Geology Reports⌕ Search

Geology topics

Clayton D. Raines

Publications and source records attributed to Clayton D. Raines.

17 recordsLinked to original sources
USGS2025

Novel adomaviruses associated with blotchy bass syndrome in black basses ( Micropterus spp. )

Black bass ( Micropterus spp. ) are the most important warmwater game fishes in the United States. They have high socioeconomic and recreational value and support an important aquaculture industry. Since 2008, fisheries managers have been reporting the observation of hyperpigmented melanistic lesions (HPMLs) on smallmouth bass ( M. dolomieu ) in different ecoregions of the United States. Similar HPMLs have been observed in largemouth bass ( M. nigricans ) since the 1980’s. Here, we report the association between novel adomaviruses and the hallmark blotchy clinical presentation of hyperpigmented lesions on the skin of smallmouth and largemouth black bass. The two adomaviruses are structurally and phylogenetically similar but share only 68.0% identity at aligned nucleotide sites and each has been found in only one host species to date. The manifestation of this skin disease appears to be seasonal (observed between the fall and spring) in both species, primarily affects adults and is of unknown health consequence. Although the significance of infection to fish health remains unclear, understanding the disease ecology of these viruses can inform biosecurity and the interjurisdictional movement of individuals. Moreover, as hyperpigmentation in other fish species is often idiopathic, our findings reframe perspectives for future investigations into this clinical presentation in other species.

Michigan, Pennsylvania, Texas, Vermont, Virginia↗
USGS2025

Sensitive environmental DNA methods for low-risk surveillance of at-risk bumble bees

Terrestrial environmental DNA (eDNA) techniques have been proposed as a means of sensitive, non-lethal pollinator monitoring. To date, however, no studies have provided evidence that eDNA methods can achieve detection sensitivity on par with traditional pollinator surveys. Using a large-scale dataset of eDNA and corresponding net surveys, we show that eDNA methods enable sensitive, species-level characterisation of whole bumble bee communities, including rare and critically endangered species such as the rusty patched bumble bee (RPBB; Bombus affinis ). All species present in netting surveys were detected within eDNA surveys, apart from two rare species in the socially parasitic subgenus Psithyrus (cuckoo bumble bees). Further, for rare non-parasitic species, eDNA methods exhibited similar sensitivity relative to traditional netting. Compared with flower eDNA samples, sequenced leaf surface eDNA samples resulted in significantly lower rates of Bombus detection, and these detections were likely attributable to high rates of background eDNA on environmental surfaces, perhaps due to airborne eDNA or eDNA movement during rainfall events. Lastly, we found that eDNA-based frequency of detection across replicate surveys was strongly associated with net-based measures of abundance across site visits. We conclude that the COI-based metabarcoding method we present is cost-effective and highly scalable for quantitative characterisation of at-risk bumble bee communities, providing a new approach for improving our understanding of species habitat associations.

Central Appalachian Mountains↗
USGS2025

Hiding in plain sight: Genomic characterization of a novel nackednavirus and evidence of diverse adomaviruses in a hyperpigmented lesion of a largemouth bass (Micropterus salmoides)

Largemouth bass (LMB; Micropterus nigricans ) are popular both as a sportfish and an aquaculture species. At present, six described viruses are associated with LMB, of which two are typically considered in cases of LMB mortality events. Advances in discovery and diagnostic capabilities using next-generation sequencing have augmented surveillance efforts and subsequently led to the discovery of novel cryptogenic viruses. Here, we present evidence of three novel viruses from a single skin sample collected from a hyperpigmented melanistic lesion of an LMB with blotchy bass syndrome associated with MnA-1 co-infection. These viruses represent recently described groups of viruses (adomaviruses and nackednaviruses) that infect fish. Both are markedly understudied and of unknown significance to fish health. This work highlights the diversity of viruses associated with LMB and further advances our understanding of the LMB virome. Application of de novo sequencing approaches presents an opportunity to explore a new frontier of host–pathogen relationships and microbes associated with changing environments.

