MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

Environmental DNA exploring the distribution of Indo-Pacific humpback dolphins and fish diversity from the Pearl River Estuary, China

Understanding the spatial distribution patterns of endangered species is crucial for their protection. However, gathering such information for cetaceans remains challenging due to their underwater life and elusive nature. Here, by conuding a three-year field ecological survey, we first employed environmental DNA (eDNA) technology to elucidate the distribution and its influencing factors of the Indo-Pacific humpback dolphins from their largest habitat, the Pearl River Estuary (PRE), China. The self-designed SCDloop primers exhibited high specificity for the dolphins and demonstrated elevated eDNA concentrations in proximity to areas with significant human activity in the PRE. Fish species detected in the PRE included most prey items consumed by the dolphins. A significant positive correlation between the occurrence of humpback dolphins and fish diversity was found, indicating the crucial role of fishery resources in the dolphins' habitat selection. Our findings support the use of eDNA technology as a supplementary tool for monitoring marine cetaceans.

DNA metabarcoding analysis revealed a silent prevalence of environmental pathogenic Leptospira in urban area of Okinawa Island, Japan

Objective

Human activities, such as agriculture, environmental manipulation, and city development, have impacted the distribution of flora, fauna, and microbes (including potential human pathogens) at the global level. This study focused on the bacterial genus Leptospira, an organism causing leptospirosis that is prevalent in tropical and subtropical regions. We hypothesized that although only a few cases of leptospirosis have been reported in the urban region of main island of Okinawa Prefecture (Okinawa Island, OKI), Japan, Leptospira is present in these regions.

Methods

Thirty-four samples were collected from rivers in urban OKI and rural Ishigaki Island (ISG) and analyzed to determine the distribution of Leptospira and mammals using environmental DNA (eDNA) metabarcoding. High-throughput sequencing analysis was performed to sequence the polymerase chain reaction products of partial leptospiral 16S rRNA and vertebrate mitochondrial 12S rRNA genes from 16 and 18 river samples of OKI and ISG, respectively, including the waters collected from Leptospira-endemic areas in ISG.

Results

Leptospira noguchii and L. interrogans-related, two Leptospira species of the P1+ clade that are pathogenic to humans and mammals, were repeatedly detected in OKI and ISG, supporting our hypothesis. The sequence numbers of the five Leptospira species of P1- and P2 clades showed significant correlations with those of cattle (Bos taurus) in OKI; however, the potential host animals for P1+ species remain unclear. The total number of leptospiral sequences obtained from the ISG samples was correlated with the distance from the mountainous woodlands.

Conclusion

The pathogenic P1+ Leptospira was distributed in urban OKI, in addition to rural ISG. The factors correlated with leptospiral detection, that is, cattle eDNAs and the distance from mountainous forests in OKI and ISG, respectively, suggest the silent prevalence of Leptospira in urban and developing regions related to human activities. The findings of the present study provide insights into public health in cities with respect to climate change and possible flood damage.

Freshwater fish community assessment using eDNA metabarcoding vs. capture-based methods: Differences in efficiency and resolution coupled to habitat and ecology

Environmental DNA (eDNA) metabarcoding has revolutionized ecological and environmental research by describing communities without relying on direct observations, making it a powerful, non-invasive, and cost-effective tool in biodiversity monitoring. However, the adoption of eDNA as a standard protocol in long-term monitoring programs, which have traditionally relied on capture-based methods, presents challenges in terms of data comparability. Here, we compared freshwater fish communities assessed through eDNA metabarcoding and electrofishing, across 35 sampling sites in the lower Tagus River basin, Portugal. For the majority of species or species-groups analysed individually (13 out of 17), a significant correspondence was observed between electrofishing and eDNA metabarcoding detections. A weaker correspondence was found between the number of specimens captured by electrofishing with the number of eDNA metabarcoding reads, with seven out of 13 taxa showing significant relationships. Species richness estimates based on the two methods were very similar at the basin level. The methods yielded significantly different species compositions, although these differences were driven by samples collected in the Tagus main channel, which is wider and has higher flow rates than tributaries. Benthic and shoreline fish communities showed similar species composition in the two methods, but this was not the case for pelagic communities, probably due to the higher water turnover of the pelagic zone and electrofishing inefficiency. Our results highlight the high potential of eDNA metabarcoding as a complementary method to electrofishing for freshwater fish monitoring, though further validation is needed to assess biases related to site-specific hydrological conditions and the ecology of the target species.

Underwater drone-based eDNA metabarcoding reveals regional differences in fish communities and early detection of alien species around the Korean Peninsula

Coastal ecosystems surrounding the Korean Peninsula are undergoing rapid environmental changes driven by global climate warming, highlighting the need for efficient methods to monitor marine biodiversity. This study aimed to analyze fish communities across four coastal regions: the East Sea, South Sea, West Sea, and Jeju using environmental DNA (eDNA) metabarcoding. Underwater drones were employed to collect water samples. A total of 63 sampling sites were surveyed, detecting 167 fish species from 72 families, encompassing tropical, subtropical, temperate, boreal, polar, and deep-water taxa. The East Sea hosted a mix of cold- and warm-water species, while Jeju exhibited a relatively high proportion of tropical and subtropical fish. Additionally, 13 alien species were identified, underscoring the utility of eDNA for the early detection of non-native taxa expanding their ranges in response to ongoing warming trends. This study further validated that eDNA sampling using underwater drones offers a rapid, non-invasive approach to biodiversity assessments, effectively addressing many of the limitations associated with traditional survey techniques. Collectively, these findings highlight the potential of eDNA to generate critical and timely data on fish assemblages the emergence of alien species, providing valuable insights to inform proactive resource management, and climate change research in marine ecosystems.

Assessing the effects of urban effluent pollution on freshwater biodiversity and community networks using eDNA metabarcoding

Aquatic ecosystems provide essential services, yet they face increasing pressures from anthropogenic activities, including land-use change, eutrophication, browning, and contaminant pollution. While the ecological effects of these stressors are documented, the impacts of complex contaminant mixtures, particularly those from wastewater treatment plant (WWTP) effluents, remain poorly understood. Mixtures effects are typically assessed using traditional species-by-species toxicological approaches, which, though the gold standard, are time-intensive, require test animals, and have limited extrapolability. New Approach Methodologies (NAMs), such as environmental DNA (eDNA), offer a non-invasive alternative, enabling broader assessments of taxa responses across trophic levels. Here, we apply an eDNA approach to assess community-wide responses to effluent discharge in the St. Lawrence River, one of North America's most diverse freshwater ecosystems. We sampled water and aquatic communities along the effluent plume of the Montréal WWTP, analyzing taxa-specific responses across trophic levels using high-throughput sequencing. We evaluated the influence of water physico-chemistry and per- and polyfluoroalkyl substances (PFAS) on aquatic beta diversity and network structure. To validate our eDNA results, we compared fish-specific detections with traditional fishing surveys. Our findings highlight how wastewater-derived contaminants influence biodiversity patterns and species interactions, with taxonomic responses varying across trophic levels. Network analyses revealed shifts in ecological stability, with changes in species connectivity and modularity influenced by effluent exposure. This study demonstrates the value of eDNA for characterizing biodiversity responses to anthropogenic stressors and provides insights into the broader implications of point-source pollution for freshwater ecosystem resilience.

Environmental DNA illuminates the darkness of mesophotic assemblages of fishes from West Indian Ocean

The advent of environmental DNA (eDNA) represents a pivotal advancement in probing mesophotic communities, offering a non-intrusive avenue for studying marine biodiversity at greater depths. Using this approach, we characterized and compared the mesophotic reef fish assemblages of two West Indian Ocean islands, Mayotte and La Réunion, which are characterized by different geo-morphological contexts. The sequences obtained were assigned taxonomically and grouped into molecular operational taxonomic units to perform richness and beta diversity analyses. The functional diversity of the assemblages was assessed using five traits, enabling each sequence to be assigned to a functional entity corresponding to a specific trait combination. On both islands, the fish assemblages exhibited a comparable level of taxonomic and functional richness, consisting mainly of piscivorous and planktivorous fishes. These assemblages were primarily composed of families such as Serranidae, consistent with expectations for the mesophotic zone. However, beta diversity analyses revealed that the two islands exhibited different taxonomic and functional structures. For example, La Réunion was characterized by a greater importance of the Muraenidae, while Mayotte displayed a higher representation of families strongly associated with coral reefs (e.g., Zanclidae or Malacanthidae). These results suggest that depth-related forcing constrains fish assemblages to some extent, but that differences in structure remains determined by other, more local factors, likely linked to the geo-morphological contexts of the islands and their habitats. This study also revealed that eDNA is a promising method for studying difficult-to-observe taxa, such as moray eels or lanternfish, and may also be relevant for monitoring species depth ranges. Overall, results highlighted the "local scale", "functionally integrative" and "temporally integrative" characteristics of eDNA for studying mesophotic reef fish assemblages. However, this study also highlights the limitations of reference DNA databases, pointing to future prospects for fully exploiting the potential of eDNA approaches in the mesophotic zones of the Indian Ocean.

