eDNA metabarcoding of avocado flowers: ‘Hass’ it got potential to survey arthropods in food production systems?

In the face of global biodiversity declines, surveys of beneficial and antagonistic arthropod diversity as well as the ecological services that they provide are increasingly important in both natural and agro-ecosystems. Conventional survey methods used to monitor these communities often require extensive taxonomic expertise and are time-intensive, potentially limiting their application in industries such as agriculture, where arthropods often play a critical role in productivity (e.g. pollinators, pests and predators). Environmental DNA (eDNA) metabarcoding of a novel substrate, crop flowers, may offer an accurate and high throughput alternative to aid in the detection of these managed and unmanaged taxa. Here, we compared the arthropod communities detected with eDNA metabarcoding of flowers, from an agricultural species (Persea americana—‘Hass’ avocado), with two conventional survey techniques: digital video recording (DVR) devices and pan traps. In total, 80 eDNA flower samples, 96 h of DVRs and 48 pan trap samples were collected. Across the three methods, 49 arthropod families were identified, of which 12 were unique to the eDNA dataset. Environmental DNA metabarcoding from flowers revealed potential arthropod pollinators, as well as plant pests and parasites. Alpha diversity levels did not differ across the three survey methods although taxonomic composition varied significantly, with only 12% of arthropod families found to be common across all three methods. eDNA metabarcoding of flowers has the potential to revolutionize the way arthropod communities are monitored in natural and agro-ecosystems, potentially detecting the response of pollinators and pests to climate change, diseases, habitat loss and other disturbances.     

Additive and interactive effects of plant genotypic diversity on arthropod communities and plant fitness

Recent research suggests that genetic diversity in plant populations can shape the diversity and abundance of consumer communities. We tested this hypothesis in a field experiment by manipulating patches of Evening Primrose ( Oenothera biennis ) to contain one, four or eight plant genotypes. We then surveyed 92 species of naturally colonizing arthropods. Genetically diverse plant patches had 18% more arthropod species, and a greater abundance of omnivorous and predacious arthropods, but not herbivores, compared with monocultures. The effects of genotypic diversity on arthropod communities were due to a combination of interactive and additive effects among genotypes within genetically diverse patches. Greater genetic diversity also led to a selective feedback, as mean genotype fitness was 27% higher in diverse patches than in monocultures. A comparison between our results and the literature reveals that genetic diversity and species diversity can have similar qualitative and quantitative effects on arthropod communities. Our findings also illustrate the benefit of preserving genetic variation to conserve species diversity and interactions within multitrophic communities.     

Plant diversity effects on arthropods and arthropod-dependent ecosystem functions in a biodiversity experiment

Biodiversity-ecosystem function experiments test how species diversity influences fundamental ecosystem processes. Historically, arthropod driven functions, such as herbivory and pest-control, have been thought to be influenced by direct and indirect associations among species. Although a number of studies have evaluated how plant diversity affects arthropod communities and arthropod-mediated ecosystem processes, it remains unclear whether diversity effects on arthropods are sufficiently consistent over time such that observed responses can be adequately predicted by classical hypotheses based on associational effects. By combining existing results from a long-term grassland biodiversity experiment (Jena Experiment) with new analyses, we evaluate the consistency of consumer responses within and across taxonomic, trophic, and trait-based (i.e. vertical stratification) groupings, and we consider which changes in arthropod community composition are associated with changes in consumer-mediated ecosystem functions.Overall, higher plant species richness supported more diverse and complex arthropod communities and this pattern was consistent across multiple years. Vegetation-associated arthropods responded more strongly to changes in plant species richness than ground-dwelling arthropods. Additionally, increases in plant species richness were associated with shifts in the species-abundance distributions for many, but not all taxa. For example, highly specialized consumers showed a decrease in dominance and an increase in the number of rare species with increasing plant species richness. Most ecosystem processes investigated responded to increases in plant species richness in the same way as the trophic group mediating the process, e.g. both herbivory and herbivore diversity increase with increasing plant species richness. In the Jena Experiment and other studies, inconsistencies between predictions based on classic hypotheses of associational effects and observed relationships between plant species richness and arthropod diversity likely reflect the influence of multi-trophic community dynamics and species functional trait distributions. Future research should focus on testing a broader array of mechanisms to unravel the biological processes underlying the biodiversity-ecosystem functioning relationships.     

