High Taxonomic Resolution Research Articles

Automated graptolite identification at high taxonomic resolution using residual networks

Graptolites, fossils significant for evolutionary studies and shale gas exploration, are traditionally identified visually by taxonomists due to their intricate morphologies and preservation challenges. Artificial intelligence (AI) holds great promise for transforming such meticulous tasks. In this paper, we demonstrate that graptolites can be identified with taxonomist accuracy using a deep learning model. We construct the most sophisticated and largest professional single organisms image dataset to date, which is composed of >34,000 images of 113 graptolite species annotated at pixel-level resolution to train the model, develop, and evaluate deep learning networks to classify graptolites. The model's performance surpassed taxonomists in accuracy, time, and generalization, achieving 86% and 81% accuracy in identifying graptolite genus and species, respectively. This AI-based method, capable of recognizing minute morphological details better than taxonomists, can be integrated into web and mobile apps, extending graptolite identification beyond research institutes and enhancing shale gas exploration efficiency.

Faunal Diet of Adult Cane Toads, Rhinella marina, in the Urban Landscape of Southwest Florida.

We investigated the diet of cane toads (Rhinella marina) inhabiting urbanized areas in southwest Florida to provide high taxonomic resolution of prey items, contrast toad diets between sampling seasons and sexes, and assess this invasive species' ecological role in the urban landscape. A pest control agency collected cane toads from two golf course communities in Naples, Florida, USA during November-December 2018 (early dry season) and June-July 2019 (early wet season), and faunal stomach contents were quantified from a random subsample of 240 adult toads (30 males and 30 females from each community and season). Yellow-banded millipedes (Anadenobolus monilicornis), big-headed ants (Pheidole spp.), and hunting billbugs (Sphenophorus venatus vestitus) were the most frequently consumed prey items and had the highest total numbers and/or volume with corresponding highest indices of relative importance. There was considerable overlap in the seasonal prey importance values for each golf course community and little if any difference in the importance values between toad sexes in each community. Nonetheless, big-headed ants were the most important prey in both communities during the wet season, while yellow-banded millipedes were the most important dry season prey in one community and hunting billbugs the most important in the other. Despite limited spatiotemporal sampling effort, our results indicated that cane toad was consuming arthropod taxa considered pests in the urban ecosystem. Further studies are needed to investigate the potential effects of human activities and environmental variability on the cane toad diet and to determine whether cane toads act as a biological control for pest populations.

DNA metabarcoding of cloacal swabs provides insight into diets of highly migratory sharks in the Mid-Atlantic Bight.

The abundances of migratory shark species observed throughout the Mid-Atlantic Bight (MAB) during productive summer months suggest that this region provides critical habitat and prey resources to these taxa. However, the principal prey assemblages sustaining migratory shark biomass in this region are poorly defined. We applied high-throughput DNA metabarcoding to shark feces derived from cloacal swabs across nine species of Carcharhinid and Lamnid sharks to (1) quantify the contribution of broad taxa (e.g., invertebrates, fishes) supporting shark biomass during seasonal residency in the MAB and (2) determine whether the species displayed distinct dietary preference indicative of resource partitioning. DNA metabarcoding resulted in high taxonomic (species-level) resolution of shark diets with actinopterygian and elasmobranch fishes as the dominant prey categories across the species. DNA metabarcoding identified several key prey groups consistent across shark taxa that are likely integral for sustaining their biomass in this region, including Atlantic menhaden (Brevoortia tyrannus), Atlantic mackerel (Scomber scombrus), and benthic elasmobranchs, including skates. Our results are consistent with previously published stomach content data for the shark species of similar size range in the Northwest Atlantic Ocean, supporting the efficacy of cloacal swab DNA metabarcoding as a minimally invasive diet reconstruction technique. The high reliance of several shark species on Atlantic menhaden could imply wasp-waist food-web conditions during the summer months, whereby high abundances of forage fishes sustain a diverse suite of migratory sharks within a complex, seasonal food web.

Unveiling invasive insect threats to plant biodiversity: Leveraging eDNA metabarcoding and saturated salt trap solutions for biosurveillance.

