Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool

The approach of combining cost-effective nanopore sequencing and emerging environmental DNA (eDNA) metabarcoding could prove to be a promising tool for biodiversity documentation, especially in Malaysia. Given the substantial funding constraints in recent years, especially in relation to the country's biodiversity, many researchers have been limited to conduct restricted research without extended monitoring periods, potentially hindering comprehensive surveys and could compromise the conservation efforts. Therefore, the present study aimed to evaluate the application of eDNA metabarcoding on freshwater fish using short reads generated through nanopore sequencing. This assessment focused on species detection in three selected rivers within the Endau Rompin Landscape in Malaysia. Additionally, the study compared levels of species detection between eDNA metabarcoding and conventional sampling methods, examined the effectiveness of primer choice, and applied both metabarcoding and shotgun sequencing to the eDNA approach. We successfully identified a total of 22 and 71 species with an identification threshold of >97% and >90%, respectively, through the MinION platform. The eDNA metabarcoding approach detected over 13% more freshwater fish species than when the conventional method was used. Notably, the distinction in freshwater fish detection between eDNA primers for 12S rRNA and cytochrome oxidase I was insignificant. The cost for eDNA metabarcoding proved to be more effective compared to conventional sampling with cost reduction at 33.4%. With favourable cost-effectiveness and increased species detection, eDNA metabarcoding could complement existing methods, enhance holistic diversity documentation for targeted habitats and facilitate effective conservation planning.

Metabarcoding read abundances of orchid mycorrhizal fungi are correlated to copy numbers estimated using ddPCR

Quantifying the abundances of fungi is key to understanding natural variation in mycorrhizal communities in relation to plant ecophysiology and environmental heterogeneity. High-throughput metabarcoding approaches have transformed our ability to characterize and compare complex mycorrhizal communities. However, it remains unclear how well metabarcoding read counts correlate with actual read abundances in the sample, potentially limiting their use as a proxy for species abundances. Here, we use droplet digital PCR (ddPCR) to evaluate the reliability of ITS2 metabarcoding data for quantitative assessments of mycorrhizal communities in the orchid species Neottia ovata sampled at multiple sites. We performed specific ddPCR assays for eight families of orchid mycorrhizal fungi and compared the results with read counts obtained from metabarcoding. Our results demonstrate a significant correlation between DNA copy numbers measured by ddPCR assays and metabarcoding read counts of major mycorrhizal partners of N. ovata, highlighting the usefulness of metabarcoding for quantifying the abundance of orchid mycorrhizal fungi. Yet, the levels of correlation between the two methods and the numbers of false zero values varied across fungal families, which warrants cautious evaluation of the reliability of low-abundance families. This study underscores the potential of metabarcoding data for more quantitative analyses of mycorrhizal communities and presents practical workflows for metabarcoding and ddPCR to achieve a more comprehensive understanding of orchid mycorrhizal communities.

Optimizing waterborne eDNA capture from waterholes in savanna systems under remote field conditions

Environmental DNA (eDNA) is used for biodiversity assessments in a variety of ecosystems across the globe, whereby different eDNA concentration, preservation and extraction methods can outperform others depending on the sampling conditions and environment. Tropical and subtropical ecosystems in Africa are among the less studied systems concerning eDNA-based monitoring. Waterholes in arid parts of southern Africa represent important agglomeration points for terrestrial mammals, and the eDNA shed into such waterbodies provides a powerful source of information for monitoring mammalian biodiversity in the surrounding area. However, the applied methods for eDNA sampling, preservation and filtering in different freshwater systems vary greatly, and rigorous protocol testing in African freshwater systems is still lacking. This study represents the first attempt to examine variations in eDNA concentration, preservation and extraction methods under remote field conditions using waterborne eDNA in a savanna system. Collected samples were heavily affected by microalgal and bacterial growth, impeding eDNA capture and PCR success. We demonstrate clear effects of the methodological choices, which also depend on the state of eDNA. A preliminary metabarcoding run showed little taxonomic overlap in mammal species detection between two metabarcoding primers tested. We recommend water filtering (using filters with pore sizes >1 μm) over centrifugation for eDNA concentration, Longmire's solution for ambient temperature sample preservation and Qiagen's DNeasy PowerSoil Pro Kit for DNA extraction of these inhibitor-prone samples. Furthermore, at least two independent metabarcoding markers should be utilized in order to maximize species detections in metabarcoding studies.

Development and validation of a DNA-based multi-species biomonitoring toolkit using a high-throughput qPCR platform: A case study of Irish shellfish species

Biomonitoring of marine life has been enhanced in recent years by the integration of innovative DNA-based approaches, which offer advantages over more laborious techniques (e.g. microscopy). However, trade-offs between throughput, sensitivity and quantitative measurements must be made when choosing between the prevailing molecular methodologies (i.e. metabarcoding or qPCR/dPCR). Thus, the aim of the present study was to demonstrate the utility of a microfluidic-enabled high-throughput quantitative PCR platform (HTqPCR) for the rapid and cost-effective development and validation of a DNA-based multi-species biomonitoring toolkit, using larvae of 23 commercially targeted bivalve and crustacean species as a case study. The workflow was divided into three main phases: definition of (off-) target taxa and establishment of reference databases (PHASE 1); selection/development and assessment of molecular assays (PHASE 2); and protocol optimization and field validation (PHASE 3). 42 assays were eventually chosen and validated. Genetic signal not only showed good correlation with direct visual counts by microscopy but also showed the ability to provide quantitative data at the highest taxonomic resolution (species level) in a time- and cost-effective fashion. This study developed a biomonitoring toolkit, demonstrating the considerable advantages of this state-of-the-art technology in boosting the developmental testing and application of panels of molecular assays for the monitoring and management of natural resources. Once developed, this approach provides a cost and time-effective alternative compared to other multi-species approaches (e.g. metabarcoding). In addition, it is transferable to a wide range of species and will aid future monitoring programmes.

Enhancing amphibian biomonitoring through eDNA metabarcoding

Surveying biodiversity has taken a quantum leap with environmental DNA (eDNA) metabarcoding, an immensely powerful approach lauded for its efficiency, sensitivity, and non-invasiveness. This approach emerges as a game-changer for the elusive realm of endangered and rare species-think nocturnal, environmentally elusive amphibians. Here, we have established a framework for constructing a reliable metabarcoding pipeline for amphibians, covering primer design, performance evaluation, laboratory validation, and field validation processes. The Am250 primer, located on the mitochondrial 16S gene, was optimal for the eDNA monitoring of amphibians, which demonstrated higher taxonomic resolution, smaller species amplification bias, and more extraordinary detection ability compared to the other primers tested. Am250 primer exhibit an 83.8% species amplification rate and 75.4% accurate species identification rate for Chinese amphibians in the in silico PCR and successfully amplified all tested species of the standard samples in the in vitro assay. Furthermore, the field-based mesocosm experiment showed that DNA can still be detected by metabarcoding even days to weeks after organisms have been removed from the mesocosm. Moreover, field mesocosm findings indicate that eDNA metabarcoding primers exhibit different read abundances, which can affect the relative biomass of species. Thus, appropriate primers should be screened and evaluated by three experimental approaches: in silico PCR simulation, target DNA amplification, and mesocosm eDNA validation. The selection of a single primer set or multiple primers' combination should be based on the monitoring groups to improve the species detection rate and the credibility of results.

Finding the perfect pairs: A matchmaking of plant markers and primers for multi-marker eDNA metabarcoding

As the scope of plant eDNA metabarcoding diversifies, so do the primers, markers and methods. A wealth of primers exists today, but their comparative evaluation is lacking behind. Similarly, multi-marker approaches are recommended but debates persist regarding barcode complementarity and optimal combinations. After a literature compilation of used primers, we compared in silico 102 primer pairs based on amplicon size, coverage and specificity, followed by an experimental evaluation of 15 primer pairs on a mock community sample covering 268 plant species and genera, and about 100 families. The analysis was done for the four most common plant metabarcoding markers, rbcL, trnL, ITS1 and ITS2 and their complementarity was assessed based on retrieved species. By focusing on existing primers, we identify common designs, promote alternatives and enhance prior-supported primers for immediate applications. The ITS2 was the best-performing marker for flowering vascular plants and was congruent to ITS1. However, the combined taxonomic breadth of ITS2 and rbcL surpassed any other combination, highlighting their high complementarity across Streptophyta. Overall, our study underscores the significance of comprehensive primer and barcode evaluations tailored to metabarcoding applications.

