more than 64 taxonomic groups of arthropods at the family level, of which 7 were visually observed or artificially introduced species, whereas the other 57 groups of arthropods, including 22 species, were not observed in the visual survey. These results show that the developed method is possible to detect the arthropod eDNA remained on plants although our sample size was small and the sequence size was unevenly distributed among the three water types tested.

Three new species of Neotropical Ceraleurodicus Hempel (Hemiptera: Aleyrodidae) found in the Natural History Museum (London) collection, with notes and a puparial key to species

In this study, three new species of whitefly in the neotropical genus Ceraleurodicus Hempel are described and illustrated based on specimens discovered in the aleyrodid collection of the Natural History Museum, London (NHMUK): Ceraleurodicus boteh Canty sp. nov., Ceraleurodicus brianeno Canty sp. nov., and Ceraleurodicus wire Canty sp. nov. Also included is a key to puparia of the ten known species in the genus, and brief descriptions and illustrations of the known puparia and adults within the genus.

Structural characterization, derivatization and antibacterial activity of secondary metabolites produced by termite-associated Streptomyces showdoensis BYF17

BACKGROUND

Insect-associated Streptomyces is a valuable resource for development of compounds with antibacterial potential. However, relatively little is known of the secondary metabolites produced by termite-associated Streptomyces.

RESULTS

Here, seven compounds including o-acetaminophenol (1), phenazine-1,6-dicarboxylic acid (2), phenylacetic acid (3), phenazinolin D (4), izumiphenazine A (5), izumiphenazine B (6) and phenazinolin E (7) were obtained from the fermentation broth of a termite-associated Streptomyces showdoensis BYF17, which was isolated from the body surfaces of Odontotermes formosanus. Two additional novel derivative compounds (6a and 6b) were synthesized via acetylation and methylation, respectively. The structures of these compounds were elucidated by spectroscopic analyses. The antibacterial bioassay showed that compound 6a displayed strong inhibitory effects against Pseudomonas syringae pv. actinidiae (Psa), with a zone of inhibition (ZOI) diameter of 20.6 mm, which was comparable to that of positive gentamicin sulfate with a ZOI value of 25.6 mm. Furthermore, the Day 5 curative activities of both compounds 6 and 6a against kiwifruit bacterial canker were 71.5%, which was higher than those of referred oxine-copper (55.0%) and ethylicin (46.8%) at a concentration of 200 μg mL^-1 . In addition, the mechanism analysis based on scanning electron microscopic observation revealed that both compounds 6 and 6a destroyed the integrity of the Psa cell membrane.

CONCLUSION

The results of biological tests showed that these bioactive compounds exhibit potent antimicrobial activities, which have the potential to be developed into new antibacterial agents. © 2023 Society of Chemical Industry.

Local stochastics and ecoclimatic situation shape phytophagous chafer assemblage composition

Very little is known about factors determining the assemblage structure of megadiverse polyphagous-herbivore scarab chafers in the tropics (Coleoptera: Scarabaeidae). Here, we examined the composition of Sri Lankan chafer assemblages and investigated whether it is influenced more by the general ecoclimatic situation, macrohabitat, or indetermined stochastic biotic and abiotic factors of each locality. We also explored the influence of the latter on separate lineages and general body size. Based on dedicated field surveys conducted during the dry and wet seasons, we examined 4847 chafer individuals of 105 species sampled using multiple UV-light traps in 11 localities covering different forest types and altitudinal zones. Assemblages were assessed for compositional similarity, species diversity, and abundance within four major eco-spatial partitions: forest types, elevational zones, localities, and macrohabitats. Our results revealed that assemblages were shaped mainly by locality stochastics (i.e., multi-factor ensemble of all biotic and abiotic environmental conditions at local scale), and to a minor extent by ecoclimatic conditions. Macrohabitat had little effect on the assemblage composition. This was true for the entire chafer assemblage as well as for all single lineages or different body size classes. However, in medium and large species the contrasts between localities were less pronounced, which was not the case for individual lineages of the assemblage. Contrasts of assemblage similarity between localities were much more evident than those for forest types and elevation zones. Significant correlation between species composition and geographic distance was found only for the assemblage of small-bodied specimens. Seasonal change (dry-wet) in species composition was minor and only measurable in a few localities. The strong turnover between examined localities corroborates with the high degree of endemism in many phytophagous chafers, particularly in Sericini. Connected with their hypothetic poor habitat specificity and polyphagy, this might also explain why so many chafer crop pests in the Asian tropics are endemics.