The negative global impacts of invasive alien species (IAS) on biodiversity are second only to habitat loss. eDNA metabarcoding allows for a faster and more comprehensive evaluation of community species composition, with a higher taxonomic resolution and less taxonomic expertise required than traditional morphological-based biosurveillance. These advantages have positioned eDNA metabarcoding as the standard method for molecular-based detection of invasive alien species, where fast and accurate detectability allows prompt responses to mitigate their adverse effects. Here, eDNA metabarcoding is used for biosurveillance of invasive alien species regulated by Canada in high-risk areas with four main objectives: i) validate the effectiveness of eDNA metabarcoding of salt trap solutions as a molecular technique for IAS detection, ii) compare detection from DNA extracts obtained from filter quarters versus whole filters, iii) benchmark two different bioinformatic pipelines (MetaWorks and mBRAVE), and iv) compare canopy and ground level trapping. eDNA from up to five IAS (Agrilus planipennis, Daktulosphaira vitifoliae, Lymantria dispar, Popillia japonica, and Trichoferus campestris) were successfully detected across years from 2017 to 2022 in southern Ontario, Canada, with successful morphological validation for all except Lymantria dispar and Trichoferus campestris. Analysis of filter quarters in contrast to whole filters was demonstrated to be insufficient for effective IAS detection in each sample. All IAS were detected in only one filter quarter, suggesting a patchy eDNA distribution on the filter. The MetaWorks and mBRAVE bioinformatics pipelines proved effective in identifying IAS, with MetaWorks yielding a higher success rate when comparing molecular and morphological identifications. Ground-level and canopy-level sampling showed differential IAS recovery rates based on the molecular detection, which also varied per collection year, with all found IAS detected at the canopy level in 2022 while only one (Lymantria dispar) in 2020. The present study ratifies the efficacy and importance of eDNA-based detection in a regulatory context and the utility of adding eDNA metabarcoding of saturated salt trap solutions, a critical tool for IAS detection.

Comparative analysis of full-length 16s ribosomal RNA genome sequencing in human fecal samples using primer sets with different degrees of degeneracy.

Next-generation sequencing has revolutionized the field of microbiology research and greatly expanded our knowledge of complex bacterial communities. Nanopore sequencing provides distinct advantages, combining cost-effectiveness, ease of use, high throughput, and high taxonomic resolution through its ability to process long amplicons, such as the entire 16s rRNA genome. We examine the performance of the conventional 27F primer (27F-I) included in the 16S Barcoding Kit distributed by Oxford Nanopore Technologies (ONT) and that of a more degenerate 27F primer (27F-II) in the context of highly complex bacterial communities in 73 human fecal samples. The results show striking differences in both taxonomic diversity and relative abundance of a substantial number of taxa between the two primer sets. Primer 27F-I reveals a significantly lower biodiversity and, for example, at the taxonomic level of the phyla, a dominance of Firmicutes and Proteobacteria as determined by relative abundances, as well as an unusually high ratio of Firmicutes/Bacteriodetes when compared to the more degenerate primer set (27F-II). Considering the findings in the context of the gut microbiomes common in Western industrial societies, as reported in the American Gut Project, the more degenerate primer set (27F-II) reflects the composition and diversity of the fecal microbiome significantly better than the 27F-I primer. This study provides a fundamentally relevant comparative analysis of the in situ performance of two primer sets designed for sequencing of the entire 16s rRNA genome and suggests that the more degenerate primer set (27F-II) should be preferred for nanopore sequencing-based analyses of the human fecal microbiome.

Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution

The study of microbiota has been revolutionized by the development of DNA metabarcoding. This sequence-based approach enables the direct detection of microorganisms without the need for culture and isolation, which significantly reduces analysis time and offers more comprehensive taxonomic profiles across broad phylogenetic lineages. While there has been an accumulating number of researches on bacteria, molecular phylogenetic analysis of fungi still remains challenging due to the lack of standardized tools and the incompleteness of reference databases limiting the accurate and precise identification of fungal taxa. Here, we present a DNA metabarcoding workflow for characterizing fungal microbiota with high taxonomic resolution. This method involves amplifying longer stretches of ribosomal RNA operons and sequencing them using nanopore long-read sequencing technology. The resulting reads were error-polished to generate consensus sequences with 99.5–100% accuracy, which were then aligned against reference genome assemblies. The efficacy of this method was explored using a polymicrobial mock community and patient-derived specimens, demonstrating the marked potential of long-read sequencing combined with consensus calling for accurate taxonomic classification. Our approach offers a powerful tool for the rapid identification of pathogenic fungi and has the promise to significantly improve our understanding of the role of fungi in health and disease.