Virginia↗
USGS2025

Scalable environmental DNA methods reveal strong associations between landscape-scale forest habitat and insect richness

While aquatic environmental DNA (eDNA) methods have reached relative maturity, terrestrial eDNA methods are nascent and have yet to reach widespread use. Field-ready applications require eDNA survey methods where samples are easy to collect by inexperienced practitioners, easy to transport between the field and lab, and easy to process thereafter. Here, we demonstrate methods that satisfy these requirements and show strong potential for characterizing diverse terrestrial eDNA samples collected from flower and leaf surfaces. We used novel methods to collect and process 236 flower eDNA samples and 21 leaf surface eDNA samples, obtaining 2,228 Arthropoda eDNA detections spanning 175 families using amplicon sequencing of two genetic markers. Detected taxa were diverse and included numerous groups of conservation concern, such as bees (Hymenoptera; Anthophila, 32 genera spanning 5 families) and Lepidoptera (209 genera from 21 families). Data reveal strong associations between insect community richness and remotely sensed measures of forest habitat, providing a quantitative perspective of relevance to insect conservation. It is increasingly clear that a variety of organisms readily disperse eDNA throughout the environment, supporting the notion that eDNA will be a powerful tool for characterizing species distributions and monitoring at-risk species. However, we conclude that researchers seeking to characterize fine-scale habitat associations or plant-pollinator interactions using eDNA will need to carefully design studies with appropriate field controls, such as the leaf surface eDNA samples collected here.

BioRxiv↗
USGS2025

Identical sequence types of Yersinia ruckeri associated with lethal disease in wild-caught invasive Blue Catfish and cultured hybrid catfish (Channel Catfish ♀ × Blue Catfish ♂) from disparate aquatic ecosystems

Objective The Blue Catfish Ictalurus furcatus is commonly raised in warmwater aquaculture in the United States to produce Channel Catfish I. punctatus × Blue Catfish hybrids. It is also a prominent aquatic invasive species of concern in the mid-Atlantic region of the United States. Here, Yersina ruckeri was isolated from moribund Blue Catfish and hybrid catfish from disparate regions of the USA. The goal of the research here was to compare these Y. ruckeri strains to each other and other known strains for which adequate sequence data was available. In addition, we sought to determine if the strain from Blue Catfish was pathogenic to Rainbow Trout Oncorhynchus mykiss . Methods Moribund hybrid catfish from culture ponds in Mississippi were processed for diagnostic evaluation in March 2016. In April 2022, a moribund Blue Catfish specimen was collected from a tributary of the Nanticoke River in Maryland. Bacterial isolates were identified and characterized using biochemical tests, antimicrobial sensitivity screening, serotyping, and complete or partial genome sequencing. Disease pathology was described via histology. The isolate from Blue Catfish was used in challenge experiments to determine if it was pathogenic to Rainbow Trout. Multilocus sequencing typing was conducted using the PubMLST database. Results Biochemical testing was consistent with Y. ruckeri . A draft genome of the Y. ruckeri isolate was assembled based on Oxford Nanopore Technology sequencing and identified a single genomic replicon (3,791,418 bp) consistent in size to other Y. ruckeri genomes and a pLT plasmid (60, 933 bp). The challenge study demonstrated no significant virulence of this isolate for Rainbow Trout ( Y. ruckeri ). This isolate was most similar to other strains isolated from ictalurids. Notably, the gyrase B gene from this isolate was identical to that of archived strains isolated from moribund Mississippi hybrid catfish aquaculture during 2016 and these isolates share identical PubMLST sequence type profiles. Similarly, they shared a pLT plasmid that differed by only 6 bp. This plasmid has never been reported from trout isolates and appears to be unique to ictalurids. Conclusions Analyses here provide preliminary genetic evidence that geographically distant (Maryland and Mississippi, USA) isolates of Y. ruckeri from ictalurids are genetically similar to each other and Y. ruckeri (strain SC09) that infects ictalurids in China. This strain is not a biothreat to Rainbow Trout at typical culture temperatures.

Journal of Aquatic Animal Health↗
USGS2025

Identifying organic contaminants at trespass cannabis grows on federal land in California, USA