Observation Bias in Metabarcoding

DNA metabarcoding is subject to observation bias associated with PCR and sequencing, which can result in observed read proportions differing from actual species proportions in the DNA extract. Here, we amplify and sequence a mock community of known composition containing marine fishes and cetaceans using four different primer sets and a variety of PCR conditions. We first compare metabarcoding observations to two different sets of expected species proportions based on total genomic DNA and on target mitochondrial template DNA. We find that calibrating observed read proportions based on template DNA concentration is most appropriate as it isolates PCR amplification bias; calibration with total genomic DNA results in bias that can be attributed to both PCR amplification bias and differing ratios of template to total genomic DNA. We then model the remaining amplification bias and find that approximately 60% can be explained by inherent species-specific DNA characteristics. These include primer-template mismatches, amplicon fragment length, and GC content, which vary somewhat across Taq polymerases. Finally, we investigate how different PCR protocols influence community composition regardless of expected proportions and find that changing protocols most strongly influence the amplification of templates with primer mismatches. Our findings suggest that using primer-template pairs without mismatches and targeting a narrow taxonomic group can yield more repeatable and accurate estimates of species' true, underlying DNA template proportions. These findings identify key factors that should be considered when designing studies that aim to apply metabarcoding data quantitatively.

The Long and the Short of It: Nanopore-Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species-Level Assignment Depend on Amplicon Lengths

To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA-based techniques and especially environmental (e)DNA metabarcoding is becoming a powerful monitoring tool. However, current approaches rely on genetic target regions under 500 bp, offering limited taxonomic resolution. We developed a method for long-read eDNA metabarcoding, using Nanopore sequencing of a longer amplicon and present DECONA, a read processing pipeline to enable improved identification of marine vertebrate species. We designed a universal primer pair targeting a 2 kb region of fish mitochondrial DNA and compared it to the commonly used MiFish primer pair targeting a ~ 170 bp region. In silico testing showed that 2 kb fragments improved accurate identification of closely related species. Analysing eDNA from a North Sea aquarium showed that sequences from both primer pairs could be assigned to most species, and additional species level assignments could be made through the 2 kb primer pair. Interestingly, this difference was opposite in eDNA from the North Sea, where not the 2 kb but the MiFish primer pair detected more species. This study demonstrates the feasibility of using long-read metabarcoding for eDNA vertebrate biodiversity assessments. However, our findings suggests that longer fragments are less abundant in environmental settings, but not in aquarium settings, suggesting that longer fragments may provide a more recent snapshot of the community. Thus, long-read metabarcoding can expand the molecular toolbox for biodiversity assessments by improving species-level identification and may be especially useful when the temporal origin of the eDNA signal is better understood.

Unraveling Fish Community Diversity and Structure in the Yellow Sea: Evidence from Environmental DNA Metabarcoding and Bottom Trawling

The use of environmental DNA (eDNA) metabarcoding to analyze fish species diversity across different aquatic ecosystems is well documented. Nonetheless, there is a gap in validating eDNA metabarcoding studies on the diversity and structure of fish communities in coastal ecosystems, particularly in comparing these findings with bottom trawl catch data. In this study, we employed eDNA metabarcoding to explore species composition and relative abundance in fish communities, taxonomic-level diversity variations, and the interplay between community structures and environmental factors in the Yellow Sea and compared these results with those obtained from bottom trawl catches. In addition, we compared the various methods used to estimate the distributions of taxonomic, phylogenetic, and functional diversity factors. We found that eDNA metabarcoding detected a greater number of species (86 vs. 41), genera (73 vs. 37), and families (42 vs. 25) than bottom trawl results at each sampling station. eDNA metabarcoding provided higher Shannon, Simpson, and Chao1 alpha diversity indices than the bottom trawl results. The PCoA results showed that eDNA metabarcoding samples could be more clearly separated at the sampling sites in the Zhuanghe (ZH) and Lianyungang (LYG) areas than bottom trawling samples. The RDA analysis indicated that temperature, along with NO3- and NH4+ concentrations, were pivotal in shaping the geographical patterns of fish communities, as identified through eDNA metabarcoding, echoing findings from bottom trawling studies. Furthermore, our findings suggest that eDNA barcoding surpasses bottom trawling in detecting taxonomic and phylogenetic diversity, as well as in uncovering greater functional diversity at the local level. Conclusively, eDNA metabarcoding emerges as a valuable complement to bottom trawling, offering a multifaceted approach to biodiversity monitoring that not only boosts efficiency but also reduces environmental impact on coastal ecosystems.

A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies

Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic approaches are used for eDNA-based community composition analysis. Simulation studies and careful evaluation of taxonomic classifiers are essential to establish reliable benchmarks to improve the accuracy and reproducibility of eDNA-based findings. Here we present a comprehensive evaluation of nine taxonomic classifiers exploring three widely used mitochondrial markers (12S rDNA, 16S rDNA and COI) in Australian marine vertebrates. Curated reference databases and exclusion database tests were used to simulate diverse species compositions, including three positive control and two negative control datasets. Using these simulated datasets ranging from 36 to 302 marker genes, we were able to identify between 19% and 89% of marine vertebrate species using mitochondrial markers. We show that MMSeqs2 and Metabuli generally outperform BLAST with 10% and 11% higher F1 scores for 12S and 16S rDNA markers, respectively, and that Naive Bayes Classifiers such as Mothur outperform sequence-based classifiers except MMSeqs2 for COI markers by 11%. Database exclusion tests reveal that MMSeqs2 and BLAST are less susceptible to false positives compared to Kraken2 with default parameters. Based on these findings, we recommend that MMSeqs2 is used for taxonomic classification of marine vertebrates given its ability to improve species-level assignments while reducing the number of false positives. Our work contributes to the establishment of best practices in eDNA-based biodiversity analysis to ultimately increase the reliability of this monitoring tool in the context of marine vertebrate conservation.

Structural Characteristics of Mitochondrial Genomes of Two Species of Mackerel and Phylogenetic Analysis of Scombridae Family

Scomberomorus guttatus and Scomberomorus commerson are both important marine economic fish species worldwide, with high scientific and ecological value. In this study, the complete mitochondrial genome sequences of these two species of mackerel were obtained by using next-generation sequencing technology, with total lengths of 16,562 bp and 16,594 bp, respectively. Like most teleosts, both species possess 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 non-coding region D-loop. The base composition showed significant AT bias (55.1%, 53.4%) and anti-G bias (16.0%, 16.2%). In their control area, the terminal-associated sequence (TAS) was identified, and a total of three core sequences with repeated "---TACAT---ATGTA---" were found. There are typical CSB-E structures and CSB-D-like structures in the central conserved domain (CD), but no CSB-F structures have been found. Meanwhile, the CSB-2 and CSB-3 structures were identified in the conserved sequence block (CSB), but the CSB-1 structure was missing. To further investigate the phylogenetic relationships within the Scombridae family, this study conducted a comparative analysis of mitochondrial genomes from 30 Scombridae species. Phylogenetic trees encompassing 60% of the documented Scombridae species were constructed using the Neighbor-Joining (NJ) and Maximum Likelihood (ML) methods. The results revealed a close evolutionary relationship between the genus Scomber and Rastrelliger, while the genus Scomberomorus exhibited closer affinities to Thunnus, Euthynnus, and Katsuwonus. At the species level, Scomberomorus guttatus diverged earlier from Scomberomorus commerson. These findings refine and update the phylogenetic relationships among Scombridae species, providing critical molecular evidence and insights for deeper exploration of their evolutionary history and genetic affinities.