Diversity and trait composition of moths respond to land-use intensification in grasslands: generalists replace specialists

Grasslands belong to the ecologically most relevant habitats in cultural landscapes, but also provide high economic value when used as meadows or pastures. Land-use intensification in grasslands negatively affects plant diversity as well as arthropod communities that depend on plants as food source and habitat, with important consequences for the provision and resilience of ecosystem functioning. In this study, we sampled grassland moth species and investigated whether species composition, diversity and life-history trait characteristics of moth communities respond to the type and intensity of land use, comparing 26 sites in three different regions of Germany. Consistent across the three regions, we found that pastures grazed by cattle, horses or sheep harbour fundamentally different moth communities than meadows (mown and fertilized grasslands). Overall land-use intensity (LUI)—i.e., grazing intensity, amount of fertilizer applied and mowing frequency taken together—significantly reduced abundance and species richness as well as diversity. Some 27.6% of the species showed significant negative responses to LUI. A shift towards generalist life-history traits was observed: in frequently mown and fertilized meadows, rare specialist species were replaced by ubiquist species, i.e., highly reproductive habitat generalists. These results show the sensitivity of moths, an important group of arthropod herbivores and pollinators, to land use change in grassland ecosystems. The functional homogenization of life-history traits in plants along land-use gradients is mirrored by their herbivore consumers, leaving high-intensity grasslands less diverse and potentially less resilient to environmental disturbances.     

Effects of ungulates on epigeal arthropods in Sierra Nevada National Park (southeast Spain)

This paper examines the effect of ungulates on epigeal arthropod communities in two common plant communities of the high mountains of the Sierra Nevada (southeast Spain). We have compared the abundance, biomass, diversity and specific composition of arthropod communities in grazed and ungrazed plots experimentally excluded from ungulates. In general, we found that arthropods were more abundant and diverse in grazed than in ungrazed plots. However, the effect of ungulates depended on the variable considered (diversity versus abundance versus biomass). Moreover, ungulates also affected species composition. This means that without affecting diversity, ungulates can still have a strong effect on arthropod communities by changing species composition. Also, the relationship between ungulates and arthropods differed depending on the year of study and the sampling period. In conclusion, our study indicates that to extrapolate the results obtained for a group of insects, a habitat or a sampling period is not appropriate for the conservation of arthropod communities.     

A diverse fossil terrestrial arthropod fauna from New Zealand: evidence from the early Miocene Foulden Maar fossil lagerstätte

Fossil evidence for the evolutionary history of terrestrial arthropods in New Zealand is extremely limited; only six pre‐Quaternary insects (Triassic to Eocene) have been recorded previously, none of Miocene age. The Foulden Maar fossil lagerstätte in Otago has now yielded a diverse arthropod assemblage, including members of the Araneae, Plecoptera, Isoptera, Hemiptera, Coleoptera, Hymenoptera, Trichoptera and Diptera. The fauna significantly emends the fossil record for the Southern Hemisphere, provides an unparalleled insight into a 23‐million‐year‐old New Zealand lake/forest palaeoecosystem and allows a first evaluation of arthropod diversity at a time coeval with or shortly after the maximum marine transgression of Zealandia in the late Oligocene. The well‐preserved arthropods chiefly represent ground‐dwelling taxa of forest floor and leaf litter habitats, mostly from sub‐families and genera that are still present in the modern fauna. They provide precisely dated fossil evidence for the antiquity of some of New Zealand's terrestrial arthropods and the first potential time calibrations for phylogenetic studies. The high arthropod diversity at Foulden Maar, together with a subtropical rainforest flora and fossil evidence for complex arthropod–plant interactions, suggests that terrestrial arthropods persisted during the Oligocene marine transgression of Zealandia.     