Despite the legalization of recreational cannabis in California, USA, illegal cannabis cultivation remains pervasive, partly through the establishment of illegal cultivation on public lands (trespass grows). These operations often illegally divert water for irrigation and perform unauthorized applications of chemical fertilizers and pesticides. This work investigates a broad suite of these chemicals, focusing on their persistence in topsoil and presence in water and bed sediment in adjacent streams. Quantitative analyses of pesticides were conducted (183 compounds in water; 176 in topsoil/bed sediment), supplemented by qualitative nontargeted screening at three trespass grows that had no active cultivation for 8 months to 2 years. Targeted multi-residue analysis of topsoil detected the insecticides bifenthrin, cyfluthrin, malathion and imidacloprid (with concentrations up to 38 ng/g dry weight, d.w.), and the fungicides fluopyram, myclobutanil, and triadimefon (concentrations up to 8.1 ng/g d.w.). No pesticides were detected in the companion water or streambed sediment samples from adjacent streams. In addition, no water samples were found to have measurable estrogenic activity. Nontargeted screening uncovered additional pesticides (i.e., spiromesifen, trinexapac) in the topsoil and cannabis-related compounds (i.e., cannabidol, delta9-tetrahydrocannabinol) in both topsoil and streambed sediment suggesting the likelihood of offsite transport of cannabis related compounds. Phthalate plasticizers, rubber-related compounds, pharmaceuticals and personal care product chemicals were detected in topsoil, water, and streambed sediment and may be related to extensive irrigation infrastructure installed at these trespass grows. This work begins to establish a contaminant profile associated with illegal cannabis growing activities, providing a foundation for future research focused on their potential ecological impacts.

California↗
USGS2025

Assessing microplastics, per- and polyfluoroalkyl substances (PFAS), and other contaminants of global concern in wadable agricultural streams

Microplastics, per- and polyfluoroalkyl substances (PFAS), antibiotic resistance genes (ARGs), pharmaceuticals and personal care products (PPCPs), and pesticides may lead to unintended environmental contamination through many pathways in multiple matrices. This statewide, multi-matrix study of contaminants of global concern (CGCs) in agricultural streams across Iowa (United States) is the first to examine multiple CGCs in water, bed sediment, and fish to understand their occurrence in small streams located in regions of intense agriculture activity. Iowa plays a pivotal role in agriculture, with more than 85% of Iowa’s landscape devoted to agriculture making it an ideal location for determining the prevalence of CGCs to provide critical baseline exposure data. Fifteen sites were sampled across a range of predominant land uses (e.g., poultry, swine); all sites had detections of microplastics in all matrices. Concentrations of PFAS varied but were detected in water and sediment; all fish had detections of perfluorooctanesulfonate (PFOS), a type of PFAS. More than 50% of water and bed sediment samples had detections of ARGs. The most frequently detected PPCP was metformin. No sites had a cumulative exposure activity ratio greater than 1.0 for chemical exposures; 13 sites were above the 0.001 precautionary threshold. Toxicity quotients calculated using Aquatic Life Benchmarks were below the 0.1 moderate risk threshold for chemical exposures for all but one site. For fish, all sites exceeded the moderate and high-risk thresholds proposed for microplastic particles for food dilution (both chronic and acute exposures) and all sites exceeded the microplastic moderate threshold proposed for chronic tissue translocation, and two sites exceeded the threshold for acute tissue translocation.

Iowa↗
USGS2025

Land application of biosolid, livestock, and drilling wastes to US farmland: A potential pathway for the redistribution of contaminants in the environment

In the United States (U.S.), waste byproducts generated from the treatment of municipal waste (biosolids), production of livestock (livestock waste), and drilling of oil and gas wells (drilling waste) are commonly applied to agricultural lands. Although this can be a cost-effective reuse/disposal practice, there is limited research on the potential for contaminant exposures and effects on ecosystems, wildlife, and human health from such land applications. In this study, we conducted extensive chemical, microbial, and toxicity analyses of biosolid, livestock, and drilling wastes just prior to land application on agricultural lands at 34 sites across the U.S. Twenty-two analytical methods were used to determine potential contaminant exposures profiles for 452 organic and 114 inorganic chemicals, nine microbial groups, estrogenicity, and cytotoxicity. Analytical results document unique and substantial chemical, microbial, and toxicity profiles for these land-applied wastes. Of the three waste byproducts, biosolids contained the greatest concentrations of household chemicals, pesticides, pharmaceuticals, per-/polyfluoroalkyl substances, calcium, and phosphorus. Livestock waste contained the greatest concentrations of total and leachable dissolved organic carbon, biogenic hormones, mycotoxins, plant estrogens, total inorganic nitrogen, and potassium. Drilling waste contained the greatest concentrations of BTEX compounds (benzene, toluene, ethylbenzene, and xylenes), polycyclic aromatic hydrocarbons, rare-earth elements, barium, strontium, and uranium–thorium series radioisotopes. Biosolid and livestock wastes had greater culturable heterotrophic bacteria, halophilic bacteria, Escherichia coli ( E. coli ), enterococci, and staphylococci concentrations, and greater microbial diversity than drilling waste. Bioassay analyses indicated that exposure to contaminants in livestock wastes and biosolids could result in estrogenic effects, whereas exposure to contaminants in drilling waste could result in cytotoxic effects. Our study documents that current reuse/disposal practices for biosolid, livestock, and drilling wastes on agricultural lands could provide a potential pathway for the redistribution of unique and complex contaminant mixtures into the environment that have bioactive, endocrine disrupting, and carcinogenic characteristics. Results of this study provide a snapshot of chemical compositions and concentrations that can be used to inform the development of best-management practices to help maximize beneficial reuse of these wastes and minimize risk to the environment and human health.