DNA Barcoding of Lepidoptera Species from the Maltese Islands: New and Additional Records, with an Insight into Endemic Diversity

This work presents the first outcomes resulting from a DNA barcode reference library of lepidopteran species from Malta. The library presented here was constructed from the specimens collected between 2015 and 2019 and covers the genetic barcodes of 146 species (ca. 25% of lepidopterous Maltese fauna), including four newly recorded Lepidoptera species from the Maltese islands: Apatema baixerasi, Bostra dipectinialis, Oiketicoides lutea, and Phereoeca praecox. The DNA reference barcode library constructed during this study was analyzed in conjunction with publicly available DNA barcodes and used to assess the ability of the local DNA barcodes to discriminate species. Results showed that each species occupies a different BOLD BIN; therefore, DNA barcoding was able to discriminate between the studied species. Our data led to the formation of 12 new BOLD BINs—that is, OTUs that were identified during this work—while nearly 46% of the barcodes generated during this study were never recorded on conspecifics, further indicating the uniqueness of genetic diversity on these central Mediterranean islands. The outcomes of this study highlight the integrative taxonomic approach, where molecular taxonomy plays an important role for biodiversity investigation in its entirety.

Discovering marine biodiversity in the 21st century

We review the current knowledge of the biodiversity of the ocean as well as the levels of decline and threat for species and habitats. The lack of understanding of the distribution of life in the ocean is identified as a significant barrier to restoring its biodiversity and health. We explore why the science of taxonomy has failed to deliver knowledge of what species are present in the ocean, how they are distributed and how they are responding to global and regional to local anthropogenic pressures. This failure prevents nations from meeting their international commitments to conserve marine biodiversity with the results that investment in taxonomy has declined in many countries. We explore a range of new technologies and approaches for discovery of marine species and their detection and monitoring. These include: imaging methods, molecular approaches, active and passive acoustics, the use of interconnected databases and citizen science. Whilst no one method is suitable for discovering or detecting all groups of organisms many are complementary and have been combined to give a more complete picture of biodiversity in marine ecosystems. We conclude that integrated approaches represent the best way forwards for accelerating species discovery, description and biodiversity assessment. Examples of integrated taxonomic approaches are identified from terrestrial ecosystems. Such integrated taxonomic approaches require the adoption of cybertaxonomy approaches and will be boosted by new autonomous sampling platforms and development of machine-speed exchange of digital information between databases.

Combining OSMAC, metabolomic and genomic methods for the production and annotation of halogenated azaphilones and ilicicolins in termite symbiotic fungi

We gathered a collection of termite mutualistic strains from French Guiana to explore the metabolites of symbiotic microorganisms. Molecular networks reconstructed from a metabolomic analysis using LC-ESI-MS/MS methodology led us to identify two families of chlorinated polyketides, i.e., azaphilones from Penicillium sclerotiorum and ilicicolins from Neonectria discophora. To define the biosynthetic pathways related to these two types of scaffolds, we used a whole genome sequencing approach followed by hybrid assembly from short and long reads. We found two biosynthetic gene clusters, including two FAD-dependent halogenases. To exploit the enzymatic promiscuity of the two identified FAD halogenases, we sought to biosynthesize novel halogenated metabolites. An OSMAC strategy was used and resulted in the production of brominated analogs of ilicicolins and azaphilones as well as iodinated analogs of azaphilones.

Emerging Evidence on Tenebrio molitor Immunity: A Focus on Gene Expression Involved in Microbial Infection for Host-Pathogen Interaction Studies

In recent years, the scientific community's interest in T. molitor as an insect model to investigate immunity and host-pathogen interactions has considerably increased. The reasons for this growing interest could be explained by the peculiar features of this beetle, which offers various advantages compared to other invertebrates models commonly used in laboratory studies. Thus, this review aimed at providing a broad view of the T. molitor immune system in light of the new scientific evidence on the developmental/tissue-specific gene expression studies related to microbial infection. In addition to the well-known cellular component and humoral response process, several studies investigating the factors associated with T. molitor immune response or deepening of those already known have been reported. However, various aspects remain still less understood, namely the possible crosstalk between the immune deficiency protein and Toll pathways and the role exerted by T. molitor apolipoprotein III in the expression of the antimicrobial peptides. Therefore, further research is required for T. molitor to be recommended as an alternative insect model for pathogen-host interaction and immunity studies.