VirMAP for cancer: Characterization of the intratumoral virome in virally associated cancers and a resource for investigators.

2568 Background: A major barrier to understanding the role of viruses in cancer progression has been the lack of sensitivity of current tools to assemble viral genomes in an untargeted way. Here, we utilize our novel VirMAP algorithm to identify eukaryotic and prokaryotic viruses associated with cancers, using RNA sequencing data from The Cancer Genome Atlas (TCGA). Methods: VirMAP was run on 16 TCGA RNASeq datasets of primary tumor tissues, with a focus on cancers with known viral associations (including cervical, head and neck, liver, stomach, esophagus and ovarian). Previously published survival data were used for exploratory analysis. Overall survival (OS) was assessed using the Kaplan-Meier method, and p-values were calculated using log-rank test. Multivariate analysis (MVA) was done using Cox proportional hazards model to control for age, sex, stage, and histology. Results: Viral sequence recovery (among 537 billion sequencing reads from 6185 patients) was at least equal to previously published algorithms such as Kraken, but with higher taxonomic resolution; overall recovery was 0.0041% from 16 tumor types. Cancers with high viral loads such as cervical cancer demonstrated high recovery rates (0.012% of all reads mapped to viral taxa, followed by 0.004% for liver, 0.0018% head and neck, 0.0016% stomach, 0.0009% esophageal, and 0.0002% ovarian). There was a wide range of viral signature richness, with cervical cancer showing the highest viral read count predominated by 18 different HPV serotypes; in contrast, stomach cancer had lower abundance but contained over 300 unique viral species. Exploratory analysis revealed novel correlations between viral signatures and OS. In cervical cancer, presence of HPV45 predicted worse survival (median OS 837 days vs 4086, p=0.0043); MVA demonstrated hazard ratio (HR) of 5.7 [2.6-11.4, p<0.0001]. In stomach cancer, patients often had more than one viral taxon present (mean 3.7, range 0-18); presence of seven or more unique taxa predicted worse OS (median OS 403 days vs 1153, p=0.0001). MVA showed HR of 1.1 for every additional taxon (p=0.0004). Across all 16 tumor types, the detection of phage virus was associated with worse OS (1073 days vs. 2094 days for non-phage virus and 2131 days for no virus, p<0.0001). Conclusions: VirMAP performs deep characterization of the tumor-associated virome in both high and low abundance settings, with generation of partial genome reconstructions and strain level taxonomic classification including phages. Further work is ongoing to optimize viral read normalization based on genome length, as well as subset analysis with disease-specific modifiers such as histology, race, and exposures. Utilizing publicly available platforms such as TCGA, clinical and correlative published data can be leveraged to better understand the nuanced pleotropic effects of the tumor virome on cancer progression.

Shallow shotgun sequencing reduces technical variation in microbiome analysis

The microbiome is known to play a role in many human diseases, but identifying key microbes and their functions generally requires large studies due to the vast number of species and genes, and the high levels of intra-individual and inter-individual variation. 16S amplicon sequencing of the rRNA gene is commonly used for large studies due to its comparatively low sequencing cost, but it has poor taxonomic and functional resolution. Deep shotgun sequencing is a more accurate and comprehensive alternative for small studies, but can be cost-prohibitive for biomarker discovery in large populations. Shallow or moderate-depth shotgun metagenomics may serve as a viable alternative to 16S sequencing for large-scale and/or dense longitudinal studies, but only if resolution and reproducibility are comparable. Here we applied both 16S and shallow shotgun stool microbiome sequencing to a cohort of 5 subjects sampled twice daily and weekly, with technical replication at the DNA extraction and the library preparation/sequencing steps, for a total of 80 16S samples and 80 shallow shotgun sequencing samples. We found that shallow shotgun sequencing produced lower technical variation and higher taxonomic resolution than 16S sequencing, at a much lower cost than deep shotgun sequencing. These findings suggest that shallow shotgun sequencing provides a more specific and more reproducible alternative to 16S sequencing for large-scale microbiome studies where costs prohibit deep shotgun sequencing and where bacterial species are expected to have good coverage in whole-genome reference databases.