Environmental Science: Processes & Impacts↗
USGS2025

Sensitive environmental DNA methods for low-risk surveillance of at-risk bumble bees

Terrestrial environmental DNA (eDNA) techniques have been proposed as a means of sensitive, non-lethal pollinator monitoring. To date, however, no studies have provided evidence that eDNA methods can achieve detection densities on par with traditional pollinator surveys. Using a large-scale dataset of eDNA and corresponding net surveys, we show that eDNA methods enable sensitive, species-level characterization of whole bumble bee communities, including rare and critically endangered species such as the rusty pathed bumble bee (RPBB; Bombus affinis ). All species present in netting surveys were detected within eDNA surveys, apart from two rare species in the socially parasitic subgenus Psithyrus (cuckoo bumble bees). Further, for rare non-parasitic species, eDNA methods exhibited similar sensitivity relative to traditional netting. Relative to flower eDNA samples, sequenced field negative controls resulted in significantly lower rates of Bombus detection, and these detections were likely attributable to high rates of background eDNA on environmental surfaces. Lastly, we found that eDNA-based frequency of detection across replicate surveys was strongly associated with net-based measures of abundance across site visits. We conclude that the method is cost-effective and highly scalable for semi-quantitative characterization of at-risk bumble bee communities, providing a new approach for improving our understanding of species habitat associations.

BioRxiv↗
USGS2025

Novel adomaviruses associated with blotchy bass syndrome in black basses (Micropterus spp.)

Black bass ( Micropterus spp. ) are the most important warmwater game fishes in the United States. They have high socioeconomic and recreational value and support an important aquaculture industry. Since 2008, fisheries managers have been reporting the observation of hyperpigmented melanistic lesions (HPMLs) on smallmouth bass ( M. dolomieu ) in different ecoregions of the United States. Similar HPMLs have been observed in largemouth bass ( M. nigricans ) since the 1980’s. Here, we report a close association between novel adomaviruses and the hallmark blotchy clinical presentation of hyperpigmented lesions on the skin smallmouth and largemouth black bass and provide evidence that satisfies Rivers’ postulates. The two adomaviruses are structurally and phylogenetically similar but share only 68.0% identity at aligned nucleotide sites and each has been found in only one host species to date. The manifestation of this skin disease appears to be seasonal in both species, primarily affects adults and is of unknown health consequence. Although the significance of infection to fish health remains unclear, understanding the disease ecology of these can inform biosecurity and the interjurisdictional movement of individuals. Moreover, as hyperpigmentation in other fish species is often idiopathic, our findings reframe perspectives for future investigations into this clinical presentation in other species.

BioRxiv↗
USGS2024

Discovery and genomic characterization of a novel hepadnavirus from asymptomatic anadromous alewife (Alosa pseudoharengus)

The alewife ( Alosa pseudoharengus) is an anadromous herring that inhabits waters of northeastern North America. This prey species is a critical forage for piscivorous birds, mammals, and fishes in estuarine and oceanic ecosystems. During a discovery project tailored to identify potentially emerging pathogens of this species, we obtained the full genome of a novel hepadnavirus (ApHBV) from clinically normal alewives collected from the Maurice River, Great Egg Harbor River, and Delaware River in New Jersey, USA during 2015–2018. This previously undescribed hepadnavirus contained a circular DNA genome of 3146 nucleotides. Phylogenetic analysis of the polymerase protein placed this virus in the clade of metahepadnaviruses (family: Hepadnaviridae ; genus: Metahepadnavirus ). There was no evidence of pathology in the internal organs of infected fish and virions were not observed in liver tissues by electron microscopy. We developed a Taqman-based quantitative (qPCR) assay and screened 182 individuals collected between 2015 and 2018 and detected additional qPCR positives (n = 6). An additional complete genome was obtained in 2018 and it has 99.4% genome nucleotide identity to the first virus. Single-nucleotide polymorphisms were observed between the two genomes, including 7/9 and 12/8 synonymous vs nonsynonymous mutations across the polymerase and surface proteins, respectively. While there was no evidence that this virus was associated with disease in this species, alewives are migratory interjurisdictional fishes of management concern. Identification of microbial agents using de novo sequencing and other advanced technologies is a critical aspect of understanding disease ecology for informed population management.