Silver nanoparticles instigate physiological, genotoxicity, and ultrastructural anomalies in midgut tissues of beetles

Silver nanoparticles (AgNPs) have long been materials of great interest in numerous fields; however, there is escalating alarm over their toxicity to public health since exposure to these particles is inevitable. This study sheds light on the deleterious impacts of AgNPs on the midgut tissues of beetles (Blaps polychresta) collected from Egypt as a biological model. The investigations were conducted on the beetles administered with a sublethal dose of AgNPs (0.03 mg/g body weight) after 30 days. Oxidative stress parameters and antioxidant enzyme activities were assessed, which exposed critical disruption in the antioxidant defense system of treated beetles. Remarkably, metallothionein (MT) gene expression was significantly increased, while reduced glutathione (GSH) level was notably decreased in midgut tissues subjected to AgNPs. These findings manifestly imply the presence of overproduction in terms of reactive oxygen species (ROS) inside the cells. Additionally, DNA impairment and apoptosis of midgut cells were appraised employing comet and flow cytometry analyses, respectively. The comet results revealed a significant increase in comet cells for the AgNPs treated beetles compared with the control group. Furthermore, the apoptosis results demonstrated a substantial diminution in viable cells with significant growth in apoptotic cells in midgut cells exposed to AgNPs, manifesting their striking correlation with comet and biochemical findings. Noticeably, the histopathological and ultrastructural inspections revealed substantial aberrations in the midgut tissues in the AgNPs treated group, substantiating the previous results. As far as we know, no research has been found that surveyed how the AgNPs at low doses affect the midgut tissues of beetles. Overall, these findings evince the aberrant influences of AgNPs on living organisms.

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.

Postembryonic development of the tracheal system of beetles in the context of aptery and adaptations towards an arid environment

The tracheal system comprises one of the major adaptations of insects towards a terrestrial lifestyle. Many aspects such as the modifications towards wing reduction or a life in an arid climate are still poorly understood. To address these issues, we performed the first three-dimensional morphometric analyses of the tracheal system of a wingless insect, the desert beetle Gonopus tibialis and compared it with a flying beetle (Tenebrio molitor). Our results clearly show that the reduction of the flight apparatus has severe consequences for the tracheal system. This includes the reduction of the tracheal density, the relative volume of the trachea, the volume of the respective spiracles and the complete loss of individual tracheae. At the same time, the reduction of wings in the desert beetle allows modifications of the tracheal system that would be impossible in an animal with a functional flight apparatus such as the formation of a subelytral cavity as a part of the tracheal system, the strong elongation of the digestive tract including its tracheal system or the respiration through a single spiracle. Finally, we addressed when these modifications of the tracheal system take place during the development of the studied beetles. We can clearly show that they develop during pupation while the larvae of both species are almost identical in their tracheal system and body shape.

A trait-based plant economic framework can help increase the value of reforestation for conservation

While reforestation is gaining momentum to moderate climate change via carbon sequestration, there is also an opportunity to use tree planting to confront declining global biodiversity. Where tree species vary in support of diversity, selecting appropriate species for planting could increase conservation effectiveness. We used a common garden experiment in Borneo using 24 native tree species to examine how variation among tree species in their support of beetle diversity is predicted by plant traits associated with "acquisitive" and "conservative" resource acquisition strategies. We evaluate three hypotheses: (1) beetle communities show fidelity to host identity as indicated by variation in abundance and diversity among tree species, (2) the leaf economic spectrum partially explains this variation as shown by beetle preferences for plant species that are predicted by plant traits, and (3) a small number of selected tree species can capture higher beetle species richness than a random tree species community. We found high variation among tree species in supporting three highly intercorrelated metrics of beetle communities: abundance, richness, and Shannon diversity. Variation in support of beetle communities was predicted by plant traits and varied by plant functional groups; within the dipterocarp family, high beetle diversity was predicted by conservative traits such as high wood density and slow growth, and in non-dipterocarps by the acquisitive traits of high foliar K and rapid growth. Using species accumulation curves and extrapolation to twice the original sample size, we show that 48 tree species were not enough to reach asymptote levels of beetle richness. Nevertheless, species accumulation curves of the six tree species with the highest richness had steeper slopes and supported 33% higher richness than a random community of tree species. Reforestation projects concerned about conservation can benefit by identifying tree species with a disproportional capacity to support biodiversity based on plant traits.