Mfind: a tool for DNA barcode analysis in angiosperms and its relationship with microsatellites using a sliding window algorithm

MAIN CONCLUSION

Mfind is a tool to analyze the impact of microsatellite presence on DNA barcode specificity. We found a significant correlation between barcode entropy and microsatellite count in angiosperm. Genetic barcodes and microsatellites are some of the identification methods in taxonomy and biodiversity research. It is important to establish a relationship between microsatellite quantification and genetic information in barcodes. In order to clarify the association between the genetic information in barcodes (expressed as Shannon's Measure of Information, SMI) and microsatellites count, a total of 330,809 DNA barcodes from the BOLD database (Barcode of Life Data System) were analyzed. A parallel sliding-window algorithm was developed to compute the Shannon entropy of the barcodes, and this was compared with the quantification of microsatellites like (AT)n, (AC)n, and (AG)n. The microsatellite search method utilized an algorithm developed in the Java programming language, which systematically examined the genetic barcodes from an angiosperm database. For this purpose, a computational tool named Mfind was developed, and its search methodology is detailed. This comprehensive study revealed a broad overview of microsatellites within barcodes, unveiling an inverse correlation between the sumz of microsatellites count and barcodes information. The utilization of the Mfind tool demonstrated that the presence of microsatellites impacts the barcode information when considering entropy as a metric. This effect might be attributed to the concise length of DNA barcodes and the repetitive nature of microsatellites, resulting in a direct influence on the entropy of the barcodes.

Fecal DNA metabarcoding helps characterize the Canada jay's diet and confirms its reliance on stored food for winter survival and breeding

Accurately determining the diet of wild animals can be challenging if food items are small, visible only briefly, or rendered visually unidentifiable in the digestive system. In some food caching species, an additional challenge is determining whether consumed diet items have been previously stored or are fresh. The Canada jay (Perisoreus canadensis) is a generalist resident of North American boreal and subalpine forests with anatomical and behavioural adaptations allowing it to make thousands of arboreal food caches in summer and fall that are presumably responsible for its high winter survival and late winter/early spring breeding. We used DNA fecal metabarcoding to obtain novel information on nestling diets and compiled a dataset of 662 published and unpublished direct observations or stomach contents identifications of natural foods consumed by Canada jays throughout the year. We then used detailed natural history information to make informed decisions on whether each item identified to species in the diets of winter adults and nestlings was best characterized as 'likely cached', 'likely fresh' (i.e., was available as a non-cached item when it appeared in a jay's feces or stomach), or 'either possible'. Of the 87 food items consumed by adults in the winter, 39% were classified as 'likely cached' and 6% were deemed to be 'likely fresh'. For nestlings, 29% of 125 food items identified to species were 'likely cached' and 38% were 'likely fresh'. Our results support both the indispensability of cached food for Canada jay winter survival and previous suggestions that cached food is important for late winter/early spring breeding. Our work highlights the value of combining metabarcoding, stomach contents analysis, and direct observations to determine the cached vs. non-cached origins of consumed food items and the identity of food caches, some of which could be especially vulnerable to degradation through climate change.

Decoding the molecular phylogenetics of ornamental catfishes (siluriformes) of North East India using DNA barcoding approach

BACKGROUND

Catfishes (order Siluriformes) are among the most diverse and widely distributed fish groups in the world. They are not only used for human consumption but are also a major part of the ornamental fish trade. Being a Biodiversity Hotspot, the North Eastern Region of India is home to a diverse population of ornamental fishes. Catfishes contain a humongous number of species; in this study, the authors have tried to elucidate the phylogenetic relationship of some important ornamental catfishes found in North East India using DNA barcodes.

METHODS AND RESULTS

In this study, we have tried to explore the phylogenetic history of 13 species (41 specimens) of ornamental catfishes spanning 12 genera and 9 families of Siluriformes using DNA barcoding. Pairwise genetic distances using Kimura 2-Parameter (K2P) were calculated at intra-specific and inter-specific levels. A Neighbor-Joining tree was constructed to understand the phylogenetic relationship among the nine different catfish families. All the specimens under this study clustered with their respective species under the same family and formed three sub-clades. However, Olyra longicaudata, belonging to the Bagridae family, did not cluster with other species from the same family. In this study, the authors have suggested a revision of the classification of O. longicaudata back to its original family, Olyridae.

CONCLUSIONS

In this study, the maximum intraspecific genetic distance of 0.03 and the minimum interspecific genetic distance of 0.14 were observed among the species. Therefore, it is evident that there is a barcoding gap among the species, which helped in the correct identification of the species. Thus, DNA barcoding helped complement the phenetic approach and also revealed a different phylogenetic relationship among the catfishes belonging to the Bagridae family.

Molecular identification of Hymenopteran insects collected by using Malaise traps from Hazarganji Chiltan National Park Quetta, Pakistan

The order Hymenoptera holds great significance for humans, particularly in tropical and subtropical regions, due to its role as a pollinator of wild and cultivated flowering plants, parasites of destructive insects and honey producers. Despite this importance, limited attention has been given to the genetic diversity and molecular identification of Hymenopteran insects in most protected areas. This study provides insights into the first DNA barcode of Hymenopteran insects collected from Hazarganji Chiltan National Park (HCNP) and contributes to the global reference library of DNA barcodes. A total of 784 insect specimens were collected using Malaise traps, out of which 538 (68.62%) specimens were morphologically identified as Hymenopteran insects. The highest abundance of species of Hymenoptera (133/538, 24.72%) was observed during August and least in November (16/538, 2.97%). Genomic DNA extraction was performed individually from 90/538 (16.73%) morphologically identified specimens using the standard phenol-chloroform method, which were subjected separately to the PCR for their molecular confirmation via the amplification of cytochrome c oxidase subunit 1 (cox1) gene. The BLAST analyses of obtained sequences showed 91.64% to 100% identities with related sequences and clustered phylogenetically with their corresponding sequences that were reported from Australia, Bulgaria, Canada, Finland, Germany, India, Israel, and Pakistan. Additionally, total of 13 barcode index numbers (BINs) were assigned by Barcode of Life Data Systems (BOLD), out of which 12 were un-unique and one was unique (BOLD: AEU1239) which was assigned for Anthidium punctatum. This indicates the potential geographical variation of Hymenopteran population in HCNP. Further comprehensive studies are needed to molecularly confirm the existing insect species in HCNP and evaluate their impacts on the environment, both as beneficial (for example, pollination, honey producers and natural enemies) and detrimental (for example, venomous stings, crop damage, and pathogens transmission).

Comparing modern identification methods for wild bees: Metabarcoding and image-based morphological taxonomic assignment

With the decline of bee populations worldwide, studies determining current wild bee distributions and diversity are increasingly important. Wild bee identification is often completed by experienced taxonomists or by genetic analysis. The current study was designed to compare two methods of identification including: (1) morphological identification by experienced taxonomists using images of field-collected wild bees and (2) genetic analysis of composite bee legs (multiple taxa) using metabarcoding. Bees were collected from conservation grasslands in eastern Iowa in summer 2019 and identified to the lowest taxonomic unit using both methods. Sanger sequencing of individual wild bee legs was used as a positive control for metabarcoding. Morphological identification of bees using images resulted in 36 unique taxa among 22 genera, and >80% of Bombus specimens were identified to species. Metabarcoding was limited to genus-level assignments among 18 genera but resolved some morphologically similar genera. Metabarcoding did not consistently detect all genera in the composite samples, including kleptoparasitic bees. Sanger sequencing showed similar presence or absence detection results as metabarcoding but provided species-level identifications for cryptic species (i.e., Lasioglossum). Genus-specific detections were more frequent with morphological identification than metabarcoding, but certain genera such as Ceratina and Halictus were identified equally well with metabarcoding and morphology. Genera with proportionately less tissue in a composite sample were less likely to be detected using metabarcoding. Image-based methods were limited by image quality and visible morphological features, while genetic methods were limited by databases, primers, and amplification at target loci. This study shows how an image-based identification method compares with genetic techniques, and how in combination, the methods provide valuable genus- and species-level information for wild bees while preserving tissue for other analyses. These methods could be improved and transferred to a field setting to advance our understanding of wild bee distributions and to expedite conservation research.