Metabarcoding of ichthyoplankton communities associated with a highly dynamic shelf region of the southwest Indian Ocean.

Drifting fish eggs and larvae (ichthyoplankton) can be identified to species using DNA metabarcoding, thus allowing for post hoc community analyses at a high taxonomic resolution. We undertook a regional-scale study of ichthyoplankton distribution along the east coast of South Africa, focused on the contrasting environments of the tropical Delagoa and subtropical Natal Ecoregions, and on exposed and sheltered shelf areas. Zooplankton samples were collected with tow nets at discrete stations along cross-shelf transects (20-200 m depth) spaced along a latitudinal gradient that incorporates a known biogeographical boundary. Metabarcoding detected 67 fish species, of which 64 matched prior distribution records of fishes from South Africa, with the remaining three known from the Western Indian Ocean. Coastal, neritic and oceanic species were present, from epi- and mesopelagic to benthopelagic and benthic adult habitats. By family, Myctophidae (10 species), Carangidae, Clupeidae, Labridae (each with 4 species) and Haemulidae (3 species) were most speciose. Ichthyoplankton community composition varied significantly with latitude, distance to coast, and distance to the shelf edge. Small pelagic fishes had the highest frequency of occurrence: Engraulis capensis, Emmelichthys nitidus and Benthosema pterotum increased in frequency towards the north, whereas Etrumeus whiteheadi increased towards the south. Chub mackerel Scomber japonicus accounted for most variability related to distance from the coast, whilst African scad Trachurus delagoa correlated with distance to the shelf edge. Dissimilarity between communities in the Delagoa and Natal Ecoregions was 98-100%, whereas neighbouring transects located within the sheltered KwaZulu-Natal Bight had lower dissimilarity (56-86%). Onshore transport of ichthyoplankton by Agulhas Current intrusions plausibly explained the abundance of mesopelagic species over the shelf. Metabarcoding followed by community analysis revealed a latitudinal gradient in the ichthyoplankton, associations with coastal and shelf-edge processes, and evidence of a spawning area in the sheltered KwaZulu-Natal Bight.

Pollen morphology of family Thymelaeaceae Juss. in India and its taxonomic implications

We provide pollen morphology and ultrastructure of 26 plant taxa, comprising 14 genera, 21 species, 1 sub-species and 3 varieties, of the Thymelaeaceae family from the Indian sub-continent using light micsoscopic (LM) and scanning electron microscopic (SEM) techniques. The principal aim was to provide new and useful information regarding the extent of the pollen morphological diversity among the Thymelaeaceae taxa and, thus, contribute to a better understanding of the taxonomy of the studied taxa. The pollen grains of the studied taxa are essentially radially symmetrical, apolar, (released as) monad, pantoporate with a typical crotonoid pattern, and spheroidal (mostly) in shape; but widespread variations with respect to the number and dispensation of pores, size, exine (ectoexine and endoexine) thickness, and the shape itself (spheroidal, sub-spheroidal and prolate spheroidal), as well as in the amb (outline) have been also recorded. Pollen identification keys, based on the pollen micro-morphological attributes, were also constructed in order to easily identify the 26 studied Thymelaeceae taxa up to species and/or varieties level (high taxonomic resolution, showing taxonomic significance). The pollen morphological attributes of the 26 studied plant taxa of the Thymelaeaceae family were subjected to Principal Component Analysis (PCA) and Hierarchical Component Analysis (HCA), which suggest four clusters. The cophenetic correlation coefficient also validates the four group of clustering. The study will significantly help in the precise pollen identification in fossil (pollen) records for the reconstruction of vegetation dynamics and contemporary climate change during the Quaternary Period in India. Moreover, the present study also helps in determining the phylogenetic and evolutionary trend on the basis of the presence or absence of exine ornamentation and having more or less apertures among the pollen grains of the 26 studied Thymelaeaceae taxa.