Exploring Large-Scale Patterns of Genetic Variation in the COI Gene among Insecta: Implications for DNA Barcoding and Threshold-Based Species Delimitation Studies

The genetic variation in the COI gene has had a great effect on the final results of species delimitation studies. However, little research has comprehensively investigated the genetic divergence in COI among Insecta. The fast-growing COI data in BOLD provide an opportunity for the comprehensive appraisal of the genetic variation in COI among Insecta. We calculated the K2P distance of 64,414 insect species downloaded from BOLD. The match ratios of the clustering analysis, based on different thresholds, were also compared among 4288 genera (35,068 species). The results indicate that approximately one-quarter of the species of Insecta showed high intraspecific genetic variation (>3%), and a conservative estimate of this proportion ranges from 12.05% to 22.58%. The application of empirical thresholds (e.g., 2% and 3%) in the clustering analysis may result in the overestimation of the species diversity. If the minimum interspecific genetic distance of the congeneric species is greater than or equal to 2%, it is possible to avoid overestimating the species diversity on the basis of the empirical thresholds. In comparison to the fixed thresholds, the “threshOpt” and “localMinima” algorithms are recommended for the provision of a reference threshold for threshold-based species delimitation studies.

Chromosome-level genome of the globe skimmer dragonfly (Pantala flavescens)

BACKGROUND

The globe skimmer dragonfly (Pantala flavescens) is a notable Odonata insect distributed in nature fields and farmlands worldwide, and it is commonly recognized as a natural enemy because it preys on agricultural pests and health pests. As one of the sister groups of winged insects, odonatan species are key to understanding the evolution of insect wings.

FINDINGS

We present a high-quality reference genome of P. flavescens, which is the first chromosome-level genome in the Palaeoptera (Odonata and Ephemeroptera). The assembled genome size was 662 Mb, with a contig N50 of 16.2 Mb. Via Hi-C scaffolding, 648 Mb (97.9%) of contig sequences were clustered, ordered, and assembled into 12 large scaffolds, each corresponding to a natural chromosome. The X chromosome was identified by sequence coverage depth. The repetitive sequences and gene density of the X chromosome are similar to those of autosomal sequences, but the X chromosome shows a much lower degree of heterozygosity. Our analysis shows that the effective population size experienced 3 declining events, which may have been caused by climate change and environmental pollution.

CONCLUSIONS

The genome of P. flavescens provides more information on the biology and evolution of insects and will help for the use of this species in pest control.

Predicting global numbers of teleomorphic ascomycetes

Sexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes? The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.

Soil Invertebrates Generate Microplastics From Polystyrene Foam Debris

To fully understand microplastics' impact on soil ecosystems, one must recognize soil organisms as not just passively enduring their negative effects, but potentially contributing to microplastics' formation, distribution, and dynamics in soil. We investigated the ability of four soil invertebrates, the cricket Acheta domesticus L. (Orthoptera: Gryllidae), the isopod Oniscus asellus L. (Isopoda: Oniscidae), larvae of the beetle Zophobas morio Fabricius (Coleoptera: Tenebrionidae), and the snail Cornu aspersum Müller (Stylommatophora: Helicidae) to fragment macroscopic pieces of weathered or pristine polystyrene (PS) foam. We placed invertebrates into arenas with single PS foam pieces for 24 h, then collected and assessed the microplastic content of each invertebrate's fecal material, its cadaver, and the sand substrate of its arena via hydrogen peroxide digestion, filtration, and fluorescent staining. All taxa excreted PS particles, though snails only to a tiny extent. Beetle larvae produced significantly more microplastics than snails, and crickets and isopods fragmented the weathered PS foam pieces more than the pristine pieces, which they left untouched. A follow-up experiment with pristine PS foam assessed the effect of different treatments mimicking exposure to the elements on fragmentation by isopods. PS foam pieces soaked in a soil suspension were significantly more fragmented than untreated pieces or pieces exposed to UV light alone. These findings indicate that soil invertebrates may represent a source of microplastics to the environment in places polluted with PS foam trash, and that the condition of macroplastic debris likely affects its palatability to these organisms.