DNA barcodes reliably differentiate between nivicolous species of Diderma (Myxomycetes, Amoebozoa) and reveal regional differences within Eurasia

The nivicolous species of the genus Diderma are challenging to identify, and there are several competing views on their delimitation. We analyzed 102 accessions of nivicolous Diderma spp. that were sequenced for two or three unlinked genes to determine which of the current taxonomic treatments is better supported by molecular species delimitation methods. The results of a haplotype web analysis, Bayesian species delimitation under a multispecies coalescent model, and phylogenetic analyses on concatenated alignments support a splitting approach that distinguishes six taxa: Diderma alpinum, D. europaeum, D. kamchaticum, D. meyerae, D. microcarpum and D. niveum. The first two approaches also support the separation of Diderma alpinum into two species with allopatric distribution. An extended dataset of 800 specimens (mainly from Europe) that were barcoded with 18S rDNA revealed only barcode variants similar to those in the species characterized by the first data set, and showed an uneven distribution of these species in the Northern Hemisphere: Diderma microcarpum and D. alpinum were the only species found in all seven intensively sampled mountain regions. Partial 18S rDNA sequences serving as DNA barcodes provided clear signatures that allowed for unambiguous identification of the nivicolous Diderma spp., including two putative species in D. alpinum.

A CRISPR-based strategy for targeted sequencing in biodiversity science

Many applications in molecular ecology require the ability to match specific DNA sequences from single- or mixed-species samples with a diagnostic reference library. Widely used methods for DNA barcoding and metabarcoding employ PCR and amplicon sequencing to identify taxa based on target sequences, but the target-specific enrichment capabilities of CRISPR-Cas systems may offer advantages in some applications. We identified 54,837 CRISPR-Cas guide RNAs that may be useful for enriching chloroplast DNA across phylogenetically diverse plant species. We tested a subset of 17 guide RNAs in vitro to enrich plant DNA strands ranging in size from diagnostic DNA barcodes of 1,428 bp to entire chloroplast genomes of 121,284 bp. We used an Oxford Nanopore sequencer to evaluate sequencing success based on both single- and mixed-species samples, which yielded mean chloroplast sequence lengths of 2,530-11,367 bp, depending on the experiment. In comparison to mixed-species experiments, single-species experiments yielded more on-target sequence reads and greater mean pairwise identity between contigs and the plant species' reference genomes. But nevertheless, these mixed-species experiments yielded sufficient data to provide ≥48-fold increase in sequence length and better estimates of relative abundance for a commercially prepared mixture of plant species compared to DNA metabarcoding based on the chloroplast trnL-P6 marker. Prior work developed CRISPR-based enrichment protocols for long-read sequencing and our experiments pioneered its use for plant DNA barcoding and chloroplast assemblies that may have advantages over workflows that require PCR and short-read sequencing. Future work would benefit from continuing to develop in vitro and in silico methods for CRISPR-based analyses of mixed-species samples, especially when the appropriate reference genomes for contig assembly cannot be known a priori.

Improving the efficiency of adaptive management methods in multiple fishways using environmental DNA

Dams and weirs impede the continuity of rivers and transit of migratory fish. To overcome this obstacle, fishways are installed worldwide; however, management after installation is important. The Miyanaka Intake Dam has three fish ladders with different flow velocities and discharges and has been under adaptive management since 2012. Fish catch surveys, conducted as an adaptive management strategy, place a heavy burden on fish. Furthermore, a large number of investigators must be mobilized during the 30-day investigation period. Thus, a monitoring method using environmental DNA that exerts no burden on fish and requires only a few surveyors (to obtain water samples) and an in-house analyst was devised; however, its implementation in a fishway away from the point of analysis and with limited flow space and its effective water sampling frequency have not been reported. Therefore, in 2019, we started a trial aiming to evaluate the methods and application conditions of environmental DNA surveys for the continuous and long-term monitoring of various fish fauna upstream and downstream of the Miyanaka Intake Dam. To evaluate the fish fauna, the results of an environmental DNA survey (metabarcoding method) for 2019 to 2022 were compared to those of a catch survey in the fishway from 2012 to 2022. The results confirmed the use of environmental DNA surveys in evaluating the contribution of fishways to biodiversity under certain conditions and introduced a novel method for sample collection.

Express barcoding with NextGenPCR and MinION for species-level sorting of ecological samples

The use of DNA barcoding is well established for specimen identification and large-scale biodiversity discovery, but remains underutilized for time-sensitive applications such as rapid species discovery in field stations, identifying pests, citizen science projects, and authenticating food. The main reason is that existing express barcoding workflows are either too expensive or can only be used in very well-equipped laboratories by highly-trained staff. We here show an alternative workflow combining rapid DNA extraction with HotSHOT, amplicon production with NextGenPCR thermocyclers, and sequencing with low-cost MinION sequencers. We demonstrate the power of the approach by generating 250 barcodes for 285 specimens within 6 h including specimen identification through BLAST. The workflow required only the following major equipment that easily fits onto a lab bench: Thermocycler, NextGenPCR, microplate sealer, Qubit, and MinION. Based on our results, we argue that simplified barcoding workflows for species-level sorting are now faster, more accurate, and sufficiently cost-effective to replace traditional morpho-species sorting in many projects.

ONTbarcoder 2.0: rapid species discovery and identification with real-time barcoding facilitated by Oxford Nanopore R10.4

Most arthropod species are undescribed and hidden in specimen-rich samples that are difficult to sort to species using morphological characters. For such samples, sorting to putative species with DNA barcodes is an attractive alternative, but needs cost-effective techniques that are suitable for use in many laboratories around the world. Barcoding using the portable and inexpensive MinION sequencer produced by Oxford Nanopore Technologies (ONT) could be useful for presorting specimen-rich samples with DNA barcodes because it requires little space and is inexpensive. However, similarly important is user-friendly and reliable software for analysis of the ONT data. It is here provided in the form of ONTbarcoder 2.0 that is suitable for all commonly used operating systems and includes a Graphical User Interface (GUI). Compared with an earlier version, ONTbarcoder 2.0 has three key improvements related to the higher read quality obtained with ONT's latest flow cells (R10.4), chemistry (V14 kits) and basecalling model (super-accuracy model). First, the improved read quality of ONT's latest flow cells (R10.4) allows for the use of primers with shorter indices than those previously needed (9 bp vs. 12-13 bp). This decreases the primer cost and can potentially improve PCR success rates. Second, ONTbarcoder now delivers real-time barcoding to complement ONT's real-time sequencing. This means that the first barcodes are obtained within minutes of starting a sequencing run; i.e. flow cell use can be optimized by terminating sequencing runs when most barcodes have already been obtained. The only input needed by ONTbarcoder 2.0 is a demultiplexing sheet and sequencing data (raw or basecalled) generated by either a Mk1B or a Mk1C. Thirdly, we demonstrate that the availability of R10.4 chemistry for the low-cost Flongle flow cell is an attractive option for users who require only 200-250 barcodes at a time.

Integrated DNA barcoding methods to identify species in the processed fish products from Chinese market

DNA-based methods are reliable for a precise identification of species in processed products. In this study, we assessed five typical DNA extraction methods from multiple aspects. Full-length and mini-length DNA barcoding were performed to detect the species substitution and mislabeling of 305 processed fish products from the Chinese market covering six processed fish products. The salt extraction method that exhibited the best overall performance was applied. All samples were successfully extracted; however, only 19.3 % of samples could be amplified using the full-DNA barcode primer set, and 90.2 % of samples could be amplified using the newly designed mini-DNA barcode primer sets (401 and 320 bp). Overall, the molecular identification results revealed that 36.4 % (111/305) of the samples were inconsistent with the labels, with commercial fraud observed in all six types of processed fish products. The survey findings provide technical references for effective fish authentication monitoring, offering insights into the seafood safety in markets.

Environmental DNA metabarcoding reveals the effects of seafloor litter and trawling on marine biodiversity

Environmental DNA (eDNA) techniques are emerging as promising tools for monitoring marine communities. However, they have not been applied to study the integrated effects of anthropogenic pressures on marine biodiversity. This study examined the relationships between demersal community species composition, key environmental features, and anthropogenic impacts such as fishing effort and seafloor litter using eDNA data in the central Tyrrhenian Sea. The results indicated that both fishing effort and seafloor litter influenced species composition and diversity. The adaptive traits of marine species played a critical role in their response to debris accumulation and fishing. Mobile species appeared to use relocation strategies, while sessile species showed flexibility in the face of disturbance. Epibiotic species relied on passive transport. The use of eDNA-based methods is a valuable resource for monitoring anthropogenic impacts during scientific surveys, enhancing our ability to monitor marine ecosystems and more effectively assess the effects of pollution.

Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity

Mosquitoes (Culicidae) represent the main vector insects globally, and they also inhabit many of the terrestrial and aquatic habitats of the world. DNA barcoding and metabarcoding are now widely used in both research and routine practices involving mosquitoes. However, these methodologies rely on information available in databases consisting of barcode sequences representing taxonomically identified voucher specimens. In this study, we assess the availability of public data for mosquitoes in the main online databases, focusing specifically on the two most widely used DNA barcoding markers in Culicidae: COI and ITS2. In addition, we test hypotheses on possible factors affecting species coverage (i.e., the percentage of species covered in the online databases) for COI in different countries and the occurrence of the DNA barcode gap for COI. Our findings showed differences in the data publicly available in the repositories, with a taxonomic or species coverage of 28.4-30.11% for COI in BOLD + GenBank, and 12.32% for ITS2 in GenBank. Afrotropical, Australian and Oriental biogeographic regions had the lowest coverages, while Nearctic, Palearctic and Oceanian had the highest. The Neotropical region had an intermediate coverage. In general, countries with a higher diversity of mosquitoes and higher numbers of medically important species had lower coverage. Moreover, countries with a higher number of endemic species tended to have a higher coverage. Although our DNA barcode gap analyses suggested that the species boundaries need to be revised in half of the mosquito species available in the databases, additional data must be gathered to confirm these results and to allow explaining the occurrence of the DNA barcode gap. We hope this study can help guide regional species inventories of mosquitoes and the completion of a publicly available reference library of DNA barcodes for all mosquito species.

A comprehensive DNA barcoding reference database for Plecoptera of Switzerland

DNA barcoding is an essential tool in modern biodiversity sciences. Despite considerable work to barcode the tree of life, many groups, including insects, remain partially or totally unreferenced, preventing barcoding from reaching its full potential. Aquatic insects, especially the three orders Ephemeroptera, Plecoptera, and Trichoptera (EPT), are key freshwater quality indicators worldwide. Among them, Plecoptera (stoneflies), which are among the most sensitive aquatic insects to habitat modification, play a central role in river monitoring surveys. Here, we present an update of the Plecoptera reference database for (meta)barcoding in Switzerland, now covering all 118 species known from this country. Fresh specimens, mostly from rare or localized species, were collected, and 151 new CO1 barcodes were generated. These were merged with the 422 previously published sequences, resulting in a dataset of 573 barcoded specimens. Our CO1 dataset was delimited in 115 CO1 clusters based on a priori morphological identifications, of which 17% are newly reported for Switzerland, and 4% are newly reported globally. Among the 115 CO1 clusters, 85% showed complete congruence with morphology. Distance-based analysis indicated local barcoding gaps in 97% of the CO1 clusters. This study significantly improves the Swiss reference database for stoneflies, enhancing future species identification accuracy and biodiversity monitoring. Additionally, this work reveals cryptic diversity and incongruence between morphology and barcodes, both presenting valuable opportunities for future integrative taxonomic studies. Voucher specimens, DNA extractions and reference barcodes are available for future developments, including metabarcoding and environmental DNA surveys.

Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes

BACKGROUND

The era of high throughput sequencing offers new paths to identifying species boundaries that are complementary to traditional morphology-based delimitations. De novo species delimitation using traditional or DNA super-barcodes serve as efficient approaches to recognizing putative species (molecular operational taxonomic units, MOTUs). Tea plants (Camellia sect. Thea) form a group of morphologically similar species with significant economic value, providing the raw material for tea, which is the most popular nonalcoholic caffeine-containing beverage in the world. Taxonomic challenges have arisen from vague species boundaries in this group.

RESULTS

Based on the most comprehensive sampling of C. sect. Thea by far (165 individuals of 39 morphospecies), we applied three de novo species delimitation methods (ASAP, PTP, and mPTP) using plastome data to provide an independent evaluation of morphology-based species boundaries in tea plants. Comparing MOTU partitions with morphospecies, we particularly tested the congruence of MOTUs resulting from different methods. We recognized 28 consensus MOTUs within C. sect. Thea, while tentatively suggesting that 11 morphospecies be discarded. Ten of the 28 consensus MOTUs were uncovered as morphospecies complexes in need of further study integrating other evidence. Our results also showed a strong imbalance among the analyzed MOTUs in terms of the number of molecular diagnostic characters.

CONCLUSION

This study serves as a solid step forward for recognizing the underlying species boundaries of tea plants, providing a needed evidence-based framework for the utilization and conservation of this economically important plant group.

A DNA barcode library of Austrian geometridae (Lepidoptera) reveals high potential for DNA-based species identification

Situated in the Eastern section of the European Alps, Austria encompasses a great diversity of different habitat types, ranging from alpine to lowland Pannonian ecosystems, and a correspondingly high level of species diversity, some of which has been addressed in various DNA barcoding projects. Here, we report a DNA barcode library of all the 476 species of Geometridae (Lepidoptera) that have been recorded in Austria. As far as possible, species were sampled from different Austrian regions in order to capture intraspecific genetic variation. In total, 2500 DNA barcode sequences, representing 438 species, were generated in this study. For complete coverage of Austrian geometrid species in the subsequent analyses, the dataset was supplemented with DNA barcodes from specimens of non-Austrian origin. Species delimitations by ASAP, BIN and bPTP methods yielded 465, 510 and 948 molecular operational taxonomic units, respectively. Congruency of BIN and ASAP partitions with morphospecies assignments was reasonably high (85% of morphospecies in unique partitions), whereas bPTP appeared to overestimate the number of taxonomic units. The study furthermore identified taxonomically relevant cases of morphospecies splitting and sharing in the molecular partitions. We conclude that DNA barcoding and sequence analysis revealed a high potential for accurate DNA-based identification of the Austrian Geometridae species. Additionally, the study provides an updated checklist of the geometrid moths of Austria.

New records of native and introduced fish species in a river basin of Western Ecuador, the Chocó-Darien Ecoregion, using DNA barcoding

DNA barcoding, based on mitochondrial markers, is widely applied in species identification and biodiversity studies. The aim of this study was to establish a barcoding reference database of fishes inhabiting the Cube River from Western Ecuador in the Chocó-Darien Global Ecoregion (CGE), a threatened ecoregion with high diversity and endemism, and evaluate the applicability of using barcoding for the identification of fish species. Barcode sequences were obtained from seven orders, 17 families, 23 genera and 26 species, which were validated through phylogenetic analysis, morphological measurements, and literature review. Our results showed that 43% of fish species in this region are endemic, confirmed the presence of known species in the area, and included the addition of three new records of native (Hoplias microlepis, Rhamdia guatemalensis and Sicydium salvini) and an introduced species (Xiphophorus maculatus) to Ecuador. In addition, eight species were barcoded for the first time. Species identification based on barcoding and morphology showed discrepancy with species lists from previous studies in the CGE, suggesting that the current baseline of western fishes of Ecuador is still incomplete. Because this study analyzed fishes from a relatively small basin (165 km2), more molecular-based studies focusing on fish are needed to achieve a robust sequence reference library of species inhabiting Western Ecuador. The new sequences of this study will be useful for future comparisons and biodiversity monitoring, supporting the application of barcoding tools for studying fish diversity in genetically unexplored regions and to develop well-informed conservation programs.

Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing

Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.

Exploitation of environmental DNA (eDNA) for ecotoxicological research: A critical review on eDNA metabarcoding in assessing marine pollution

The rise in worldwide population has led to a noticeable spike in the production, consumption, and transportation of energy and food, contributing to elevated environmental pollution. Marine pollution is a significant global environmental issue with ongoing challenges, including plastic waste, oil spills, chemical pollutants, and nutrient runoff, threatening marine ecosystems, biodiversity, and human health. Pollution detection and assessment are crucial to understanding the state of marine ecosystems. Conventional approaches to pollution evaluation usually represent laborious and prolonged physical and chemical assessments, constraining their efficacy and expansion. The latest advances in environmental DNA (eDNA) are valuable methods for the detection and surveillance of pollution in the environment, offering enhanced sensibility, efficacy, and involvement. Molecular approaches allow genetic information extraction from natural resources like water, soil, or air. The application of eDNA enables an expanded evaluation of the environmental condition by detecting both identified and unidentified organisms and contaminants. eDNA methods are valuable for assessing community compositions, providing indirect insights into the intensity and quality of marine pollution through their effects on ecological communities. While eDNA itself is not direct evidence of pollution, its analysis offers a sensitive tool for monitoring changes in biodiversity, serving as an indicator of environmental health and allowing for the indirect estimation of the impact and extent of marine pollution on ecosystems. This review explores the potential of eDNA metabarcoding techniques for detecting and identifying marine pollutants. This review also provides evidence for the efficacy of eDNA assessment in identifying a diverse array of marine pollution caused by oil spills, harmful algal blooms, heavy metals, ballast water, and microplastics. In this report, scientists can expand their knowledge and incorporate eDNA methodologies into ecotoxicological research.