Plant diversity accurately predicts insect diversity in two tropical landscapes

Plant diversity surely determines arthropod diversity, but only moderate correlations between arthropod and plant species richness had been observed until Basset et al. (Science, 338, 2012 and 1481) finally undertook an unprecedentedly comprehensive sampling of a tropical forest and demonstrated that plant species richness could indeed accurately predict arthropod species richness. We now require a high‐throughput pipeline to operationalize this result so that we can (i) test competing explanations for tropical arthropod megadiversity, (ii) improve estimates of global eukaryotic species diversity, and (iii) use plant and arthropod communities as efficient proxies for each other, thus improving the efficiency of conservation planning and of detecting forest degradation and recovery. We therefore applied metabarcoding to Malaise‐trap samples across two tropical landscapes in China. We demonstrate that plant species richness can accurately predict arthropod (mostly insect) species richness and that plant and insect community compositions are highly correlated, even in landscapes that are large, heterogeneous and anthropogenically modified. Finally, we review how metabarcoding makes feasible highly replicated tests of the major competing explanations for tropical megadiversity.     

Temporal dynamics in non-additive responses of arthropods to host-plant genotypic diversity

Genotypic diversity within host‐plant populations has been linked to the diversity of associated arthropod communities, but the temporal dynamics of this relationship, along with the underlying mechanisms, are not well understood. In this study, we employed a common garden experiment that manipulated the number of genotypes within patches of Solidago altissima, tall goldenrod, to contain 1, 3, 6 or 12 genotypes m^?2 and measured both host‐plant and arthropod responses to genotypic diversity throughout an entire growing season. Despite substantial phenological changes in host plants and in the composition of the arthropod community, we detected consistent positive responses of arthropod diversity to host‐plant genotypic diversity throughout all but the end of the growing season. Arthropod richness and abundance increased with genotypic diversity by up to～65%. Furthermore, arthropod responses were non‐additive for most of the growing season, with up to 52% more species occurring in mixtures than the number predicted by summing the number of arthropods associated with component genotypes in monoculture. Non‐additive arthropod responses were likely driven by concurrent non‐additive increases in host‐plant aboveground biomass. Qualitative differences among host‐plant genotypes were also important early in the season, when specialist herbivores dominated the arthropod community. Neither arthropod diversity nor flower number was associated with genotypic diversity at the end of the growing season, when generalist floral‐associated herbivores dominated. Taken together, these results show that focusing on the temporal dynamics in the quantity and quality of co‐occurring host‐plant genotypes and associated community composition can help uncover the mechanisms that link intraspecific host‐plant diversity to the structure of arthropod communities. Furthermore, consistent non‐additive effects in genotypically diverse plots may limit the predictability of the arthropod community based solely on the genetic make‐up of a host‐plant patch.     

A global synthesis of the effects of diversified farming systems on arthropod diversity within fields and across agricultural landscapes

Agricultural intensification is a leading cause of global biodiversity loss, which can reduce the provisioning of ecosystem services in managed ecosystems. Organic farming and plant diversification are farm management schemes that may mitigate potential ecological harm by increasing species richness and boosting related ecosystem services to agroecosystems. What remains unclear is the extent to which farm management schemes affect biodiversity components other than species richness, and whether impacts differ across spatial scales and landscape contexts. Using a global metadataset, we quantified the effects of organic farming and plant diversification on abundance, local diversity (communities within fields), and regional diversity (communities across fields) of arthropod pollinators, predators, herbivores, and detritivores. Both organic farming and higher in‐field plant diversity enhanced arthropod abundance, particularly for rare taxa. This resulted in increased richness but decreased evenness. While these responses were stronger at local relative to regional scales, richness and abundance increased at both scales, and richness on farms embedded in complex relative to simple landscapes. Overall, both organic farming and in‐field plant diversification exerted the strongest effects on pollinators and predators, suggesting these management schemes can facilitate ecosystem service providers without augmenting herbivore (pest) populations. Our results suggest that organic farming and plant diversification promote diverse arthropod metacommunities that may provide temporal and spatial stability of ecosystem service provisioning. Conserving diverse plant and arthropod communities in farming systems therefore requires sustainable practices that operate both within fields and across landscapes.     