Metabarcoding reveals massive species diversity of Diptera in a subtropical ecosystem

Diptera is often considered to be the richest insect group due to its great species diversity and broad ecological versatility. However, data on dipteran diversity from subtropical ecosystems have hitherto been scarce, due to the lack of studies conducted at an appropriate large scale. We investigated the diversity and composition of Diptera communities on Tianmu Mountain, Zhejiang, China, using DNA metabarcoding technology, and evaluated their dynamic responses to the effects of slope aspect, season, and altitudinal zone. A total of 5,092 operational taxonomic units (OTUs) were discovered and tentatively assigned to 72 dipteran families, including 2 family records new for China and 30 family records new for the locality. Cecidomyiidae, Sciaridae, and Phoridae were the predominant families, representing 53.6% of total OTUs, while 52 families include >95% unidentified and presumed undescribed species. We found that the community structure of Diptera was significantly affected by aspect, seasonality (month) and elevation, with richer diversity harbored in north-facing than south-facing slopes, and seasonality a more profound driver of community structure and diversity than elevation. Overall, massive species diversity of Diptera communities was discovered in this subtropical ecosystem of east China. The huge diversity of potentially undescribed species only revealed by metabarcoding now requires more detailed taxonomic study, as a step toward an evolutionary integration that accumulates information on species' geographic ranges, ecological traits, functional roles, and species interactions, and thus places the local communities in the context of the growing knowledge base of global biodiversity and its response to environmental change.

DiversityScanner: Robotic handling of small invertebrates with machine learning methods

Invertebrate biodiversity remains poorly understood although it comprises much of the terrestrial animal biomass, most species and supplies many ecosystem services. The main obstacle is specimen-rich samples obtained with quantitative sampling techniques (e.g., Malaise trapping). Traditional sorting requires manual handling, while molecular techniques based on metabarcoding lose the association between individual specimens and sequences and thus struggle with obtaining precise abundance information. Here we present a sorting robot that prepares specimens from bulk samples for barcoding. It detects, images and measures individual specimens from a sample and then moves them into the wells of a 96-well microplate. We show that the images can be used to train convolutional neural networks (CNNs) that are capable of assigning the specimens to 14 insect taxa (usually families) that are particularly common in Malaise trap samples. The average assignment precision for all taxa is 91.4% (75%-100%). This ability of the robot to identify common taxa then allows for taxon-specific subsampling, because the robot can be instructed to only pick a prespecified number of specimens for abundant taxa. To obtain biomass information, the images are also used to measure specimen length and estimate body volume. We outline how the DiversityScanner can be a key component for tackling and monitoring invertebrate diversity by combining molecular and morphological tools: the images generated by the robot become training images for machine learning once they are labelled with taxonomic information from DNA barcodes. We suggest that a combination of automation, machine learning and DNA barcoding has the potential to tackle invertebrate diversity at an unprecedented scale.

Knowledge, attitudes and control practices regarding venomous arthropods among staff and students in a Nigerian public university campus

BACKGROUND

The objectives of this study were to assess the knowledge, attitudes and control practices among the staff and students of Nnamdi Azikiwe University (NAU), Awka, Anambra State, Nigeria, regarding venomous arthropods.

METHODS

The knowledge, attitudes and control practices regarding venomous arthropods were assessed in 350 participants.

RESULTS

The respondents were aware of the presence of venomous arthropods at NAU and they had seen them on campus, with spiders (40.44%) being the most common and electric ants (1.39%) being the least common. The control practices applied to limit the activities of these arthropods included keeping the environment clean (40.80%), the use of insecticides (37.33%), the use of repellents (8.68%), spraying houses with kerosene (7.81%), spraying of fuel on the arthropods (3.47%), screening of houses (1.39%) and the use of bed nets (0.52%).