Improving an endangered marine species distribution using reliable and localized environmental DNA detections combined with trawl captures

The description of marine fish distributions generally relies on trawl survey observations. For rare species, sporadic catches necessitate the combination of multiannual trawl surveys to accurately describe the distribution, limiting short term monitoring. Recent studies suggest that combining traditional capture methods and environmental DNA (eDNA) detections enhance rare species' occurrence. In this study, the reliability and localization of eDNA detections (single- and multi-species) of an endangered marine species, the Atlantic wolffish Anarhichas lupus, was assessed during fine scale surveys. eDNA was detected at all six stations sampled with Niskin bottles over caves housing one or two A. lupus. Detections from samples collected with syringes by divers along a 15 m transect perpendicular to each cave were limited to the fish cave entrance. Trawl-captures and eDNA detections were then combined to test if the species distribution is improved for broad scale surveys. The station-based frequency of species occurrence was 13% with trawl captures and increased to 23% when combined with eDNA detections. Single-species detections were generally more sensitive than multi-species detections. Our results showed that a rare marine species distribution improves combining traditional methods and eDNA detections in oceanographic surveys. Strategies for integrating optimal eDNA detections in marine surveys are discussed.

Evaluation of Fish Species Detection in the Northwestern Pacific using eDNA Metabarcoding: A Mock Community Approach

BACKGROUND

Metabarcoding of environmental DNA (eDNA), a technique using high-throughput sequencing, has transformed biodiversity monitoring by identifying organisms from DNA fragments present in the environment. This method, particularly useful for aquatic ecosystems, allows for non-invasive species monitoring, helping to provide insight into ecosystem composition and taxonomic diversity. The objective of this study was to assess the efficacy of eDNA metabarcoding for fish species identification in a model community from the northeast Pacific Ocean using 12S ribosomal RNA (12S rRNA) marker.

METHODS

Water samples were collected from the tank of the Primorsky Aquarium, which contains fish species from the Sea of Japan, Sea of Okhotsk, and Bering Sea. DNA was extracted using syringe filters and enriched with polymerase chain reaction (PCR) of mitochondrial 12S rRNA fragment, followed by sequencing on Illumina platform. The resulting reads were processed using the bayesian generalized uncertainty modeling (BEGUM) pipeline and their taxonomic diversity was assessed by basic local alignment search tool (BLAST) search. Using in silico PCR, we also assessed the possible association of detection failures of some species with the presence of primer-to-target sequence mismatches.

RESULTS

From a fish community of only 20 species in the tank, we identified 56 operational taxonomic units (OTUs) corresponding to 28 genera. Among these OTUs, 20 species were unambiguously classified by BLAST-based analysis, though only 9 of them corresponded to the species actually present in the tank. Significant problems included inconsistent reference data and marker biases that affected the accuracy of species identification. In addition to DNA contamination from feed, contamination from the water source may have introduced extraneous DNA into the samples. Also, using in silico PCR analysis with a small number of available reference sequences, we demonstrated a significantly higher number of primer mismatches for species that were not identified.

CONCLUSIONS

This study highlights the relative efficacy of eDNA metabarcoding for fish species identification, but also highlights the need to improve reference databases and minimise contamination, searching for references and primers to improve accuracy. Further research should focus on optimising marker selection and controlling methodological bias to ensure robust biodiversity estimates.

Environmental DNA metabarcoding: Current applications and future prospects for freshwater fish monitoring

Fish, as the top predators in freshwater, greatly contribute to maintain ecosystem stability. There has been a sharp decline in freshwater fish stocks due to multiple factors, both natural and anthropogenic. Effective and accurate monitoring of freshwater fish is necessary to inform on ecosystem health and guide environmental management practices. Traditional survey methods are gradually unable to meet the growing monitoring needs. Environmental DNA (eDNA) metabarcoding provides a high sensitivity, fast and affordable approach for surveying and monitoring of aquatic biology. However, due to the limitations of incomplete databases and non-standardized procedures, the use of eDNA techniques for monitoring freshwater fish remains less mature compared to traditional fish monitoring methods. To systematically review the current applications and future prospects of the eDNA metabarcoding for freshwater fish monitoring, this article: (i) summarizes relevant researches on freshwater fish monitoring using eDNA technology (e.g., methodologies, resource surveys, habitat assessments, etc.) over the past decade. (ii) outlines the methodology of eDNA metabarcoding in freshwater fish monitoring, proposes a standardized process for eDNA methods, and suggests ways to eliminate detection errors. (iii) analyzes the current challenges of the eDNA metabarcoding application in resource surveys and ecological quality assessments of freshwater fish. The eDNA technology can be used as a better alternative or supplement to traditional survey methods for monitoring the diversity, biomass, population distribution, and spawning behaviors of freshwater fish, in particular, it has a prominent advantage in monitoring endangered and rare fish species. (iv) investigates the application of eDNA technology in investigating the impact of human activities and invasive species on freshwater fish, and emphasizes the eDNA's potential in assessing the impacts of water projects (e.g., dam construction or removal, water diversion project) on fish habitats, and the effectiveness of fish passage and invasive fish control efforts. (v) discusses the future prospects of eDNA-based freshwater fish monitoring, both in terms of technology and application. This review provides a guidance for the future development and application of eDNA technology in freshwater fish monitoring and ecological quality assessments.

Exploring technical improvements for environmental nucleic acids-based biodiversity assessment and management in coastal ecosystems

Assessing and conserving marine biodiversity remain critical global challenges, particularly in highly disturbed coastal regions. The use of environmental DNA (eDNA)-metabarcoding has revolutionized biodiversity assessment and management; however, the prevalence of both false positives and negatives continues to be a significant concern. To address these technical errors, we tested two potential methodological improvements in the highly disturbed Guangdong-Hong Kong-Macao Greater Bay Area: (1) the use of random whole-genome amplification (WGA) to reduce false negatives derived from low eDNA concentration, and (2) the application of environmental RNA (eRNA)-metabarcoding to mitigate false positives arising from eDNA contamination by human activities. Using fish communities as our target, we found that WGA enhanced downstream PCR amplification for metabarcoding but significantly reduced the detection of rare taxa, altered community structure, and increased false negatives (p < 0.001 for all tests). Interestingly, WGA led to higher levels of false negatives in more biodiverse communities. eDNA-metabarcoding revealed that 20.9%-23.6% of detected taxa were pure freshwater species (false positives) incapable of surviving in estuarine and coastal regions, highlighting the often-overlooked eDNA contamination in disturbed coastal ecosystems. In contrast, eRNA-metabarcoding significantly reduced false positives (p < 0.001), with error taxa accounting for only 2.5%-6.3% of all detections. Comparisons between eDNA and eRNA metabarcoding further revealed differences in their rare taxa recovery capacity. The findings provide critical insights into method selection for biodiversity assessment and management in highly disturbed coastal regions and highlight the need for further technical improvement of eDNA and eRNA-based biodiversity monitoring and conservation in aquatic ecosystems.

Selecting Competent Reverse Transcription Strategies to Maximise Biodiversity Recovery With eRNA Metabarcoding

Both environmental DNA (eDNA) and environmental RNA (eRNA) have been widely adopted for biodiversity assessment. While eDNA often persists longer in environments, eRNA offers a more current view of biological activities. In eRNA metabarcoding, extracted eRNA is reverse transcribed into complementary DNA (cDNA) for metabarcoding. However, the efficacy of various reverse transcription strategies has not been evaluated. Here we compared the biodiversity recovery efficiency of three strategies: random priming with hexamers, oligo(dT) priming and taxa-specific priming using Mifish-U for fish in both high- and low-biodiversity regions. Our results demonstrate that reverse transcription strategies significantly impact biodiversity recovery. Random priming consistently detected the highest number of taxa in both low- and high-biodiversity regions. In low-biodiversity areas, oligo(dT) performed comparably to random hexamers; however, in high-biodiversity regions, random hexamers outperformed oligo(dT), particularly in recovering rare taxa. While taxa-specific priming was comparable to the other strategies for high-abundance taxa, it was less effective for rare taxa, thus limiting its utility for comprehensive biodiversity assessment. These differences are largely due to the multiple binding sites for random hexamers compared to the fewer or absent sites with oligo(dT) and taxa-specific primers under high eRNA degradation. Combining random hexamers and oligo(dT) significantly improved taxa recovery, especially for low-abundance species, supporting its best practice in eukaryotes. For prokaryotes or genes lacking polyadenylation, random priming is favoured over taxa- or gene-specific priming. Collectively, these findings underscore the critical importance of selecting appropriate reverse transcription strategies in eRNA metabarcoding, with significant implications for effective biodiversity monitoring and conservation efforts.

Checklist of ichthyoplankton of NORI-D polymetallic nodule exploration claim (eastern Clarion-Clipperton Zone) during winter 2021

Background

There been increasing interest in polymetallic nodule mining within the Clarion-Clipperton Zone (CCZ). Polymetallic nodule mining within NORI-D will release a sediment plume within the water column and a previous mining collector test within the Nauru Ocean Resources Inc. (NORI-D) contract area released surface pollution from mining tailings. The mid-water plume, as well as accidental surface pollution, indicate that polymetallic nodule mining could impact surface plankton. Although the ichthyoplankton within the eastern tropical Pacific have been well-studied, recent data from within polymetallic nodule mining licence areas is lacking. Environmental Expedition C5e conducted an environmental baseline assessment of both pelagic and benthic fauna within the NORI-D region of the CCZ, which included the opportunistic collection of ichthyoplankton.