Abstract 641: VirMAP for cancer: Characterization of the intratumoral virome in virally-associated cancers and a resource for investigators

Abstract Background: A major barrier to understanding the role of viruses in cancer progression has been the lack of sensitivity of current tools to identify and assemble viral genomes in an untargeted way. Here, we utilize our novel VirMAP algorithm to identify eukaryotic and prokaryotic viruses associated with cancers, using RNA sequencing data from The Cancer Genome Atlas (TCGA). Methods: VirMAP was used to analyze TCGA RNA-Seq data derived from primary tumor tissues, with a focus on cancers with known viral associations (cervical, ovarian, head and neck, liver, stomach and esophagus). Previously published survival data were matched with viral signatures for exploratory analysis. Ancom-BC, a differential abundance pipeline, was utilized to screen for viruses which drive outcome. Overall survival (OS) was assessed using the Kaplan-Meier method, and p-values were calculated using log-rank test. Multivariate analysis (MVA) was done using the Cox proportional hazards model to control for age, sex, stage, and histology. Results: Viral sequence recovery (among 723 billion sequencing reads from 2090 patients) was at least equal to previously published algorithms such as Kraken, but with higher taxonomic resolution. Cancers with high viral loads such as cervical cancer demonstrated high recovery rates (0.012% of all sequencing reads mapped to viral taxa, followed by 0.004% for liver, 0.0018% for head and neck squamous cell, 0.0016% for stomach, 0.0009% for esophageal, and 0.0002% for ovarian). There was a wide range of viral signature richness, with cervical cancer showing the highest viral read count predominated by HPV serotypes; in contrast, stomach cancer had lower abundance but contained over 300 unique viral taxa. Exploratory clinical analysis revealed novel correlations between viral signatures and OS. In cervical cancer, presence of HPV45 predicted worse survival (median OS 837 days vs 4086, p=0.0043); MVA demonstrated hazard ratio (HR) of 5.7 [2.6-11.4, p<0.0001]. In stomach cancer, patients often had more than one viral taxon present (mean 3.7, range 0-18); presence of 7 or more unique taxa predicted worse OS (median OS 403 days vs 1153, p=0.0001). MVA showed HR 1.1 for every additional taxon (p=0.0004). Conclusions: VirMAP performs deep characterization of the tumor-associated virome in both high and low abundance settings, with generation of partial genome reconstructions and strain level taxonomic classification. Utilizing publicly available platforms such as TCGA, clinical and correlative published data can be leveraged to better understand the nuanced pleotropic effects of the tumor virome on cancer progression. Citation Format: Yongwoo D. Seo, Neal Bhutiani, Matthew C. Wong, Ashish V. Damania, Golnaz Morad, Matthew Lastrapes, Alexander J. Lazar, Jennifer A. Wargo, Nadim J. Ajami. VirMAP for cancer: Characterization of the intratumoral virome in virally-associated cancers and a resource for investigators [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 641.

Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis

BackgroundFor a sustainable production of food, research on agricultural soil microbial communities is inevitable. Due to its immense complexity, soil is still some kind of black box. Soil study designs for identifying microbiome members of relevance have various scopes and focus on particular environmental factors. To identify common features of soil microbiomes, data from multiple studies should be compiled and processed. Taxonomic compositions and functional capabilities of microbial communities associated with soils and plants have been identified and characterized in the past few decades. From a fertile Loess–Chernozem-type soil located in Germany, metagenomically assembled genomes (MAGs) classified as members of the phylum Thaumarchaeota/Thermoproteota were obtained. These possibly represent keystone agricultural soil community members encoding functions of relevance for soil fertility and plant health. Their importance for the analyzed microbiomes is corroborated by the fact that they were predicted to contribute to the cycling of nitrogen, feature the genetic potential to fix carbon dioxide and possess genes with predicted functions in plant-growth-promotion (PGP). To expand the knowledge on soil community members belonging to the phylum Thaumarchaeota, we conducted a meta-analysis integrating primary studies on European agricultural soil microbiomes.ResultsTaxonomic classification of the selected soil metagenomes revealed the shared agricultural soil core microbiome of European soils from 19 locations. Metadata reporting was heterogeneous between the different studies. According to the available metadata, we separated the data into 68 treatments. The phylum Thaumarchaeota is part of the core microbiome and represents a major constituent of the archaeal subcommunities in all European agricultural soils. At a higher taxonomic resolution, 2074 genera constituted the core microbiome. We observed that viral genera strongly contribute to variation in taxonomic profiles. By binning of metagenomically assembled contigs, Thaumarchaeota MAGs could be recovered from several European soil metagenomes. Notably, many of them were classified as members of the family Nitrososphaeraceae, highlighting the importance of this family for agricultural soils. The specific Loess-Chernozem Thaumarchaeota MAGs were most abundant in their original soil, but also seem to be of importance in other agricultural soil microbial communities. Metabolic reconstruction of Switzerland_1_MAG_2 revealed its genetic potential i.a. regarding carbon dioxide (CO_2) fixation, ammonia oxidation, exopolysaccharide production and a beneficial effect on plant growth. Similar genetic features were also present in other reconstructed MAGs. Three Nitrososphaeraceae MAGs are all most likely members of a so far unknown genus.ConclusionsOn a broad view, European agricultural soil microbiomes are similarly structured. Differences in community structure were observable, although analysis was complicated by heterogeneity in metadata recording. Our study highlights the need for standardized metadata reporting and the benefits of networking open data. Future soil sequencing studies should also consider high sequencing depths in order to enable reconstruction of genome bins. Intriguingly, the family Nitrososphaeraceae commonly seems to be of importance in agricultural microbiomes.

Heatwave restructures marine intertidal communities across a stress gradient.

Significant questions remain about how ecosystems that are structured by abiotic stress will be affected by climate change. Warmer temperatures are hypothesized to shift species along abiotic gradients such that distributions track changing environments where physical conditions allow. However, community-scale impacts of extreme warming in heterogeneous landscapes are likely to be more complex. We investigated the impacts of a multiyear marine heatwave on intertidal community dynamics and zonation on a wave-swept rocky coastline along the Central Coast of British Columbia, Canada. Leveraging an 8-year time series with high seaweed taxonomic resolution (116 taxa) that was established 3 years prior to the heatwave, we document major shifts in zonation and abundance of populations that led to substantial reorganization at the community level. The heatwave was associated with shifts in primary production away from upper elevations through declines in seaweed cover and partial replacement by invertebrates. At low elevations, seaweed cover remained stable or recovered rapidly following decline, being balanced by increases in some species and decreases in others. These results illustrate that, rather than shifting community zonation uniformly along abiotic stress gradients, intense and lasting warming events may restructure patterns of ecological dominance and reduce total habitability of ecosystems, especially at extreme ends of pre-existing abiotic gradients.

Diets of two non-native praying mantids (Tenodera sinensis and Mantis religiosa) show consumption of arthropods across all ecological roles

Introduced predators may affect native arthropod communities and alter the ecosystem services these native species provide. While mantids are known to have a broad diet in terms of consuming taxa from a number of different orders, we currently lack the high taxonomic resolution on the prey species consumed. Without knowing the identity and frequency of species in the diets of introduced mantids, it is difficult to estimate the ecological impacts of these species on local food webs and ecosystem services. To address these issues, we used DNA metabarcoding to identify prey in the diets of two introduced mantids (Tenodera sinensis and Mantis religiosa) in old fields. While both species fed on a broad diversity of taxa across 22 orders, T. sinensis mantids exhibited higher alpha diversity in diet items than M. religiosa mantids. Total beta diversity of mantid diets was moderate (0.39–0.485) across both species, although M. religiosa samples exhibited higher total beta diversity than T. sinensis samples. Herbivorous, predatory and pollinator prey species were the most important contributors to detected patterns of beta diversity. However, degree of diet overlap varied across sites and mantid species, where mantid diets at sites dominated by the same species of mantid were more similar than compared to mantid diets at sites dominated by a different mantid species.