In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses

During the most recent decade, environmental DNA metabarcoding approaches have been both developed and improved to minimize the biological and technical biases in these protocols. However, challenges remain, notably those relating to primer design. In the current study, we comprehensively assessed the performance of ten COI and two 16S primer pairs for eDNA metabarcoding, including novel and previously published primers. We used a combined approach of in silico, in vivo‐mock community (33 arthropod taxa from 16 orders), and guano‐based analyses to identify primer sets that would maximize arthropod detection and taxonomic identification, successfully identify the predator (bat) species, and minimize the time and financial costs of the experiment. We focused on two insectivorous bat species that live together in mixed colonies: the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy's bat (Myotis emarginatus). We found that primer degeneracy is the main factor that influences arthropod detection in silico and mock community analyses, while amplicon length is critical for the detection of arthropods from degraded DNA samples. Our guano‐based results highlight the importance of detecting and identifying both predator and prey, as guano samples can be contaminated by other insectivorous species. Moreover, we demonstrate that amplifying bat DNA does not reduce the primers' capacity to detect arthropods. We therefore recommend the simultaneous identification of predator and prey. Finally, our results suggest that up to one‐third of prey occurrences may be unreliable and are probably not of primary interest in diet studies, which may decrease the relevance of combining several primer sets instead of using a single efficient one. In conclusion, this study provides a pragmatic framework for eDNA primer selection with respect to scientific and methodological constraints.     

Long‐term nutrient addition alters arthropod community composition but does not increase total biomass or abundance

A simple bottom–up hypothesis predicts that plant responses to nutrient addition should determine the response of consumers: more productive and less diverse plant communities, the usual result of long‐term nutrient addition, should support greater consumer abundances and biomass and less consumer diversity. We tested this hypothesis for the response of an aboveground arthropod community to an uncommonly long‐term (24‐year) nutrient addition experiment in moist acidic tundra in arctic Alaska. This experiment altered plant community composition, decreased plant diversity and increased plant production and biomass as a deciduous shrub, Betula nana, became dominant. Consistent with strong effects on the plant community, nutrient addition altered arthropod community composition, primarily through changes to herbivore taxa in the canopy‐dwelling arthropod assemblage and detritivore taxa in the ground assemblage. Surprisingly, however, the loss of more than half of plant species was accompanied by negligible changes to diversity (rarefied richness) of arthropod taxa (which were primarily identified to family). Similarly, although long‐term nutrient addition in this system roughly doubles plant production and biomass, arthropod abundance was either unchanged or decreased by nutrient addition, and total arthropod biomass was unaffected. Our findings differ markedly from the handful of terrestrial studies that have found bottom‐up diversity cascades and productivity responses by consumers to nutrient addition. This is probably because unlike grasslands and salt marshes (where such studies have historically been conducted), this arctic tundra community becomes less palatable, rather than more so, after many years of nutrient addition due to increased dominance of B. nana. Additionally, by displacing insulating mosses and increasing the cover of shrubs that cool and shade the canopy microenvironment, fertilization may displace arthropods keenly attuned to microclimate. These results indicate that terrestrial arthropod assemblages may be more constrained by producer traits (i.e. palatability, structure) than they are by total primary production or producer diversity.     

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.     