New Jersey↗
USGS2024

Seasonal mortality of Wild Atlantic Menhaden (Brevoortia tyrannus) is caused by a virulent clone of Vibrio (Listonella) anguillarum; Implications for biosecurity along the Atlantic Coastal United States

Atlantic menhaden are a highly migratory marine species in the Eastern United States that suffer from seasonal chronic mortality. Affected fish show neurologic signs referred to as spinning disease, including circling at the surface and erratic corkscrew swimming before death. We investigated three similar menhaden mortality events consistent with spinning disease in coastal New Jersey and New York between 2020 and 2021 to understand the cause. A unique strain of Vibrio (Listonella) anguillarum (serogroup O3) was detected regularly in high loads, particularly in the brains of moribund fish, by both metagenomics and bacterial isolation. The most common histopathological changes in moribund fish were hemorrhagic meningitis, encephalitis, pyknosis, and karyorrhexis of hematopoietic tissues in the kidney and spleen. Whole genome sequencing of isolates from moribund fish representing a wide spatial and temporal range showed that they were nearly identical clones, suggesting it to be a pathogenic strain circulating in the population. Though V. anguillarum is believed to be the main pathogen associated with spinning disease and mortality, Yersinia ruckeri (serotype O1) was isolated from smaller numbers of fish. Considering the highly migratory nature of Atlantic menhaden throughout the eastern United States and their use as bait for other fisheries, these findings identify potential biosecurity challenges that should be considered in Atlantic salmon aquaculture, fisheries, and emerging marine aquaculture in the region.

Transboundary and Emerging Diseases↗
USGS2023

Prospects of pollinator community surveillance using terrestrial environmental DNA metagenetics

Current pollinator survey methods exhibit bias, require highly-trained practitioners, and are difficult to scale to large sample sizes. High-throughput sequencing of terrestrial eDNA could provide a complementary tool for studying pollinator communities, but eDNA methods have not been extensively evaluated. We conducted metagenetic analysis of whole arthropod community eDNA from 20 flower and seven honey bee-collected pollen samples and compared eDNA-derived data with traditional netting-based surveys of the pollinator communities present during sampling. We focused our analysis on Anthophila (bees) and detected eight bee genera belonging to four families across COI, 16S, and 28S markers. Results varied considerably by marker and eDNA substrate. Detected bee genera were plausible for the study system and about 43 percent of total bee genera were detected with both eDNA and net-based surveys, though netting resulted in more detections across a wider diversity of genera. Data from sequenced controls suggest that eDNA identifications were unlikely to have resulted from cross-contamination. Our results demonstrate that bee communities can be documented with eDNA techniques and that the choice of marker and substrate substantially influences detection. Future improvements to our methods are required, but eDNA surveys appear well-suited to characterize diverse pollinator communities and provide novel sampling perspectives within plant-pollinator networks. Future efforts should focus on improving the selection of markers available for pollinator eDNA metagenetics, addressing taxonomic gaps within reference sequence databases and optimizing sampling and eDNA isolation protocols. We anticipate that such improvements are highly feasible and that eDNA will be a useful tool to those who study pollinators and plant-pollinator interactions.

Environmental DNA↗
USGS2023

Evaluating brook trout egg and alevin survival at different temperatures in simulated karst environments with marl sedimentation