TICI: a taxon-independent community index for eDNA-based ecological health assessment

Global biodiversity is declining at an ever-increasing rate. Yet effective policies to mitigate or reverse these declines require ecosystem condition data that are rarely available. Morphology-based bioassessment methods are difficult to scale, limited in scope, suffer prohibitive costs, require skilled taxonomists, and can be applied inconsistently between practitioners. Environmental DNA (eDNA) metabarcoding offers a powerful, reproducible and scalable solution that can survey across the tree-of-life with relatively low cost and minimal expertise for sample collection. However, there remains a need to condense the complex, multidimensional community information into simple, interpretable metrics of ecological health for environmental management purposes. We developed a riverine taxon-independent community index (TICI) that objectively assigns indicator values to amplicon sequence variants (ASVs), and significantly improves the statistical power and utility of eDNA-based bioassessments. The TICI model training step uses the Chessman iterative learning algorithm to assign health indicator scores to a large number of ASVs that are commonly encountered across a wide geographic range. New sites can then be evaluated for ecological health by averaging the indicator value of the ASVs present at the site. We trained a TICI model on an eDNA dataset from 53 well-studied riverine monitoring sites across New Zealand, each sampled with a high level of biological replication (n = 16). Eight short-amplicon metabarcoding assays were used to generate data from a broad taxonomic range, including bacteria, microeukaryotes, fungi, plants, and animals. Site-specific TICI scores were strongly correlated with historical stream condition scores from macroinvertebrate assessments (macroinvertebrate community index or MCI; R2 = 0.82), and TICI variation between sample replicates was minimal (CV = 0.013). Taken together, this demonstrates the potential for taxon-independent eDNA analysis to provide a reliable, robust and low-cost assessment of ecological health that is accessible to environmental managers, decision makers, and the wider community.

Morpho-anatomical characterization and DNA barcoding of Artemesia vulgaris L

Artemisia vulgaris L. belongs to Asteraceae, is a herbal plant that has various benefits in the medical field, so that its use in the medical field can be explored optimally, the plant must be thoroughly identified. This study aims to identify A. vulgaris both in terms of descriptive morpho-anatomy and DNA barcoding using BLAST and phylogenetic tree reconstruction. The morpho-anatomical character was observed on root, stem, and leaf. DNA barcoding analysis was carried out through amplification and alignment of the rbcL and matK genes. All studies were conducted on three samples from Taman Husada (Medicinal Plant Garden) Graha Famili Surabaya, Indonesia. The anatomical slide was prepared by the paraffin method. Morphological studies revealed that the leaves of A. vulgaris both on the lower-middle part and on the upper part of the stem have differences, especially in the character of the stipules, petioles, and incisions they have. Meanwhile, from the study of anatomy, A. vulgaris has an anomocytic type of stomata and its distribution is mostly on the ventral part of the leaves. Through the BLAST process and phylogenetic tree reconstruction, the plant sequences being studied are closely related to several species of the genus Artemisia as indicated by a percentage identity above 98% and branch proximity between taxa in the reconstructed phylogenetic tree.

DNA barcoding for the assessment of marine and coastal fish diversity from the Coast of Mozambique

The ichthyological provinces of Mozambique are understudied hotspots of global fish diversity. In this study, we applied DNA barcoding to identify the composition of the fish fauna from the coast of Mozambique. A total of 143 species belonging to 104 genera, 59 families, and 30 orders were identified. The overall K2P distance of the COI sequences within species ranged from 0.00% to 1.51%, while interspecific distances ranged from 3.64% to 24.49%. Moreover, the study revealed 15 threatened species according to the IUCN Red List of Threatened Species, with elasmobranchs being the most represented group. Additionally, the study also uncovered four new species that were not previously recorded in this geographic area, including Boleophthalmus dussumieri, Maculabatis gerrardi, Hippocampus kelloggi, and Lethrinus miniatus. This study represents the first instance of utilizing molecular references to explore the fish fauna along the Mozambican coast. Our results indicate that DNA barcoding is a dependable technique for the identification and delineation of fish species in the waters of Mozambique. The DNA barcoding library established in this research will be an invaluable asset for advancing the understanding of fish diversity and guiding future conservation initiatives.

DNA barcoding of Notopterygii Rhizoma et Radix (Qiang-huo) and identification of adulteration in its medicinal services

Safety concerns, stemming from the presence of complex and unpredictable adulterants, permeate the entire industrial chain of traditional Chinese medicines (TCMs). The Notopterygii Rhizoma et Radix (NReR) from the Apiaceae family, commonly known as "Qiang-huo", is a widely used herbal medicine. The recent surge in its demand has given rise to a proliferation of counterfeit and substituted products in the market. Traditional identification presents inherent limitations, while DNA mini-barcoding, reliant on sequencing a short-standardized region, has received considerable attention as a new potential means to identify processed medicinal materials. In this study, we constructed a comprehensive Internal Transcribed Spacer 2 (ITS2) matrix encompassing genuine NReR and their commonly found adulterants for the first time. Leveraging this matrix, we conducted a thorough assessment of the genetic profiles and sources of NReR available in the Chinese herbal medicine market. Following established DNA barcoding protocols, the intra-specific genetic divergences within NReR species were found to be lower than the inter-specific genetic divergences from other species. Among the 120 samples that were successfully amplified, ITS2 exhibits an outstanding species-level identification efficiency of 100% when evaluated using both the BLASTN and neighbor-joining (NJ) tree methods. We concluded that ITS2 is a mini-barcode that has shown its potential and may become a universal mini-barcode for the quality control of "Qiang-huo", thereby ensuring the safety of clinical medication.

A comprehensive DNA barcoding of Indian freshwater fishes of the Indus River system, Beas

The Beas River is one of the important rivers of the Indus River system located in Himachal Pradesh, India, that harbors a diverse range of freshwater fish species. The present study employed COI gene to investigate the ichthyofaunal diversity of river Beas. Through the sequencing of 203 specimens from Beas River, we identified 43 species, belonging to 31 genera, 16 families, and 10 orders. To analyze the genetic divergence and phylogeny of identified species, 485 sequences of Indian origin were retrieved from BOLD, resulting in a dataset of 688 sequences. Our findings consistently revealed a hierarchical increase in the mean K2P genetic divergence within species (0.80%), genus (9.06%), and families (15.35%). Automated Barcode Gap discovery, Neighbour Joining, and Bayesian inference consensus tree methodologies were employed to determine the putative species and their phylogeny, successfully delimiting most of the species with only a few exceptions. The results unveiled six species exhibiting high intra-species divergence (> 2%), suggesting the presence of sibling species and falsely identified sequences on online databases. The present study established the first DNA barcoding-based inventory of freshwater fish species in the Beas River providing comprehensive insights into economically exploited endangered and vulnerable species. In order to ensure the sustainable use of aquatic resources in the Beas River, we recommend the implementation of species measures to protect biodiversity and genetic resources.

Plant-derived environmental DNA complements diversity estimates from traditional arthropod monitoring methods but outperforms them detecting plant-arthropod interactions

Our limited knowledge about the ecological drivers of global arthropod decline highlights the urgent need for more effective biodiversity monitoring approaches. Monitoring of arthropods is commonly performed using passive trapping devices, which reliably recover diverse communities, but provide little ecological information on the sampled taxa. Especially the manifold interactions of arthropods with plants are barely understood. A promising strategy to overcome this shortfall is environmental DNA (eDNA) metabarcoding from plant material on which arthropods leave DNA traces through direct or indirect interactions. However, the accuracy of this approach has not been sufficiently tested. In four experiments, we exhaustively test the comparative performance of plant-derived eDNA from surface washes of plants and homogenized plant material against traditional monitoring approaches. We show that the recovered communities of plant-derived eDNA and traditional approaches only partly overlap, with eDNA recovering various additional taxa. This suggests eDNA as a useful complementary tool to traditional monitoring. Despite the differences in recovered taxa, estimates of community α- and β-diversity between both approaches are well correlated, highlighting the utility of eDNA as a broad scale tool for community monitoring. Last, eDNA outperforms traditional approaches in the recovery of plant-specific arthropod communities. Unlike traditional monitoring, eDNA revealed fine-scale community differentiation between individual plants and even within plant compartments. Especially specialized herbivores are better recovered with eDNA. Our results highlight the value of plant-derived eDNA analysis for large-scale biodiversity assessments that include information about community-level interactions.