The limited spatial scale of dispersal in soil arthropods revealed with whole‐community haplotype‐level metabarcoding

Soil arthropod communities are highly diverse and critical for ecosystem functioning. However, our knowledge of spatial structure and the underlying processes of community assembly are scarce, hampered by limited empirical data on species diversity and turnover. We implement a high‐throughput sequencing approach to generate comparative data for thousands of arthropods at three hierarchical levels: genetic, species and supra‐specific lineages. A joint analysis of the spatial arrangement across these levels can reveal the predominant processes driving the variation in biological assemblages at the local scale. This multihierarchical approach was performed using haplotype‐level COI metabarcoding of entire communities of mites, springtails and beetles from three Iberian mountain regions. Tens of thousands of specimens were extracted from deep and superficial soil layers and produced comparative phylogeographic data for >1,000 codistributed species and nearly 3,000 haplotypes. Local assemblage composition differed greatly between grasslands and forests and, within each habitat, showed strong spatial structure and high endemicity. Distance decay was high at all levels, even at the scale of a few kilometres or less. The local distance decay patterns were self‐similar for the haplotypes and higher hierarchical entities, and this fractal structure was similar in all regions, suggesting that uniform processes of limited dispersal determine local‐scale community assembly. Our results from whole‐community metabarcoding provide insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. If generalized across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod diversity on Earth.     

Plant genotypic diversity and environmental stress interact to negatively affect arthropod community diversity

Many studies have found positive relationships between plant diversity and arthropod communities, but the interactive effects of plant genetic diversity and environmental stress on arthropods are not well documented. In this study, we investigated the consequences of plant genotypic diversity, watering treatment, and its interaction for the ground-dwelling arthropod community in an experimental common garden of quaking aspen (Populus tremuloides Michx.). We found that varying plant genotypic diversity and watering treatment altered multivariate arthropod community composition and structure. Arthropod biodiversity and richness showed a distinct response to the plant diversity × watering treatment interaction, declining sharply in water-limited genotypic mixtures. Abundance of arthropod functional groups did not show any response to diversity or the plant diversity × watering treatment interaction, but varied in their response to watering treatment, with predator and detritivore abundance increasing and parasitoid abundance decreasing in well-watered blocks. Our results conflict with most previous studies, and suggest that environmental stress can substantially change the nature of the plant-arthropod diversity relationship. Additionally, we suggest that the plant-arthropod diversity relationship is dependent on the type of plant and arthropod species sampled, and that the association between tree diversity and ground-dwelling arthropods may be much different than more commonly studied grassland species and herbivorous arthropods.     

An experimental test of the effect of plant functional group diversity on arthropod diversity

Characteristics used to categorize plant species into functional groups for their effects on ecosystem functioning may also be relevant to higher trophic levels. In addition, plant and consumer diversity should be positively related because more diverse plant communities offer a greater variety of resources for the consumers. Thus, the functional group composition and richness of a plant community may affect the composition and diversity of the herbivores and even higher trophic levels associated with that community. We tested this hypothesis by sampling arthropods with a vacuum sampler (34 531 individuals of 494 species) from an experiment in which we manipulated plant functional group richness and composition. Plant manipulations included all combinations of three functional groups (forbs, C₃ graminoids, and C₄ graminoids) removed zero, one, or two at a time from grassland plots at Cedar Creek Natural History Area, MN. Although total arthropod species richness was unrelated to plant functional group richness or composition, the species richness of some arthropod orders was affected by plant functional group composition. Two plant characteristics explained most of the effects of plant functional groups on arthropod species richness. Nutritional quality, a characteristic related to ecosystem functioning, and taxonomic diversity, a characteristic not used to designate plant functional groups, seemed to affect arthropod species richness both directly and indirectly. Thus, plant functional groups designated for their effects on ecosystem processes will only be partially relevant to consumer diversity and abundance.     