New information

Ichthyoplankton were collected within NORI-D from November-December 2021 using two plankton nets and a Remotely Operated Vehicle (ROV). Here, we present a checklist of ichthyoplankton within the NORI-D licence area during this winter campaign. Eighteen samples were collected and identified through morphology, with a limited number identified through genetic sequencing. Specimens were from five orders, including Argentiniformes, Stomiiformes, Myctophiformes, Beloniformes and Scombriformes. This checklist will aid contractors and scientists conducting work within the CCZ to examine how wastewater discharge from polymetallic nodule mining could impact fish reproduction and ichthyoplankton survival.

Feeding Habits of Leopards and Leopard Cats in the Fragmented Forests Surrounding the Kathmandu Valley

Large-scale anthropogenic developments in the metropolitan areas of Nepal and the rural to urban influx of people have exacerbated human-wildlife conflicts across human-altered landscapes of Nepal. The Kathmandu Valley has experienced large-scale urbanization and has subsequently witnessed substantial incidents of human-wildlife conflicts given the increasing levels of human encroachment into remnant wildlife habitats. Here, we applied DNA metabarcoding in combination with geospatial analysis to study the feeding ecology of two urban carnivores, the leopard (Panthera pardus) and the leopard cat (Prionailurus bengalensis), in the forests surrounding the Kathmandu Valley and to check whether the leopards' predation on domestic animals contributes to human-leopard conflict in this region and to obtain a baseline data on the dietary habits of the poorly studied leopard cat. We found that leopards were highly dependent on domestic animals in areas dominated by human-use activities (agricultural and built-up areas), whereas leopard cats mostly predated on wild rodents. Through our work, we highlight the importance of domestic prey in the diets of urban carnivores like leopards and demonstrate the influence human-induced habitat disturbance has on the ecology of local wildlife. This study generates critical information which will help to inform conflict mitigation strategies and conservation planning for the two carnivore species, in addition to identifying areas within the region that are susceptible to human-wildlife conflicts.

Environmental DNA/RNA metabarcoding for noninvasive and comprehensive monitoring and assessment of marine fishes

Marine fisheries resources are under increasing threat, necessitating the development of new effective monitoring and management strategies. Environmental DNA (eDNA) and RNA (eRNA) metabarcoding has emerged as a non-invasive and sensitive alternative method for monitoring fish biodiversity and fisheries resources and assessing the fisheries impact of anthropogenic activities. Here, we summarize crucial technical details about eDNA metabarcoding for marine fish monitoring and provide meta-analytical trends in primer selection and sample size, assessment standards, fish and fisheries databases, reference fish genomic databases, and other relevant metrics. The pressing need for better reference databases and standardization methods is discussed. We further highlight the potency of emerging eDNA metabarcoding studies for monitoring global fish diversity and revealed regional study hotspots in South China, Atlantic and Mediterranean Seas. The innovative advances in using eDNA/eRNA metabarcoding for fish diversity monitoring and assessment from the detection of rare or invasive species to branching applications in biomass estimation, population genetics, food web analysis, fish migration and feeding studies were reviewed. We also explore the potential of eRNA metabarcoding as an upcoming extension of eDNA metabarcoding in marine fish monitoring and assessment with improved functional relevance. We envision the integration of eDNA/eRNA metabarcoding-based fish monitoring methods with traditional monitoring approaches to significantly improve marine fish surveillance, ecological research, and conservation efforts.

Monitoring the Land and Sea: Enhancing Efficiency Through CRISPR-Cas Driven Depletion and Enrichment of Environmental DNA

Characterizing biodiversity using environmental DNA (eDNA) represents a paradigm shift in our capacity for biomonitoring complex environments, both aquatic and terrestrial. However, eDNA biomonitoring is limited by biases toward certain species and the low taxonomic resolution of current metabarcoding approaches. Shotgun metagenomics of eDNA enables the collection of whole ecosystem data by sequencing all molecules present, allowing characterization and identification. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated proteins (Cas)-based methods have the potential to improve the efficiency of eDNA metagenomic sequencing of low-abundant target organisms and simplify data analysis by enrichment of target species or nontarget DNA depletion before sequencing. Implementation of CRISPR-Cas in eDNA has been limited due to a lack of interest and support in the past. This perspective synthesizes current approaches of CRISPR-Cas to study underrepresented taxa and advocate for further application and optimization of depletion and enrichment methods of eDNA using CRISPR-Cas, holding promise for eDNA biomonitoring.

Comparative analysis of community composition and network structure between phyllosphere endophytic and epiphytic fungal communities of Mussaenda pubescens

The phyllosphere constitutes a critical habitat for microorganisms, exerting profound influences on host vitality, developmental dynamics, reproductive functions, and stress resilience. However, the diversity and network structure of endophytic and epiphytic fungal communities within this microecosystem have not been thoroughly explored. In this investigation, high-throughput sequencing technologies were employed to assess the diversity, community composition, and network structure of endophytic and epiphytic fungal communities associated with Mussaenda pubescens across six geographically distinct locations in Southeast China. The results revealed significant differences in community composition and diversity between endophytic and epiphytic fungi, with pronounced geographical variation observed within these phyllosphere fungal communities. Network analysis indicated that epiphytic fungal networks possess enhanced complexity compared with their endophytic counterparts, although the latter exhibit greater network stability. Moreover, stochastic processes were identified as pivotal in shaping the composition of these fungal communities. This research substantially enriches our comprehension of the diversity and organizational mechanisms of phyllosphere fungal communities, providing novel insights into the modalities of species coexistence and the stability of community equilibrium within ecosystems.IMPORTANCEThis study employs high-throughput sequencing technologies to explore the fungal communities within the phyllosphere of Mussaenda pubescens across Southeast China, offering significant insights into plant mycobiome. It demonstrates geographical variations in these fungal communities, with epiphytic fungi exhibiting more complex interaction networks compared with the endophytic fungi. Crucially, the research indicates that stochastic processes play a substantial role in the composition of fungal communities. These findings enhance our comprehension of plant-associated microecosystems and underscore the intricate interplay of randomness in maintaining ecosystem stability and diversity.

An optimized eDNA protocol for fish tracking in estuarine environments

Environmental DNA (eDNA) is revolutionizing how we investigate biodiversity in aquatic and terrestrial environments. It is increasingly used for detecting rare and invasive species, assessing biodiversity loss and monitoring fish communities, as it is considered a cost-effective and noninvasive approach. Some environments, however, can be challenging for eDNA analyses. Estuarine systems are highly productive, complex environments, but samples collected from these settings may exhibit PCR inhibition and a low fish read recovery. Here we present an approach for detecting fish in turbid, highly productive estuarine systems. The workflow includes bead-based extraction, inhibition removal, high fidelity and specificity DNA polymerase (Platinum SuperFi II) and multiplexing the universal MiFish primers. By applying this hybrid method to a variety of complex estuarine samples with known inhibition, we have more than doubled the number of recovered fish species while removing most of the off-target amplification.

Revealing Elasmobranch Distributions in Turbid Coastal Waters: Insights From Environmental DNA and Particle Tracking

Many sharks, rays and skates are highly threatened and vulnerable to overexploitation, as such reliable monitoring of elasmobranchs is key to effective management and conservation. The mobile and elusive nature of these species makes monitoring challenging, particularly in temperate waters with low visibility. Environmental DNA (eDNA) methods present an opportunity to study these species in the absence of visual identification or invasive techniques. However, eDNA data alone can be difficult to interpret for species monitoring, particularly in a marine setting where its distribution can be influenced by water currents. In this study, we investigated the spatial and temporal distribution of elasmobranch species in two Special Areas for Conservation (SAC) off the coast of Wales. We took monthly eDNA samples for 1 year (starting September 2020 and March 2022 for the northern and southern SACs, respectively), and used metabarcoding to reveal the presence of elasmobranch species. We combined these data with hydrodynamic modelling and particle tracking methods to simulate the potential origins of the detected eDNA. We detected 11 elasmobranch species, including the critically endangered angelshark (Squatina squatina) and tope (Galeorhinus galeus). Most detections were in the spring and the fewest in the autumn. The particle tracking simulations predicted that eDNA was shed, on average, approximately 7 km and 15 km (in the northern and southern SACs, respectively) from the sampling stations at which it was detected. These results show that the two SACs represent important areas for elasmobranchs in the United Kingdom and demonstrate that eDNA methods combined with particle tracking simulations can represent a new frontier for monitoring marine species.