CONCLUSIONS

An assessment and determination of knowledge, attitudes and control practices regarding venomous arthropods among the staff and students of NAU is necessary in order to improve the preventive measures to reduce injuries caused by venomous arthropod encounters, which are some of the most underestimated health hazards in tropical regions, including southeastern Nigeria, affecting primarily rural communities. According to the findings of our study, students and staff at NAU are rarely involved in life-threatening incidents as a result of their encounters with venomous arthropods and most apply several globally accepted standard practices for the control of venomous arthropods.

The transposable element-rich genome of the cereal pest Sitophilus oryzae

BACKGROUND

The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions.

RESULTS

We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis.

CONCLUSIONS

Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

Sheltered life beneath elytra: three new species of Eutarsopolipus (Acari, Heterostigmatina, Podapolipidae) parasitizing Australian ground beetles

In this study, we conducted a summer sampling of carabid beetles in eastern Australia to identify their associated parasitic mites. Here, we describe three new species of the genus Eutarsopolipus from under the elytra (forewings) of three native carabid species (Coleoptera: Carabidae): Eutarsopolipus paryavae n. sp. (pterostichi group) from Geoscaptus laevissimus Chaudoir; Eutarsopolipus pulcher n. sp. (leytei group) from Gnathaphanus pulcher (Dejean); and Eutarsopolipus chlaenii n. sp. (myzus group) from Chlaenius flaviguttatus Macleay. We further provide an identification key of the world species of pterostichi and leytei species groups as well as closely related species of the myzus group possessing similar characters including short cheliceral stylets. The significant diversity of Eutarsopolipus recovered here suggests that the current knowledge about Australian podapolipid mites (specially Eutarsopolipus) is still in its infancy and deserves further study.

ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone

BACKGROUND

DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via "innovation through subtraction" and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to < 10 cents, and allows fast turnaround from specimen to sequence by using the portable MinION sequencer.

RESULTS

We describe how tagged amplicons can be obtained and sequenced with the real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells ("R10.3") which suggest that each run can generate barcodes for > 10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (> 99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018.

CONCLUSIONS

We propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle ("Flongle") while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project.

Analysis of endemism of world arthropod distribution data supports biogeographic regions and many established subdivisions

We analyzed 769 242 occurrence records for 115 424 species of terrestrial arthropods, from three biodiversity repositories (Global Biodiversity Information Facility (GBIF), Natural History Museum, London, and "Sistema de Informação Distribuído para Coleções Biológicas" (SpeciesLink)), to test the use of global-scale data points for quantitative assessments of areas of endemism. The data include Insecta (105,941 species), Arachnida (7984 species), Myriapoda (1229) and terrestrial crustaceans (270 Branchiopoda). The species were assigned to 14 543 higher taxonomic groups because such groups often characterize larger areas of endemism. Putative areas of endemism were visualized as sets of cells displaying unique groups of species without the assumption of hierarchical relationships. Yet, the use of 10° grid cells recovered many large areas broadly corresponding to biogeographic Regions (Nearctic, Neotropical, Panamanian, Palaearctic, Afrotropical, Australian, Oceanian and Oriental) albeit with the limits poorly defined. An analysis of 5° grids resulted in 306 sets included in the different biogeographic Realms: Afrotropical, Australian, Madagascan, Nearctic, Neotropical, Oceanian, Oriental, Palaearctic, Saharo-Arabian and Sino-Japanese. The Panamanian Realm comprises 89 partly overlapping sets, crossing the Nearctic and Neotropical boundaries. A total of 7338 species of Insecta were endemic to some areas (Sino-Japanese, Afrotropical, Panamanian, Palaearctic, among others), followed by Arachnida (412 spp) and 105 species in other clades ranked as "classes". Six sets were supported only by genera, except for Panamanian sets that were supported by genera and families. Many of the species in the dataset are included in IUCN red lists, but probably most of those have distributions more restricted than global areas of endemism; only 102 appear as endemic to some area (Neartic, Madagascan, Panamanian, Afrotropical, among others). The results show that data from global databases can be used to identify areas of endemism on a worldwide basis but-owing to their incompleteness-only at a relatively coarse level. At the level of resolution currently allowed by such databases, such global studies are only complementary to studies where areas are determined subjectively by systematists (instead of actual point records), or studies using point records in datasets for specific taxonomic groups curated and compiled by specialists.