Plant Diversity Impacts Decomposition and Herbivory via Changes in Aboveground Arthropods

Loss of plant diversity influences essential ecosystem processes as aboveground productivity, and can have cascading effects on the arthropod communities in adjacent trophic levels. However, few studies have examined how those changes in arthropod communities can have additional impacts on ecosystem processes caused by them (e.g. pollination, bioturbation, predation, decomposition, herbivory). Therefore, including arthropod effects in predictions of the impact of plant diversity loss on such ecosystem processes is an important but little studied piece of information. In a grassland biodiversity experiment, we addressed this gap by assessing aboveground decomposer and herbivore communities and linking their abundance and diversity to rates of decomposition and herbivory. Path analyses showed that increasing plant diversity led to higher abundance and diversity of decomposing arthropods through higher plant biomass. Higher species richness of decomposers, in turn, enhanced decomposition. Similarly, species-rich plant communities hosted a higher abundance and diversity of herbivores through elevated plant biomass and C:N ratio, leading to higher herbivory rates. Integrating trophic interactions into the study of biodiversity effects is required to understand the multiple pathways by which biodiversity affects ecosystem functioning.     

Interactive effects of keystone rodents on the structure of desert grassland arthropod communities

Certain species play particularly large roles in ecosystems, and are often referred to as keystones. However, little is known about the interactive effects of these species where they co-occur. Prairie dogs ( Cynomys spp.) and banner-tailed kangaroo rats Dipodomys spectabilis are commonly considered keystone species of grassland ecosystems, creating a mosaic of unique habitats on the landscape through ecosystem engineering and herbivory. We examined the separate and interactive effects of these species on the structure of grassland arthropod communities. We conducted a cross-site study at two locations in the northern Chihuahuan Desert, and evaluated the impacts of these rodents on ground-dwelling arthropod and grasshopper communities in areas where prairie dogs and kangaroo rats co-occurred compared to areas where each rodent species occurred alone. Our results demonstrate that prairie dogs ( C. gunnisoni and C. ludovicianus ) and banner-tailed kangaroo rats had keystone-level impacts on arthropod communities both separately and interactively. Their burrow systems provided important habitats for multiple trophic and taxonomic groups of arthropods, and increased overall arthropod abundance and species richness. Many arthropods also were attracted to the aboveground habitats around the mounds and across the landscapes where the rodents occurred. Detritivores, predators, ants, grasshoppers, and rare rodent burrow inhabitants were especially associated with prairie dog and kangaroo rat activity. The impacts of prairie dogs and kangaroo rats were unique, and the habitats they created supported different assemblages of arthropods. Where both rodent species co-occurred, there was greater heterogeneity and arthropod diversity on the landscape. Our results suggest that the interaction of multiple keystones, especially those with engineering roles, results in unique and more diverse communities in time and space.     

Diversity cascades in alfalfa fields: from plant quality to agroecosystem diversity

To examine top-down and bottom-up influences on managed terrestrial communities, we manipulated plant resources and arthropod abundance in alfalfa (Medicago sativa L.) fields. We modified arthropod communities using three nonfactorial manipulations: pitfall traps to remove selected arthropods, wooden crates to create habitat heterogeneity, and an arthropod removal treatment using a reversible leaf blower. These manipulations were crossed with fertilizer additions, which were applied to half of the plots. We found strong effects of fertilizer on plant quality and biomass, and these effects cascaded up to increase herbivore abundance and diversity. The predator community also exhibited a consistent positive effect on the maintenance of herbivore species richness and abundance. These top-down changes in arthropods did not cascade down to affect plant biomass; however, plant quality (saponin content) increased with higher herbivore densities. These results corroborate previous studies in alfalfa that show complex indirect effects, such as trophic cascades, can operate in agricultural systems, but the specifics of the interactions depend on the assemblages of arthropods involved.     

Toward accurate species‐level metabarcoding of arthropod communities from the tropical forest canopy

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