Inter-colony and inter-annual variation in discard use by albatross chicks revealed using isotopes and regurgitates

Effective marine ecosystem monitoring is critical for sustainable management. Monitoring seabird diets can convey important information on ecosystem health and seabird–fishery interactions. The diet of breeding black-browed albatross (Thalassarche melanophris) has previously been assessed using stomach content analysis (SCA) or stable isotope analysis (SIA), but not both methods together. Combining dietary sampling approaches reduces biases associated with using single methods. This study combines SCA and SIA to study the diet of black-browed albatross chicks, with a specific focus on fishery discard consumption, at two Falkland Islands colonies (New Island 51°43′S, 61°18′W and Steeple Jason Island 51°01′S, 61°13′W) during two consecutive breeding seasons (2019 and 2020). SCA provided high taxonomic resolution of short-term diet and priors for stable isotope mixing models, with multiple measures of dietary items (e.g. numeric frequency N%, frequency of occurrence FO%). By contrast, SIA of down feathers provided a single and more integrated dietary signal from throughout chick development. Although the two methods disagreed on the dominant prey group (SCA—crustacean; SIA—pelagic fish), the complementary information suggested a chick diet dominated by natural prey (SCA: 74%–93% [FO], 44%–98% [N]; SIA: minimum 87%–95% contribution). Nonetheless, SCA revealed that a high proportion of breeding adults do take discards. We detected consistent colony-specific diets in relation to prey species, but not in relation to higher discard use. Overall, discard consumption was highest in 2020, the year characterised by the poorest foraging conditions. Our results have implications for fisheries management and future dietary studies assessing discard use.

Multiple Approaches to the Trophic Role of Mesopelagic Fish around the Iberian Peninsula.

Myctophids, commonly vertical migrators, and partial and non-migrant stomiiforms constitute most of the mesopelagic biomass, and transport organic matter throughout the food web from the surface to the ocean's depths. Both the diet and trophic structure of twenty-nine species of mesopelagic fish collected around the Iberian Peninsula were studied through the analysis of stomach contents, quantifying food items with a high taxonomic resolution. The investigation covered oligotrophic to productive habitats, with sampling stations distributed in five discrete zones of the western Mediterranean Sea and the northeastern Atlantic Ocean. The geographic environmental conditions, migratory behavior, and species-specific body sizes allowed for the identification of some major feeding patterns for these fish communities. The trophic niche of migrant myctophids showed a high overlap, with copepods as the primary prey category. The diet composition of generalist myctophids (e.g., Ceratoscopelus maderensis and Hygophum benoiti) reflected the distinct zooplanktonic communities between zones. Large stomiiforms (Chauliodus spp., Sigmops elongatus) preferred feeding on micronekton, while the smallest stomiiforms (e.g., Argyropelecus spp., Cyclothone spp., Vinciguerria spp.) preyed on copepods and ostracods. Given the relevance of the mesopelagic fish communities for commercially exploited species and, therefore, for maintaining the sustainability of the fisheries' activity in the zones analyzed, the information provided in the present study is essential for a better understanding of the biology and ecology of these species.

Profiling Blautia at high taxonomic resolution reveals correlations with cognitive dysfunction in Chinese children with Down syndrome.

Down syndrome (DS), the presence of a supernumerary chromosome 21, is associated with cognitive dysfunction caused by early neurodegenerative processes. Alterations in the gut microbiota were observed in Chinese children with DS, and the genus Blautia was associated with cognitive function in these children. Therefore, it is crucial to understand the detailed composition of this group at the species level and to explore the effect of specific species on cognitive function. In this study, Blautia-specific amplicon sequencing was conducted to identify the specific Blautia species in 15 children with DS and 15 matched healthy children. The taxonomic analyses suggested that the Blautia taxa were clustered by disease status. The diversity of Blautia at the species level differed between DS patients and healthy controls, with the abundances of Blautia massiliensis and Blautia argi decreasing in DS children, while Blautia faecis was increased. Acetic acid, one of the metabolites of Blautia, was significantly reduced in the DS group. Of particular interest, Kyoto Encyclopaedia of Genes and Genomes analysis revealed decreased modules related to starch and sucrose metabolism and glycolysis. In addition, B. argi was positively related to DS cognitive scores, and B. faecis was negatively related to cognitive function, implying its role on the DS cognitive impairments. Our study has important implications for understanding the important effects of specific species of Blautia on cognitive function and thus possibly provides a new strategy for future studies of cognitive improvement in individuals with DS.