Complete mitochondrial genome of Lepidocephalichthysberdmorei and its phylogenetic status within the family Cobitidae (Cypriniformes)

In this study, the complete mitochondrial genome of Lepidocephalichthysberdmorei was first determined by the primer walking sequence method. The complete mitochondrial genome was 16,574 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (D-loop). The gene arrangement pattern was identical to that of other teleosts. The overall base composition was 29.9% A, 28.5% T, 25.5% C, and 16.1% G, with an A+T bias of 58.4%. Furthermore, phylogenetic analyses were conducted based on 13 PCGs from the mitochondrial genomes of 18 cobitid species using with three different methods (Neighbor-joining, Maximum likelihood, and Bayesian inference). All methods consistently showed that the four species of the genus Lepidocephalichthys form a monophyletic group. This study would provide effective molecular information for the Lepidocephalichthys species as well as novel genetic marker for the study of species identification.

Contrasting pollution responses of native and non-native fish communities in anthropogenically disturbed estuaries unveiled by eDNA metabarcoding

Understanding the influence of environmental pollutants on the assembly mechanisms of estuarine fish communities is vital for addressing conservation challenges in these biodiverse ecosystems. Although significant research has explored the toxic impacts of pollutants such as petroleum, heavy metals, and eutrophication on individual species and populations, their effects on community assembly processes and the differential responses of native versus non-native fish at the meta-community level remain inadequately understood. This study utilized environmental DNA (eDNA) metabarcoding to analyze fish community diversity across 28 subtropical estuaries in China, assessing how these pollutants affect community composition and assembly mechanisms. Results indicated that eDNA was 2.54 times more effective than traditional methods in species identification, while also enabling the detection of a higher number of non-native fish species and more diverse functional guilds within estuarine ecosystems. A significant distance decay pattern (p < 0.05) was observed among native fish, whereas non-native species exhibited non-significant patterns. Neutral and null models showed that non-native species had significantly higher migration rates (0.005939 vs 0.001757) and a greater contribution of stochastic processes (82.38 % vs 70.59 %) compared to native species. Additionally, distance-based redundancy analysis (db-RDA), variance partitioning analysis (VPA), and correlation analyses revealed that native species were strongly constrained by environmental factors, particularly oil, Hg, Zn, Pb, Cr6+, and NH4+, while non-native species displayed notable resilience to these pollutants. These findings highlight the potential for non-native species to disproportionately influence community dynamics and assembly through unrestricted random dispersal amid environmental disturbances. This research clarifies the contrasting ecological responses of native and non-native fish communities to anthropogenic pressures in estuarine environments, offering essential insights into ecosystem resilience and informing biodiversity conservation strategies in rapidly changing coastal ecosystems.

A systematic survey of environmental DNA in Palau's lakes and waterfalls reveals an increase in Leptospira levels after flooding

Objective

Leptospirosis is an important bacterial zoonosis which is widespread in tropical and subtropical islands and influences human and animal health which has secondary economic effects. Although leptospirosis is endemic in Palau, an Oceanian Pacific Island country, few systematic surveys of potential risk factors for Leptospira infection, such as weather and host animals, have been conducted in the natural environment. We used environmental DNA metabarcoding to assess the distribution, species diversity, and abundance of pathogenic Leptospira in this endemic region to investigate the potential environmental risks.

Methods

Forty-two paired water samples, representing fine and rainy weather conditions, were collected from four representative waterfalls and lakes on Babeldaob Island, the largest island in Palau. High-throughput sequencing analysis was conducted for polymerase chain reaction products of leptospiral 16S rRNA and vertebrate animal mitochondrial 12S rRNA genes.

Results

We revealed greater Leptospira diversity and abundance in samples collected after continuous rain, particularly in the presence of flooding, compared with samples collected under typhoon, monsoon, or fine weather conditions. From same samples, six mammalian species including cats (Felis catus), mice (Mus musculus), Yap flying fox (Pteropus yapensis), rats (Rattus spp.), and pigs (Sus scrofa) were repeatedly detected. These may be candidates of host animals of Leptospira in Palau; however, their detection was not clearly correlated with that of Leptospira.

Conclusion

We repeatedly detected several species of pathogenic Leptospira from water samples of a wide region of Babeldaob Island. We confirmed that Leptospira contamination in freshwater environments increased under rainy conditions, particularly in the presence of flooding. This information could be used to improve public health control measures in this region.

A simple and cost-effective extraction for piscine environmental DNA metabarcoding using guanidine hydrochloride method

Environmental DNA (eDNA) metabarcoding is a valuable tool for assessing aquatic biodiversity, but the high cost and complexity of DNA extraction pose challenges for widespread adoption, especially in developing countries. This study presents a cost-effective eDNA extraction method using a guanidine hydrochloride (GuHCl) buffer, proteinase-K digestion, and isopropanol precipitation to improve the detection of fish communities. Comparison with the Qiagen DNeasy Blood & Tissue Kit using MiFish universal primers showed that the GuHCl protocol detected more fish species in freshwater samples, with comparable performance in relative read abundance metrics. However, the GuHCl method exhibited higher PCR inhibition in brackish samples, likely due to salinity and natural inhibitors. The results suggest that the GuHCl-based method is a viable alternative, offering enhanced sensitivity for low-abundance species in freshwater samples and cost savings. This protocol facilitates large-scale eDNA metabarcoding for ecological studies and conservation management efforts.•The GuHCl protocol identified a greater diversity of fish species in freshwater samples than the Qiagen kit, but detected fewer species in brackish water samples.•Both extraction methods demonstrated robust positive correlations in metrics of relative read abundance.

Bridging the gaps through environmental DNA: A review of critical considerations for interpreting the biodiversity data in coral reef ecosystems

Coral reefs, the rainforests of the sea, are vital hotspots for marine biodiversity. However, the persistent challenge of climate change directly threatens the delicate balance of coral reef ecosystems, impacting myriad species and critical ecosystem services. Therefore, this comprehensive review critically discusses the associated challenges in assessing and preserving coral reef diversity, emphasizing the need for novel biomonitoring techniques due to the elusive and cryptic nature of many reef organisms. The review focuses on environmental DNA (eDNA) analysis as a non-invasive tool for coral species monitoring at various ecological levels. The review highlights that using eDNA in coral reef monitoring requires careful consideration of multiple factors, such as strategic assay development, optimization, and marker selection, substrate selection, and sample volume, which are critical for maximizing the probability of species detection. Moreover, integrating environmental RNA (eRNA) provides additional insights into temporal aspects advancing the coral reef biodiversity research and conservation efforts.

Dammed coastal waterways are less diverse, more homogenous, and dominated by non-native species: Comprehensive insights from quantitative analysis of environmental DNA

Small dams are commonplace worldwide and impact local and regional aquatic diversity by altering habitats and disrupting dispersal networks. Quantifying the local and regional impacts of dams requires nearly comprehensive species occurrence data. We used environmental DNA (eDNA) metabarcoding to test theoretical predictions about the impacts of dams on local and regional bony fish diversity within the Chesapeake Bay Watershed, USA. We analyzed eDNA from 465 sampling points within 34 waterbodies documenting the distributions of 61 species. On average, dammed waterbodies had approximately half (48 %) as many species per site as undammed (lower alpha diversity) and more homogenous species composition (lower beta diversity). Native migratory species were less than one tenth (0.08) as likely to be detected at dammed sites than undammed sites, native resident (non-migratory) species were one third (0.34) as likely, whereas introduced species were 2.6 times more likely to be detected. Our sampling and bioinformatics methods were validated by a diverse mock community control. Our results suggest that dams in coastal waterways homogenize fish metacommunities, reduce local biodiversity through dispersal limitation and habitat alteration, and favor the dominance of lentic-adapted introduced species while potentially restricting the spread of introduced catfish. Decisions to construct or decommission dams should consider local and regional impacts on biodiversity.