New prospects of environmental RNA metabarcoding research in biological diversity, ecotoxicological monitoring, and detection of COVID-19: a critical review

Ecosystems are multifaceted and complex systems and understanding their composition is crucial for the implementation of efficient conservation and management. Conventional approaches to biodiversity surveys can have limitations in detecting the complete range of species present. In contrast, the study of environmental RNA (eRNA) offers a non-invasive and comprehensive method for monitoring and evaluating biodiversity across different ecosystems. Similar to eDNA, the examination of genetic material found in environmental samples can identify and measure many species, including ones that pose challenges to traditional methods. However, eRNA is degraded quickly and therefore shows promise in detection of living organisms closer to their actual location than eDNA methods. This method provides a comprehensive perspective on the well-being of ecosystems, facilitating the development of focused conservation approaches to save at-risk species and uphold ecological equilibrium. Furthermore, eRNA has been recognized as a valuable method for the identification of COVID-19 in the environment, besides its established uses in biodiversity protection. The SARS-CoV-2 virus, which is accountable for the worldwide epidemic, releases RNA particles into the surrounding environment via human waste, providing insights into the feasibility of detecting it in wastewater and other samples taken from the environment. In this article, we critically reviewed the recent research activities that use the eRNA method, including its utilization in biodiversity conservation, ecological surveillance, and ecotoxicological monitoring as well as its innovative potential in identifying COVID-19. Through this review, the reader can understand the recent developments, prospects, and challenges of eRNA research in ecosystem management and biodiversity conservation.

Extracting, filtering and simulating cellular barcodes using CellBarcode tools

Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of barcode types supported or the analysis strategies implemented. As such, there is a need for more versatile and efficient tools for barcode extraction, as well as for tools to investigate which factors impact barcode detection and which filtering strategies to best apply. Here we introduce the package CellBarcode and its barcode simulation kit, CellBarcodeSim, that allows efficient and versatile barcode extraction and filtering for a range of barcode types from bulk or single-cell sequencing data using a variety of filtering strategies. Using the barcode simulation kit and biological data, we explore the technical and biological factors influencing barcode identification and provide a decision tree on how to optimize barcode identification for different barcode settings. We believe that CellBarcode and CellBarcodeSim have the capability to enhance the reproducibility and interpretation of barcode results across studies.

How reliable is metabarcoding for pollen identification? An evaluation of different taxonomic assignment strategies by cross-validation

Metabarcoding is a powerful tool, increasingly used in many disciplines of environmental sciences. However, to assign a taxon to a DNA sequence, bioinformaticians need to choose between different strategies or parameter values and these choices sometimes seem rather arbitrary. In this work, we present a case study on ITS2 and rbcL databases used to identify pollen collected by bees in Belgium. We blasted a random sample of sequences from the reference database against the remainder of the database using different strategies and compared the known taxonomy with the predicted one. This in silico cross-validation (CV) approach proved to be an easy yet powerful way to (1) assess the relative accuracy of taxonomic predictions, (2) define rules to discard dubious taxonomic assignments and (3) provide a more objective basis to choose the best strategy. We obtained the best results with the best blast hit (best bit score) rather than by selecting the majority taxon from the top 10 hits. The predictions were further improved by favouring the most frequent taxon among those with tied best bit scores. We obtained better results with databases containing the full sequences available on NCBI rather than restricting the sequences to the region amplified by the primers chosen in our study. Leaked CV showed that when the true sequence is present in the database, blast might still struggle to match the right taxon at the species level, particularly with rbcL. Classical 10-fold CV-where the true sequence is removed from the database-offers a different yet more realistic view of the true error rates. Taxonomic predictions with this approach worked well up to the genus level, particularly for ITS2 (5-7% of errors). Using a database containing only the local flora of Belgium did not improve the predictions up to the genus level for local species and made them worse for foreign species. At the species level, using a database containing exclusively local species improved the predictions for local species by ∼12% but the error rate remained rather high: 25% for ITS2 and 42% for rbcL. Foreign species performed worse even when using a world database (59-79% of errors). We used classification trees and GLMs to model the % of errors vs. identity and consensus scores and determine appropriate thresholds below which the taxonomic assignment should be discarded. This resulted in a significant reduction in prediction errors, but at the cost of a much higher proportion of unassigned sequences. Despite this stringent filtering, at least 1/5 sequences deemed suitable for species-level identification ultimately proved to be misidentified. An examination of the variability in prediction accuracy between plant families showed that rbcL outperformed ITS2 for only two of the 27 families examined, and that the % correct species-level assignments were much better for some families (e.g. 95% for Sapindaceae) than for others (e.g. 35% for Salicaceae).

DNA and RNA Stability of Marine Microalgae in Cold-Stored Sediments and Its Implications in Metabarcoding Analyses

The ever-increasing applications of metabarcoding analyses for environmental samples demand a well-designed assessment of the stability of DNA and RNA contained in cells that are deposited or buried in marine sediments. We thus conducted a qPCR quantification of the DNA and RNA in the vegetative cells of three microalgae entrapped in facsimile marine sediments and found that >90% of DNA and up to 99% of RNA for all microalgal species were degraded within 60 days at 4 °C. A further examination of the potential interference of the relic DNA of the vegetative cells with resting cyst detection in sediments was performed via a metabarcoding analysis in artificial marine sediments spiked with the vegetative cells of two Kareniaceae dinoflagellates and the resting cysts of another three dinoflagellates. The results demonstrated a dramatic decrease in the relative abundances of the two Kareniaceae dinoflagellates in 120 days, while those of the three resting cysts increased dramatically. Together, our results suggest that a positive detection of microalgae via metabarcoding analysis in DNA or RNA extracted from marine sediments strongly indicates the presence of intact or viable cysts or spores due to the rapid decay of relic DNA/RNA. This study provides a solid basis for the data interpretation of metabarcoding surveys, particularly in resting cyst detection.

Description and genomic characterization of Cohnella caldifontis sp. nov., isolated from hot springs in Yunnan province, south-west China

A bacterial strain, Gram staining positive, strictly aerobic, rod-shaped, motile bacterium with flagellum and endospore-forming, designated strain YIM B05605T, was isolated from soil sampled in Hamazui hot springs, Tengchong City, Yunnan province, China. Optimum growth for the strain occurred at pH 7.0 and 45 °C. MK-7 was the main menaquinone in the strain YIM B05605T. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PME), unidentified glycolipid (GL), three unknown aminophospholipids (APLs) and unidentified polarlipid (PL) were part of the polar lipid profile. The major fatty acids were anteiso-C15:0 and iso-C16:0. The DNA G + C content of the type strain was 58.76%. Genome-based phylogenetic analysis confirmed that strain YIM B05605T formed a distinct phylogenetic cluster within the genus Cohnella. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strain YIM B05605T with the most related species C. fontinalis YT-1101T were 73.42% and 15.7%. Functional analysis by NR, Swiss-prot, Pfam, eggNOG, GO, KEGG databases revealed that strain YIM B05605T has 13 genes related to the sulfur cycle, 2 genes related to the nitrogen cycle. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizations, strain YIM B05605T could be classified as a novel species of the genus Cohnella, for which the name Cohnella caldifontis sp. nov., is proposed. The type strain is YIM B05605T (= CGMCC 1.60052T = KCTC 43462T = NBRC 115921T).

Disclosing the hidden nucleotide sequences: a journey into DNA barcoding of raptor species in public repositories

BACKGROUND

In nucleotide public repositories, studies discovered data errors which resulted in incorrect species identification of several accipitrid raptors considered for conservation. Mislabeling, particularly in cases of cryptic species complexes and closely related species, which were identified based on morphological characteristics, was discovered. Prioritizing accurate species labeling, morphological taxonomy, and voucher documentation is crucial to rectify spurious data.

OBJECTIVE

Our study aimed to identify an effective DNA barcoding tool that accurately reflects the efficiency status of barcodes in raptor species (Accipitridae).

METHODS

Barcode sequences, including 889 sequences from the mitochondrial cytochrome c oxidase I (COI) gene and 1052 sequences from cytochrome b (Cytb), from 150 raptor species within the Accipitridae family were analyzed.

RESULTS

The highest percentage of intraspecific nearest neighbors from the nearest neighbor test was 88.05% for COI and 95.00% for Cytb, suggesting that the Cytb gene is a more suitable marker for accurately identifying raptor species and can serve as a standard region for DNA barcoding. In both datasets, a positive barcoding gap representing the difference between inter-and intra-specific sequence divergences was observed. For COI and Cytb, the cut-off score sequence divergences for species identification were 4.00% and 3.00%, respectively.