Comparative performance of a multi‐locus barcoding approach to enhance taxonomic resolution of New Zealand mosquitoes (Diptera: Culicidae)

AbstractMosquitoes (Diptera: Culicidae) pose a serious threat to human health globally and the accurate identification of mosquito species is fundamental to entomological diagnostics and surveillance implementing effective vector control and management. However, cryptic species complexes, incomplete or damaged specimens, and juvenile life stages complicates the task. Molecular characterisation has shown the potential to identify the mosquito species accurately and overcomes the difficulties that morphological diagnosis face. Here, we assessed the effectiveness of a multi‐locus barcoding approach using cytochrome c oxidase subunit I (COI), internal transcribed spacer 1 (ITS1) and internal transcribed spacer 2 (ITS2) regions to identify the New Zealand mosquito species (n = 16) at the highest taxonomic resolution, which can make diagnosis more accurate and efficient. Our results show that most of the New Zealand mosquito species could be distinctly separated from each other as well as from other exotic species using either of these barcoding regions (i.e., COI, ITS1 and ITS2). The assessment of taxonomic discriminatory power of COI, ITS1 and ITS2 barcodes suggests that ITS2 can better distinguish the New Zealand closely‐related species. Two closely‐related endemic species from the Culex pervigilans species complex (Cx. rotoruae and Cx. pervigilans) were difficult to distinguish using COI and ITS1 regions. However, the ITS2 barcode could detect a greater genetic variation among individuals of those two species and demonstrate the potential to resolve the relationships among them to provide better resolution as a complementary to COI. Overall, this study provides a reference DNA barcode database of COI and ITS2 for New Zealand mosquito species, which will aid in their accurate identification at a higher taxonomic resolution and corroborate the traditional morphological approaches to perform better species discrimination among closely‐related species complex. The study also assessed the preliminary genetic diversity of the mosquito species from different regions of New Zealand, which can be used as a baseline for uncovering the environmental and geographical effect on genomic variations among New Zealand mosquito populations in the future.

Faecal metabarcoding provides improved detection and taxonomic resolution for non-invasive monitoring of gastrointestinal nematode parasites in wild moose populations

BackgroundAlthough wild ungulate populations are heavily monitored throughout Europe, we understand little of how parasites affect population dynamics, and there is no systematic, long-term monitoring of parasite diversity and parasite loads. Such monitoring is in part hampered by a lack of time- and cost-effective assay methodologies with high sensitivity and good taxonomic resolution. DNA metabarcoding has been successfully used to characterize the parasitic nemabiome with high taxonomic resolution in a variety of wild and domestic hosts. However, in order to implement this technique in large-scale, potentially non-invasive monitoring of gastrointestinal parasitic nematodes (GIN), protocol optimization is required to maximize biodiversity detection, whilst maintaining time- and cost-effectiveness.MethodsFaecal samples were collected from a wild moose population and GIN communities were characterized and quantified using both parasitological techniques (egg and larva counting) and DNA metabarcoding of the ITS2 region of rDNA. Three different isolation methods were compared that differed in the volume of starting material and cell lysis method.ResultsSimilar nematode faunas were recovered from all samples using both parasitological and metabarcoding methods, and the approaches were largely congruent. However, metabarcoding assays showed better taxonomic resolution and slightly higher sensitivity than egg and larvae counts. The metabarcoding was not strictly quantitative, but the proportion of target nematode sequences recovered was correlated with the parasitologically determined parasite load. Species detection rates in the metabarcoding assays were maximized using a DNA isolation method that included mechanical cell disruption and maximized the starting material volume.ConclusionsDNA metabarcoding is a promising technique for the non-invasive, large-scale monitoring of parasitic GINs in wild ungulate populations, owing to its high taxonomic resolution, increased assay sensitivity, and time- and cost-effectiveness. Although metabarcoding is not a strictly quantitative method, it may nonetheless be possible to create a management- and conservation-relevant index for the host parasite load from this data. To optimize the detection rates and time- and cost-effectiveness of metabarcoding assays, we recommend choosing a DNA isolation method that involves mechanical cell disruption and maximizes the starting material volume.Graphical

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

Abstract 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.