Novel Drop-Sampler for Simultaneous Collection of Stereo-Video, Environmental DNA and Oceanographic Data

There is an increasing interest in environmental DNA (eDNA) as a method to survey marine biota, enhancing traditional survey methods, and a need to ground truth eDNA-based interpretations with visual surveys to understand biases in both the eDNA and visual datasets. We designed and tested a rapidly deployable, robust method pairing water sampling for eDNA collection and stereo-video imagery, comparing inferred fish assemblages with interspersed baited remote underwater video (stereo-BRUV) samples. The system is capable of rapidly collecting simultaneous wide-field stereo-video imagery, oceanographic measurements and multiple water samples across a range of habitats and depths (up to 600 m). A platform demonstration was conducted in a no-take National Park Zone of the Ningaloo Marine Park, Western Australia, with samples being collected whilst the system is resting on the seafloor. Combining simultaneous visual survey data with eDNA species estimates increased the total diversity of the fish assemblage by ca. 6.5% over eDNA estimates alone, whilst the analysis of the assemblage composition sampled by each method revealed significant differences. The platform demonstration highlights the biases of each sampling method and their complementarity to one another. We suggest that these biases will be better understood by advancements that allow eDNA metabarcoding to discriminate the abundance and life stage of marine biota. Furthermore, investigation of the relationship between eDNA metabarcoding data and concomitant imagery-derived length, age and habitat data is needed.

eDNA technology reveals fish species diversity and ecological corridor function in large raft mussel aquaculture area in the East China Sea

Human activities have transformed coastal environments by introducing numerous artificial structures that impact local ecosystems. Our study investigated fish species diversity in the mussel farm (MF) and the surrounding natural reef habitat (NH) around Gouqi Island in the East China Sea (ECS). Gouqi Island, which hosts the largest mussel farm in ESC, is also a critical region for marine fish activity. We monitored fish species diversity across four seasons for the first time using eDNA technology in December (winter) 2022, March (spring), June (summer), and September (autumn) 2023. We recorded a total of 55 fish species across 49 genera, 33 families, and 10 orders. Alpha diversity analysis revealed that species diversity peaked in summer throughout the year. Diversity in the mussel farming area was significantly higher than in the natural reef habitat. Principal Component Analysis (PCA) and Analysis of Similarities (ANOSIM) confirmed significant differences in community composition between the two habitats (p < 0.01), with a more stable community structure in the mussel farm. This indicates that the mussel farming area supports a distinct fish community compared to the surrounding natural waters. The dominant fish family in the mussel farm was Sciaenidae, which includes several economically valuable species and could be a target for resource conservation. Additionally, the mussel farm hosted numerous migratory fish species exhibiting clear seasonal patterns, suggesting that the farm serves as an important ecological corridor utilized by these species throughout their life cycles.

Ecological forensic testing: Using multiple primers for eDNA detection of marine vertebrates in an estuarine lagoon subject to anthropogenic influences

Many critical aquatic habitats are in close proximity to human activity (i.e., adjacent to residences, docks, marinas, etc.), and it is vital to monitor biodiversity in these and similar areas that are subject to ongoing urbanization, pollution, and other environmental disruptions. Environmental DNA (eDNA) metabarcoding is an accessible, non-invasive genetic technique used to detect and monitor species diversity and is a particularly useful approach in areas where traditional biodiversity monitoring methods (e.g., visual surveys or video surveillance) are challenging to conduct. In this study, we implemented an eDNA approach that used a combination of three distinct PCR primer sets to detect marine vertebrates within a canal system of Biscayne Bay, Florida, an ecosystem representative of challenging sampling conditions and a myriad of impacts from urbanization. We detected fish species from aquarium, commercial, and recreational fisheries, as well as invasive, cryptobenthic, and endangered vertebrate species, including charismatic marine mammals such as the protected West Indian manatee, Trichechus manatus. Our results support the potential for eDNA analyses to supplement traditional biodiversity monitoring methods and ultimately serve as an important tool for ecosystem management. This approach minimizes stress or disturbance to organisms and removes the intrinsic risk and logical limitations of SCUBA diving, snorkeling, or deploying sensitive equipment in areas that are subject to high vessel traffic and/or low visibility. Overall, this work sets the framework to understand how biodiversity may change over different spatial and temporal scales in an aquatic ecosystem heavily influenced by urbanization and validates the use of eDNA as a complementary approach to traditional ecological monitoring methods.

eDNA metabarcoding reveals differences in fish diversity and community structure in Danjiang River

Fish diversity, an important indicator of aquatic ecosystem health, is declining due to water pollution, overfishing, climate change, and invasive species. Effective surveying and monitoring are required to protect fish diversity. Here, a high-sensitivity environmental DNA (eDNA) metabarcoding technique was used to investigate fish diversity in the Danjiang River, Shaanxi Province, China. In total, 59 species were identified in eight orders, 19 families, and 40 genera. Cypriniformes and Perciformes were the main groups in the survey area, while Cyprinidae accounted for 50.85% of the total fish species. Rhinogobius similis (19%), Hemibarbus umbrifer (11%), Gnathopogon herzensteini (10%), Triplophysa stewarti (8%), and Zacco platypus (7%) were the dominant species. Eight rare and two exotic fish species were identified. Combined with analysis of historical data, the richness of fish identified using eDNA metabarcoding was significantly higher than that of fish captured in ground cages. Temperature, pH, and oxidation-reduction potential are the main environmental factors that affect the spatial distribution of fish communities. These results suggest that eDNA metabarcoding could be a new tool with broad application prospects; however, local databases must be improved. This study provides theoretical data and a methodological reference for protecting and managing fish diversity in the Qinling Mountains.

A potential tool for marine biogeography: eDNA-dominant fish species differ among coastal habitats and by season concordant with gear-based assessments

Effective ocean management asks for up-to-date knowledge of marine biogeography. Here we compare eDNA and gear-based assessments of marine fish populations using an approach that focuses on the commonest species. The protocol takes advantage of the "hollow curve" of species abundance distributions, with a minority of species comprising the great majority of individuals or biomass. We analyzed new and published teleost eDNA metabarcoding surveys from three neighboring northwest Atlantic coastal locations representing sandy, rocky, or estuary habitat. Fish eDNA followed a hollow curve species abundance distribution at each location-the 10 commonest taxa accounted for more than 90% of eDNA copies. Top ten taxa were designated eDNA-dominant species (eDDS) and categorized as habitat-associated (top 10 in one study) or as shared. eDDS by category were similarly abundant in concurrent bottom trawl and seine surveys. eDDS habitat category profiles correctly classified most (94%-100%) individual eDNA and capture measurements within surveys and recognized estuarine sites in other regional eDNA and seine studies. Using a category metric like that for habitats, eDDS demonstrated strong seasonal turnover concordant with trawl catch weights. eDNA seasonal profiles applied to historical trawl and seine records highlighted known long-term trends in mid-Atlantic fish populations. This study provides evidence that eDNA-abundant fish species differ among coastal habitats and by season consistent with gear-based assessments. Grouping abundant species by category facilitated comparisons among habitats and integration with established surveys. eDNA metabarcoding of dominant fish species potentially offers a useful tool for marine biogeography and ocean monitoring.

Exploring riverine aquatic animal diversity and establishing aquatic ecological monitoring approaches tailored to the Qinling region via eDNA technology

This study thoroughly examines biodiversity and aquatic ecosystems across 14 sampled sites within the Shitou River basin by utilizing environmental DNA technology. Through integrated analysis and high-throughput sequencing, the study elucidates a diverse array of biodiversity, encompassing 27 fish species and 341 freshwater benthic macroinvertebrates (FBM) species. Using various biodiversity indices, we found significant differences in diversity and stability across different environments. Regions with more complex habitats had higher species richness and evenness. Further analyses showed complex relationships between diversity metrics for FBM and fish, indicating potential interactions between these groups. The standardized mean score (SMS) was developed to aid in the assessment of water quality. Specifically, SMS scoring revealed that sites STH3, STH4, and STH14 excelled across multiple dimensions, earning an "Excellent" rating, while site STH12 was rated as "Poor" due to subpar performance across several metrics. This project not only enhances current understanding regarding aquatic ecological dynamics but also establishes a strong foundation for detailed environmental evaluation and monitoring, aligned with the priorities of contemporary ecological management and caution.

Environmental DNA as a complementary tool for biodiversity monitoring: A multi-technique and multi-trophic approach to investigate cetacean distribution and feeding ecology

The use of environmental DNA (eDNA) to assess the presence of biological communities has emerged as a promising monitoring tool in the marine conservation landscape. Moreover, advances in Next-Generation Sequencing techniques, such as DNA metabarcoding, enable multi-species detection in mixed samples, allowing the study of complex ecosystems such as oceanic ones. We aimed at using these molecular-based techniques to characterize cetacean communities, as well as potential prey on the northern coast of Mainland Portugal. During four seasonal campaigns (summer 2021 to winter 2022/2023), seawater samples were collected along with visual records of cetacean occurrence. The eDNA isolated from 64 environmental samples was sequenced in an Illumina platform, with universal primers targeting marine vertebrates. Five cetacean species were identified by molecular detection: common dolphin (Delphinus delphis), bottlenose dolphin (Tursiops truncatus), Risso's dolphin (Grampus griseus), harbor porpoise (Phocoena phocoena) and fin whale (Balaenoptera physalus). Overall, except for the latter (not sighted during the campaigns), this cetacean community composition was similar to that obtained through visual monitoring, and the complementary results suggest their presence in the region all year round. In addition, the positive molecular detections of Balaenoptera physalus are of special relevance since there are no records of this species reported on scientific bibliography in the area. The detection of multiple known prey of the identified dolphins indicates an overlap between predator and prey in the study area, which suggests that these animals may use this coastal area for feeding purposes. While this methodological approach remains in a development stage, the present work highlights the benefits of using eDNA to study marine communities, with specific applications for research on cetacean distribution and feeding ecology.