CONCLUSION

Greater accuracy was demonstrated for the Cytb gene, making it the preferred primary DNA barcoding marker for raptors.

Wing geometric morphometrics and DNA barcoding to distinguish three closely related species of Armigeres mosquitoes (Diptera: Culicidae) in Thailand

Armigeres subalbatus, a mosquito species widely found in Thailand and other Asian countries, serves as a vector for filarial parasites, affecting both humans and animals. However, the surveillance of this vector is complicated because of its morphological similarity to two other species, Armigeres dohami and Armigeres kesseli. To differentiate these morphologically similar species, our study employed both wing geometric morphometrics (GM) and DNA barcoding, offering a comprehensive approach to accurately identify these closely related Armigeres species in Thailand. Our GM analyses based on shape demonstrated significant accuracy in differentiating Armigeres species. Specifically, the outline-based GM method focusing on the 3rd posterior cell exhibited an accuracy rate of 82.61%, closely followed by the landmark-based GM method with 81.54%. Both these GM techniques effectively distinguished Ar. subalbatus from Ar. dohami and Ar. kesseli. Regarding DNA barcoding, our investigation of pairwise intra- and interspecific divergences revealed a "barcoding gap". Furthermore, the results of species confirmation using both species delimitation methods including the automatic barcode gap discovery method (ABGD) and the Multi-rate Poisson tree process (mPTP) were consistent with those of morphological identification, sequence comparisons with the GenBank and Barcode of Life Data System (BOLD) databases, and the neighbor-joining tree construction. These consistent results emphasize the efficacy of DNA barcoding in the precise identification of Armigeres species.

Is the metabarcoding ripe enough to be applied to the authentication of foodstuff of animal origin? A systematic review

Food authentication using molecular techniques is of great importance to fight food fraud. Metabarcoding, based on the next-generation sequencing (NGS) technologies, allowing large-scale taxonomic identification of complex samples via massive parallel sequencing of fragments (called DNA barcodes) simultaneously, has become increasingly popular in many scientific fields. A systematic review to answer the question "Is the metabarcoding ripe enough to be applied to the authentication of foodstuff of animal origin?" is presented. The inclusion criteria were focused on the selection of scientific papers (SPs) only applying metabarcoding to foodstuff of animal origin collected on the market. The 23 included SPs were first analyzed with respect to the metabarcoding phases: library preparation (target genes, primer pairs, and fragment length), sequencing (NGS platforms), and final data analysis (bioinformatic pipelines). Given the importance of primer selection, the taxonomic coverage of the used primers was also evaluated. In addition, the SPs were scored based on the use of quality control measures (procedural blanks, positive controls, replicates, curated databases, and thresholds to filter the data). A lack of standardized protocols, especially with respect to the target barcode/s and the universal primer/s, and the infrequent application of the quality control measures, leads to answer that metabarcoding is not ripe enough for authenticating foodstuff of animal origin. However, the observed trend of the SP quality improvement over the years is encouraging. Concluding, a proper protocol standardization would allow a wider use of metabarcoding by both official and private laboratories, enabling this method to become the primary for the authentication of foodstuffs of animal origin.

Assessing three soil removal methods for environmental DNA analysis of mock forensic geology evidence

Soil is useful in criminal investigations as it is highly variable and readily transferred. Forensic geologists use several different techniques to removal soil from evidence prior to the analysis of inorganic components. There has been recent interest from the forensic science community to analyze environmental deoxyribonucleic acid (eDNA) associated with soil to augment existing forensic analyses. Notably however, limited research has been conducted to compare commonly used soil removal methods for downstream eDNA analysis. In this study, three soil removal methods were assessed: picking/scraping, sonication, and swabbing. Three mock evidence types (t-shirts, boot soles, and trowels) were sampled in triplicate with each removal method (n = 27). Soil samples underwent DNA isolation, quantification, and amplification of four genomic barcode regions: 16S for bacteria, ITS1 for fungi, ITS2 for plants, and COI for arthropods. Amplicons were prepared into libraries for DNA sequencing on an Illumina® MiniSeq. DNA concentrations were highest in picked/scraped samples and were statistically significant compared with swabbed and sonicated samples. Amplicon sequence variants (ASVs) were identified, and removal methods had no impact on the recovery of the total number of target ASVs. Additionally, when assessing each sample in multidimensional space, picked/scraped samples tended to cluster separately from swabbed and sonicated samples. The soil core used a reference in this study also clustered with the picked/scraped samples, indicating that these samples may be more reflective of the communities collected from soil cores. Based on these data, we identified that picking/scraping is an acceptable soil removal method for eDNA analysis.

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics

Recent technological innovations have enabled the high-throughput quantification of gene expression and epigenetic regulation within individual cells, transforming our understanding of how complex tissues are constructed1-6. However, missing from these measurements is the ability to routinely and easily spatially localize these profiled cells. We developed a strategy, Slide-tags, in which single nuclei within an intact tissue section are tagged with spatial barcode oligonucleotides derived from DNA-barcoded beads with known positions. These tagged nuclei can then be used as an input into a wide variety of single-nucleus profiling assays. Application of Slide-tags to the mouse hippocampus positioned nuclei at less than 10 μm spatial resolution and delivered whole-transcriptome data that are indistinguishable in quality from ordinary single-nucleus RNA-sequencing data. To demonstrate that Slide-tags can be applied to a wide variety of human tissues, we performed the assay on brain, tonsil and melanoma. We revealed cell-type-specific spatially varying gene expression across cortical layers and spatially contextualized receptor-ligand interactions driving B cell maturation in lymphoid tissue. A major benefit of Slide-tags is that it is easily adaptable to almost any single-cell measurement technology. As a proof of principle, we performed multiomic measurements of open chromatin, RNA and T cell receptor (TCR) sequences in the same cells from metastatic melanoma, identifying transcription factor motifs driving cancer cell state transitions in spatially distinct microenvironments. Slide-tags offers a universal platform for importing the compendium of established single-cell measurements into the spatial genomics repertoire.

Airborne environmental DNA captures terrestrial vertebrate diversity in nature

The current biodiversity and climate crises highlight the need for efficient tools to monitor terrestrial ecosystems. Here, we provide evidence for the use of airborne eDNA analyses as a novel method for detecting terrestrial vertebrate communities in nature. Metabarcoding of 143 airborne eDNA samples collected during 3 days in a mixed forest in Denmark yielded 64 bird, mammal, fish and amphibian taxa, of which the detected 57 'wild' taxa represent over a quarter of the around 210 terrestrial vertebrates that occur in the overall area. We provide evidence for the spatial movement and temporal patterns of airborne eDNA and for the influence of weather conditions on vertebrate detections. This study demonstrates airborne eDNA for high-resolution biomonitoring of vertebrates in terrestrial systems and elucidates its potential to guide global nature management and conservation efforts in the ongoing biodiversity crisis.

Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons

Periodic monitoring can provide important information for the protection of endangered fish, sustainable use of fishery resources and management of alien species. Previous studies have attempted to monitor fish using non-invasive environmental DNA (eDNA) technology, generally employing quantitative PCR to quantify the eDNA concentration. However, the throughput was limited. High-throughput metabarcoding technology can detect the DNA of multiple species simultaneously in a single experiment but does not provide sufficient quantification. In this study, we applied a quantitative metabarcoding approach to simultaneously quantify the eDNA concentration of an entire fish assemblage in a small reservoir over two summer seasons. Traditional surveys were also conducted to investigate the individuals of fish. The eDNA concentrations were quantified using quantitative metabarcoding, and the fish species detected using this approach were highly consistent with the results of traditional fish monitoring. A significant positive relationship was observed between the eDNA concentration and fish species abundance. Seasonal changes in fish community structure were estimated using eDNA concentrations, which may reveal the activity seasons of different fish. The eDNA concentrations of different fish species peaked at different water temperatures, reflecting the differential responses of fish species to this environmental factor. Finally, by detecting outlier eDNA concentrations, the spawning activities of 13 fish species were estimated, 12 of which were roughly consistent with the current knowledge of fish spawning periods. These results indicate that quantitative eDNA metabarcoding with dozens of sampling times is useful for the simultaneous ecological monitoring of multiple fish species.