Brook trout ( Salvelinus fontinalis ) have been extirpated from many karst-geology streams in West Virginia; however, the causes are not fully understood. Specifically, the impact of calcareous precipitate (marl), which is common in hard-water environments, has not been evaluated as an im- pediment to juvenile survival. Accordingly, two lab-based studies were conducted to determine if brook trout egg and alevin survival is inhibited by marl. In the first study, three aeration treatments were applied to water from a limestone spring source (13–14 C; ~300 mg L–1 hardness), resulting in different pH levels and an increasing degree of marl precipitate. Treatments included raw/untreated (RU; no marl), once-aerated (OA; limited marl), and continuously aerated (CA; significant marl) water. Brook trout eggs obtained from a local hatchery were fertilized and stocked among gravel-filled trays receiving each water type. Mortality occurred faster in CA water where marl coated egg surfaces, but cumulative survival was negligible for all water types. After 53 days, no surviving alevins remained in RU or CA, and 1% survival was observed in OA water. However, extra eggs maintained in a marl-producing system at 8 C without gravel demonstrated >50% survival. A second study was carried out to investigate this discrepancy. Survival was evaluated at three temperatures with and without gravel while producing a thin coating of marl. Increased prevalence of alevin deformities and significantly lower survival were observed at 13.7 C versus 8.1 and 11.2 C, but gravel inclusion did not affect these variables. Potentially harmful effects of marl were observed; however, juvenile brook trout survival was higher during Study 2. This research suggests that brook trout reintroduction efforts in karst-geology streams should be focused on microhabitats with limited marl production and adequate water temperatures for juvenile survival.

Journal of the Southeastern Association of Fish an↗
USGS2023

Effects of hard water precipitates on early life stage brook trout

Brook trout (Salvelinus fontinalis) have been extirpated from many karst-geology streams in West Virginia; however, the causes are not fully understood. Specifically, the impact of calcareous precipitate (marl), which is common in hard-water environments, has not been evaluated as an impediment to juvenile survival. Accordingly, two lab-based studies were conducted to determine if brook trout egg and alevin survival is inhibited by marl. In the first study, three aeration treatments were applied to a limestone spring source (13–14 C; ~300 mg L-1 hardness), resulting in different pH levels and an increasing degree of marl precipitate. Treatments included: raw/untreated (RU; no marl), once-aerated (OA; limited marl), and continuously aerated (CA; significant marl) water. Brook trout eggs obtained from a local hatchery were fertilized and stocked among gravel-filled trays receiving each water type. Mortality occurred faster in CA water where marl coated egg surfaces; however, cumulative survival was negligible for all water types. After 53 days, no surviving alevins remained in RU or CA, and 1% survival was observed in OA water; however, extra eggs maintained in a marl-producing system at 8 C without gravel demonstrated > 50% survival. A second study was carried out to investigate this discrepancy. Survival was evaluated at three temperatures with and without gravel while producing a thin coating of marl. Increased prevalence of alevin deformities and significantly lower survival were observed at 13.7 C versus 8.1 and 11.2 C, but gravel inclusion did not affect these variables. Potentially harmful effects of marl were observed; however, juvenile brook trout survival was higher during Study 2. This research suggests that brook trout reintroduction efforts in karst-geology streams should be focused on microhabitats with limited marl production and adequate water temperatures for juvenile survival.

Hatchery International↗
USGS2022

Comparison of microscopy and metabarcoding to identify pollen used by the critically endangered rusty patched bumble bee, Bombus affinis

Taxonomic analysis of pollen collected by bees can provide insights into their host plant use, providing information about the plant species selected for targeted conservation strategies. The two main identification approaches used are morphological analysis of pollen samples affixed to microscope slides (i.e., microscopic palynology) and molecular analysis of samples. Both methods are widely used for freshly collected materials and have been compared in multiple studies, yet their application to archived samples remains to be explored. Archived samples may be particularly useful for the study of rare or protected species, particularly when historical foraging patterns are uncertain. We used both methods to analyse pollen collected by the endangered rusty patched bumble bee species, Bombus affinis Cresson, applied to museum-archived specimens. Pollen samples were removed from the corbiculae of bumble bees originally collected in Michigan between 1914 and 1974. Samples included 24 rusty patched bumble bees each with large pollen loads on both corbiculae, allowing for pollen from the same bee to be analysed using both methods. DNA metabarcoding detected more plant taxa than light microscopy, and DNA barcoding also had higher taxonomic resolution when compared to taxa determined using light microscopy. In many instances, pollen could only be confidently identified to tribe or family with light microscopy. Discrepancy between methods decreased when taxa identified via DNA metabarcoding were binned into ecologically relevant groups corresponding to those identified using light microscopy. Although binning demonstrated smaller within-method variance, there was still minimal correspondence between the two methods. Results indicate there are benefits and biases unique to each method and highlight the utility of binning taxonomic results to morphological or ecological groupings.

Insect Conservation and Diversity↗