Temporal variation characteristics of microbial aerosols in the goose house environment

1. Preventing disease is important in poultry production systems, but this has mainly been studied in chickens. The aim of this study is to explore the impact of microbial aerosols in intensive goose house environments.2. To evaluate the environmental quality of geese housing, fine particulate matter (PM2.5) was collected using an ambient air particulate matter sampler. High-throughput sequencing was used to analyse bacterial diversity and relative abundance. Results showed that the number of general and operational taxonomic units (OTUs) were 1,578 and 19 112 in all PM2.5 samples. Firmicutes, Bacteroidota, Proteobacteria, Acidobacterota were the four most abundant phyla in PM2.5.3. Compared with bacterial phyla in the PM2.5 from chicken houses, those in the genus Acidobacterota were increased in goose housing. There are various genera of bacteria present in PM2.5, and their composition was similar across different samples. No significant change was observed in the diversity of microbiota in the PM2.5, although multiple pathogenic bacteria were detected.4. A prediction function showed that a variety of bacterial phyla correlated positively with the human diseases.5. In summary, the microbial aerosols in the goose shed pose significant risks to the health of the geese. Regular monitoring of the composition of microbial aerosols is important for the healthy growth of geese and disease prevention and control.

Unraveling the Mitogenomic Characteristics and Phylogenetic Implications of Leuciscus merzbacheri (Zugmayer, 1912), an Endangered Fish in the Junggar Basin of Xinjiang, Northwest China

BACKGROUND

Leuciscus merzbacheri is a rare and endangered fish in Xinjiang, China. As a representative species of the fauna in the Junggar Basin, it is of high economic and scientific value. The genetic data are still limited, and the mitochondrial genomic characteristics remain unexplored.

METHODS

A high-throughput sequencing method was used to obtain the complete mitogenome of L. merzbacheri.

RESULTS

The full length of the circular DNA was 16,609 bp, and it consisted of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs and 2 non-coding regions. The overall nucleotide compositions of both the mitogenome and PCGs showed an obvious AT preference with percentages of 54.20% and 53.60%, respectively. Three commonly used amino acids were Leu (16.43%), Ala (8.95%) and Thr (7.85%) in turn. All tRNAs could form the typical clover structures excluding tRNA-Ser AGY. The presumed secondary structures of two rRNAs contained several stem-loop domains, and the structure of 12S rRNA seemed to be more stable than that of 16S rRNA. Extended termination sequence regions (ETASs), central conserved regions (CSB-F, CSB-E and CSB-D), and conserved sequence regions (CSB-1, CSB-2 and CSB-3) were identified in the control region. The phylogenetic tree showed that L. merzbacheri was recovered with strong supports as a sister to the other members of the genus. The location in the outermost branch implied that it might be a relatively ancient species among its congeners.

CONCLUSIONS

This study would complement the genetic data on L. merzbacheri and contribute to a better understanding of molecular evolution in Leuciscus as well.

Endemic Radiation of African Moonfish, Selene dorsalis (Gill 1863), in the Eastern Atlantic: Mitogenomic Characterization and Phylogenetic Implications of Carangids (Teleostei: Carangiformes)

This study offers an in-depth analysis of the mitochondrial genome of Selene dorsalis (Gill 1863), a species native to the Eastern Atlantic Ocean. The circular mitochondrial DNA molecule measures 16,541 base pairs and comprises 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and a control region (CR). The nucleotide composition exhibits a notable adenine-thymine (AT) bias, accounting for 53.13%, which aligns with other species in the Carangidae family. Most PCGs initiate with the ATG codon, with the exception of Cytochrome C oxidase subunit I, which starts with GTG. Analysis of relative synonymous codon usage reveals that leucine and serine are the most prevalent amino acids in the mitochondrial genome of S. dorsalis and its congeners (S. vomer and S. setapinnis). All tRNAs display the typical cloverleaf structure, though tRNA Serine (S1) lacks a dihydrouracil arm. Pairwise comparisons of synonymous and nonsynonymous substitutions for all PCGs yielded values below '1', indicating strong purifying selection. The CR spans 847 bp, representing 5.12% of the mitochondrial genome, and is characterized by high AT content (62.81%). It is situated between tRNA-Pro (TGG) and tRNA-Phe (GAA). The CR contains conserved sequence blocks, with CSB-1 being the longest at 22 bp and CSB-D the shortest at 18 bp. Phylogenetic analysis, using Bayesian and Maximum-likelihood trees constructed from concatenated PCGs across 72 species, successfully differentiates S. dorsalis from other carangids. This study also explores how ocean currents and gyres might influence lineage diversification and parapatric speciation of Selene species between the Atlantic and Pacific Oceans. These results highlight the importance of the mitochondrial genome in elucidating the structural organization and evolutionary dynamics of S. dorsalis and its relatives within marine ecosystems.

Application of Synchronous Evaluation-Diagnosis Model with Quantitative Stressor-Response Analysis (SED-QSR) to Urban Lake Ecological Status: A Proposed Multiple-Level System

Ecological integrity assessment and degradation diagnosis are used globally to evaluate the health of water bodies and pinpoint critical stressors. However, current studies mainly focus on separate evaluation or diagnosis, leading to an inadequate exploration of the relationship between stressors and responses. Here, based on multiple data sets in an urban lake system, a synchronous evaluation-diagnosis model with quantitative stressor-response analysis was advanced, aiming to improve the accuracy of evaluation and diagnosis. The weights for key physicochemical stressors were quantitatively determined in the sequence of NDAVIadj > CODMn > TP > NH4+-N by the combination of generalized additive model and structural equation modeling, clarifying the most significant effects of aquatic vegetation on the degradation of fish assemblages. Then, sensitive biological metrics were screened by considering the distinct contributions of four key stressors to alleviate the possible deviation caused by common methods. Finally, ecological integrity was evaluated by summing the key physicochemical stressors and sensitive biological metrics according to the model-deduced weights instead of empirical weights. Our system's diagnosis and evaluation results achieved an accuracy of over 80% when predicting anthropogenic stress and biological status, which highlights the great potential of our multiple-level system for ecosystem management.

Multi-method survey rediscovers critically endangered species and strengthens Madagascar's freshwater fish conservation

Freshwater ecosystems are crucial for global biodiversity through supporting plant and animal species and providing essential resources. These ecosystems are under significant threat, particularly in island environments such as Madagascar. Our study focuses on the Amboaboa River basin, home to the rare and endemic fish species Rheocles derhami, last recorded in 2013. To assess the status of this and other threatened fish species including Ptychochromis insolitus and Paretroplus gymnopreopercularis, and to understand freshwater fish population dynamics in this biodiversity hotspot, we conducted a comprehensive survey using both environmental DNA (eDNA) and traditional fishing methods. While traditional methods effectively captured a diverse range of species, including several invasive aliens and the critically endangered endemic species that were the focus of this study, the eDNA approach detected only a fraction of these introduced species and struggled to identify some critically endangered endemics at the species level. This highlights the value of combining methods to enhance species detection. We also investigated the trade-offs associated with multi-primer assessments in eDNA analysis, focusing on three different primer combinations targeting the 12S mitochondrial gene: MiFish, Tele02, and Riaz. Additionally, we provided 12S reference barcodes for 10 species across 9 genera of fishes from the region to increase the coverage of the public reference databases. Overall, our study elucidates the current state of freshwater biodiversity in the Amboaboa River basin and underscores the value of employing multiple methods for effective conservation strategies.