New species and new records of genus Buellia (lichenized Ascomycota, Caliciaceae) from Pakistan using electron microscopy and DNA barcoding techniques

Three new species Buellia darelensis, B. densitheca, B. kashmirensis and two new records B. elegans and B. taishanensis are added to the lichen biota of Pakistan. Buellia darelensis and B. kashmirensis share the same habitats found on the rock while B. densitheca colonized on bark of Pinus hardwoods in the Himalayan forest, Pakistan. Morphological, chemical, and phylogenetic analyses were carried out to elucidate the placement of these species and to support the delimitation of the new taxa. Detailed descriptions and figures for the species are given, and a key to all known buellioid species from Pakistan is provided. RESEARCH HIGHLIGHTS: During recent explorations of lichens from different regions of Pakistan, we observed specimens that could not be readily assigned to any known species. A phylogenetic analysis of the internal transcribed spacer nrDNA region confirms their position within the genus Buellia, and morphological data showed distinctiveness of three species from other known species of the genus. We therefore describe these specimens as new species to science, and two species are as new records for the country. Pakistan exhibits a large altitudinal variation, with climatic conditions and a diverse vegetation that supports a diverse and conspicuous lichen biota. The nature reserves have abundant biological resources, and it is expected that more new species of lichen may be discovered in the future.

Conservation in a litre of air

Since Ficetola et al. (2008) alerted ecologists and conservation biologists to the existence of environmental DNA (eDNA), the number of studies using eDNA has exploded, with a rapidly increasing diversity of research, monitoring, and management objectives. Initial applications focused on amphibians and fishes while today's taxonomic targets span the phylogenetic tree. The environmental media that are sampled have expanded from freshwater to saltwater to soils, and, most recently, to air. In this issue of Molecular Ecology Resources, Lynggaard et al. (Molecular Ecology Resources, 2023) use eDNA captured on air filters to census vertebrate biodiversity in a forest. With a three day, six sample period, 143 sample effort in a nature park in a rural area of Zealand, Denmark, their wild species detections comprised about 25% of the terrestrial vertebrates that are known to occur in the area, including about 33% of the mammal, 17% of the bird, and 60% of the amphibian species. This study demonstrates that air sampling for eDNA has the potential to become a powerful standard method for terrestrial biodiversity assessment that is complementary to traditional methods (e.g., trapping, visual and acoustic observation, collection of scat and hair).

Species delimitation by DNA barcoding reveals undescribed diversity in Stelliferinae (Sciaenidae)

Stelliferinae is the third most speciose subfamily of Sciaenidae, with 51 recognized species arranged in five genera. Phylogenies derived from both morphological and molecular data support the monophyly of this subfamily, although there is no general consensus on the intergeneric relationships or the species diversity of this group. We used the barcoding region of the cytochrome oxidase C subunit I (COI) gene to verify the delimitation of Stelliferinae species based on the Automatic Barcode Gap Discovery (ABGD), Generalized Mixed Yule Coalescence (GMYC), and Bayesian Poisson Tree Process (bPTP) methods. In general, the results of these different approaches were congruent, delimiting 30-32 molecular operational taxonomic units (MOTUs), most of which coincided with valid species. Specimens of Stellifer menezesi and Stellifer gomezi were attributed to a single species, which disagrees with the most recent review of this genus. The evidence also indicated that Odontoscion xanthops and Corvula macrops belong to a single MOTU. In contrast, evidence also indicates presence of distinct lineages in both Odontoscion dentex and Bairdiella chrysoura. Such results are compatible with the existence of cryptic species, which is supported by the genetic divergence and haplotype genealogy. Therefore, the results of the present study indicate the existence of undescribed diversity in the Stelliferinae, which reinforces the need for an ample taxonomic review of the fish in this subfamily.

taxalogue: a toolkit to create comprehensive CO1 reference databases

Background

Taxonomic identification through DNA barcodes gained considerable traction through the invention of next-generation sequencing and DNA metabarcoding. Metabarcoding allows for the simultaneous identification of thousands of organisms from bulk samples with high taxonomic resolution. However, reliable identifications can only be achieved with comprehensive and curated reference databases. Therefore, custom reference databases are often created to meet the needs of specific research questions. Due to taxonomic inconsistencies, formatting issues, and technical difficulties, building a custom reference database requires tremendous effort. Here, we present taxalogue, an easy-to-use software for creating comprehensive and customized reference databases that provide clean and taxonomically harmonized records. In combination with extensive geographical filtering options, taxalogue opens up new possibilities for generating and testing evolutionary hypotheses.

Methods

taxalogue collects DNA sequences from several online sources and combines them into a reference database. Taxonomic incongruencies between the different data sources can be harmonized according to available taxonomies. Dereplication and various filtering options are available regarding sequence quality or metadata information. taxalogue is implemented in the open-source Ruby programming language, and the source code is available at https://github.com/nwnoll/taxalogue. We benchmark four reference databases by sequence identity against eight queries from different localities and trapping devices. Subsamples from each reference database were used to compare how well another one is covered.

Results

taxalogue produces reference databases with the best coverage at high identities for most tested queries, enabling more accurate, reliable predictions with higher certainty than the other benchmarked reference databases. Additionally, the performance of taxalogue is more consistent while providing good coverage for a variety of habitats, regions, and sampling methods. taxalogue simplifies the creation of reference databases and makes the process reproducible and transparent. Multiple available output formats for commonly used downstream applications facilitate the easy adoption of taxalogue in many different software pipelines. The resulting reference databases improve the taxonomic classification accuracy through high coverage of the query sequences at high identities.

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

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

Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest

Soils harbour a rich arthropod fauna, but many species are still not formally described (Linnaean shortfall) and the distribution of those already described is poorly understood (Wallacean shortfall). Metabarcoding holds much promise to fill this gap, however, nuclear copies of mitochondrial genes, and other artefacts lead to taxonomic inflation, which compromise the reliability of biodiversity inventories. Here, we explore the potential of a bioinformatic approach to jointly "denoise" and filter nonauthentic mitochondrial sequences from metabarcode reads to obtain reliable soil beetle inventories and address open questions in soil biodiversity research, such as the scale of dispersal constraints in different soil layers. We sampled cloud forest arthropod communities from 49 sites in the Anaga peninsula of Tenerife (Canary Islands). We performed whole organism community DNA (wocDNA) metabarcoding, and built a local reference database with COI barcode sequences of 310 species of Coleoptera for filtering reads and the identification of metabarcoded species. This resulted in reliable haplotype data after considerably reducing nuclear mitochondrial copies and other artefacts. Comparing our results with previous beetle inventories, we found: (i) new species records, potentially representing undescribed species; (ii) new distribution records, and (iii) validated phylogeographic structure when compared with traditional sequencing approaches. Analyses also revealed evidence for higher dispersal constraint within deeper soil beetle communities, compared to those closer to the surface. The combined power of barcoding and metabarcoding contribute to mitigate the important shortfalls associated with soil arthropod diversity data, and thus address unresolved questions for this vast biodiversity fraction.

FishDNAIDs: DNA barcoding as a tool in the development and validation in silico and in vitro of detection systems to four species of Characiformes of commercial importance in the Brazilian Amazon

BACKGROUND

The COI mitochondrial gene has been chosen as the "DNA barcode in animals" and the large quantity of genetic information in public databanks gives solid support for the use of DNA barcoding as a promising tool for the development of a specific molecular detection system.

METHODS AND RESULTS

The present study aimed to develop a Specific Molecular Detection System (SMDS: FishDNAIDs) (primers and probe sets) for the following four target species: Prochilodus nigricans, Potamorhina altamazonica, Psectrogaster rutiloides and Triportheus angulatus, in qPCR assays. In silico and in vitro tests (using gDNA) were performed to test these sets. The database generated contained the cytochrome c oxidase subunit I (COI) nucleotide sequence for 183 specimens of Characiformes, distributed in 34 species representing eight families. In silico, primers designed for the target species amplified different species from the same genus, except for P. rutiloides, which amplified only the target species. In the in vitro test, using the SYBRGreentm and TaqMan® fluorescence systems, both sets detected the respective target species (P. nigricans, P. altamazonica, P. rutiloides and T. angulatus). In the qPCR assays using SYBRGreentm, species considered to be related were also detected, in addition to the target species, with the exception of P. amazonica and P. essequibensis (correlated to P. rutiloides). All target species were detected in the qPCR assays using the TaqMan® system; however, with the SMDS PALT, the target species P. altamazonica was detected with low CT values (22.21 ± 0.17) as well as the correlates of P. latior and P. pristigaster, though with high CT values (23.51 ± 0.19 and 30.21 ± 0.95). This assay uniquely identifies known adult tissue samples from all four species.

CONCLUSIONS

The primers and probe sets developed can act as powerful tools for detecting the target Characiformes species.