Human activities strengthen the influence of deterministic processes in the mechanisms of fish community assembly in tropical rivers of Yunnan, China

Human-induced global alterations have worsened the severe decrease in fish biodiversity in rivers. To successfully reduce the pace of reduction in fish diversity, it is crucial to prioritize the understanding of how human activities impact the processes that shape and maintain fish diversity. Traditional fish survey methods are based on catch collection and morphological identification, which is often time-consuming and ineffective. Hence, these methods are inadequate for conducting thorough and detailed large-scale surveys of fish ecology. The rapid progress in molecular biology techniques has transformed environmental DNA (eDNA) technique into a highly promising method for studying fish ecology. In this work, we conducted the first systematic study of fish diversity and its formation and maintenance mechanism in the Xishuangbanna section of the Lancang River using eDNA metabarcoding. The eDNA metabarcoding detected a total of 159 species of freshwater fishes spanning 13 orders, 34 families, and 99 genera. The fishes in the order cypriniformes were shown to be overwhelmingly dominant. At different intensities of anthropogenic activity, we found differences in fish community composition and assembly. The analysis of the Sloan's neutral community model fitting revealed that stochastic processes were the dominant factor in the shaping of fish communities in the Xishuangbanna section of the Lancang River. We have further confirmed this result by using the phylogenetic normalized stochasticity ratio. Furthermore, our findings indicate that as human activities get more intense, the influence of stochastic processes on the shaping of fish communities decreases, while the influence of deterministic processes eventually becomes more prominent. Finally, we discovered that salinity positively correlated with fish community changes in the high-intensity anthropogenic sample sites, but all environmental factors had little effect on fish community changes in the low-intensity and moderate-intensity anthropogenic sample sites. Our study not only validated the potential application of eDNA metabarcoding for monitoring fish diversity in tropical rivers, but also revealed how fish communities respond to human activities. This knowledge will serve as a solid foundation for the protection of fish resources in tropical rivers.

New insights into biologic interpretation of bioinformatic pipelines for fish eDNA metabarcoding: A case study in Pearl River estuary

Environmental DNA (eDNA) metabarcoding is an emerging tool for monitoring biological communities in aquatic ecosystems. The selection of bioinformatic pipelines significantly impacts the results of biodiversity assessments. However, there is currently no consensus on the appropriate bioinformatic pipelines for fish community analysis in eDNA metabarcoding. In this study, we compared three bioinformatic pipelines (Uparse, DADA2, and UNOISE3) using real and mock (constructed with 15/30 known fish) communities to investigate the differences in biological interpretation during the data analysis process in eDNA metabarcoding. Performance evaluation and diversity analyses revealed that the choice of bioinformatic pipeline could impact the biological results of metabarcoding experiments. Among the three pipelines, the operational taxonomic units (OTU)-based pipeline (Uparse) showed the best performance (sensitivity: 0.6250 ± 0.0166; compositional similarity: 0.4000 ± 0.0571), the highest richness (25-102) and minimal inter-group differences in alpha diversity. It suggested the OTU-based pipeline possessed superior capability in fish diversity monitoring compared to ASV/ZOTU-based pipeline. Additionally, the Bray-Curtis distance matrix achieved the highest discriminative effect in the PCoA (43.3%-53.89%) and inter-group analysis (P < 0.01), indicating it was better at distinguishing compositional differences or specific genera of fish community at different sampling sites than other distance matrices. These findings provide new insights into fish community monitoring through eDNA metabarcoding in estuarine environments.

DNA metabarcoding unveils the hidden species composition in fish surimi: Implications for the management of unlabeled and mixed seafood products

Fish surimi products are traditional foods primarily made from fish meat and may contain a complex species composition. In Taiwan, the abundant fishery resources and diverse fish species lead to local catches being widely used as ingredients in fish surimi products. However, due to growing market demand and increasingly scarce resources, some surimi products contain sensitive species, such as sharks, posing potential threats to the ecological environment and biodiversity. In this study, by applying metabarcoding techniques, we analyzed 120 fish surimi product samples from different brands and types throughout the four seasons in Taiwan's market. The main fish species identified included milkfish (Chanos chanos), dolphinfish (Coryphaena hippurus), Pomfret (Taractes rubescens), swordfish (Istiophorus spp.) and cartilaginous. Moreover, at least 37 species of cartilaginous fish, including 26 endangered species, were found. Through comprehensive and accurate species identification of surimi product ingredients, we unveiled the usage of sensitive species in products on the market. This finding is important for the surimi industry's quality control and market supervision. Furthermore, it can promote the sustainable use of Taiwan's fishery resources and protect biodiversity.

Spatiotemporal changes of pelagic food webs investigated by environmental DNA metabarcoding and connectivity analysis

Environmental DNA metabarcoding (eDNA metaB) is fundamental for monitoring marine biodiversity and its spread in coastal ecosystems. We applied eDNA metaB to seawater samples to investigate the spatiotemporal variability of plankton and small pelagic fish, comparing sites with different environmental conditions across a coast-to-offshore gradient at river mouths along the Campania coast (Italy) over 2 years (2020-2021). We found a marked seasonality in the planktonic community at the regional scale, likely owing to the hydrodynamic connection among sampling sites, which was derived from numerical simulations. Nonetheless, spatial variability among plankton communities was detected during summer. Overall, slight changes in plankton and fish composition resulted in the potential reorganization of the pelagic food web at the local scale. This work supports the utility of eDNA metaB in combination with hydrodynamic modelling to study marine biodiversity in the water column of coastal systems. This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

Multi-marker DNA metabarcoding for precise species identification in ichthyoplankton samples

Ichthyoplankton monitoring is crucial for stock assessments, offering insights into spawning grounds, stock size, seasons, recruitment, and changes in regional ichthyofauna. This study evaluates the efficiency of multi-marker DNA metabarcoding using mitochondrial cytochrome c oxidase subunit I (COI), 12S rRNA and 16S rRNA gene markers, in comparison to morphology-based methods for fish species identification in ichthyoplankton samples. Two transects with four coastal distance categories were sampled along the southern coast of Portugal, being each sample divided for molecular and morphological analyses. A total of 76 fish species were identified by both approaches, with DNA metabarcoding overperforming morphology-75 versus 11 species-level identifications. Linking species-level DNA identifications with higher taxonomic morphological identifications resolved several uncertainties associated with traditional methods. Multi-marker DNA metabarcoding improved fish species detection by 20-36% compared to using a single marker/amplicon, and identified 38 species in common, reinforcing the validity of our results. PERMANOVA analysis revealed significant differences in species communities based on the primer set employed, transect location, and distance from the coast. Our findings underscore the potential of DNA metabarcoding to assess ichthyoplankton diversity and suggest that its integration into routine surveys could enhance the accuracy and comprehensiveness of fish stock assessments.

Examination of sequence variations in partial mitochondrial 12S gene amongst damselfish species as references for DNA barcoding

Accurate species identification, based on DNA barcoding, can be achieved when sufficient sequence variations are present amongst species in the sampled marker. In general, the ability to discriminate species decreases with shorter sequences; however, shorter regions have a merit in amplification success by the polymerase chain reaction. In either case, it is important to investigate sequence variations amongst species before barcoding to understand its reliability and limitations. In this study, we investigate how accurately short, but hypervariable portion of the mitochondrial 12S ribosomal RNA (12S) gene (MiFish region with approximately 180 bp) is used to identify each species in diversified pomacentrid fishes compared with the longer region of the same gene (approximately 750 bp). We prepared three datasets with 301 sequences of the MiFish region for 150 species, the same 301 of sequences of the longer 12S region and 476 sequences of the MiFish region for 183 species. Neighbour-joining (NJ) analyses and genetic distance analyses revealed several indistinguishable pairs of species in these DNA regions. Although the number of such pairs was larger in the MiFish region, 83.6% (153 of 183) of species possessed respective unique sequences even in the MiFish region (versus 96.0% [144 of 150 species] in the longer 12S region). A part of indistinguishable pairs of species might have caused by mitochondrial DNA introgressions and taxonomically unresolved problems. Our analysis clarified the effectiveness and limitations of species identification using DNA barcoding for Pomacentridae and the sequences we provided here contribute to the expansion of references for pomacentrid mitochondrial 12S sequences.

Environmental DNA Reveals the Impact of Submarine Groundwater Discharge on the Spatial Variability of Coastal Fish Diversity

Submarine groundwater discharge (SGD) has recently been recognized as an influential factor in coastal ecosystems; however, little research has been conducted on its effects on coastal fish diversity. To investigate the relationship between SGD and fish diversity, we conducted a survey at the coastal island scale using the environmental DNA (eDNA) method. Our findings indicate that fish species richness and functional richness peak at stations with high SGD. Environmental variables, such as salinity, dissolved inorganic nitrogen (DIN) concentration, and SGD, significantly influence fish diversity. Carnivore fish richness was negatively correlated with salinity, while planktivore fish richness was positively correlated. Additionally, SGD and DIN concentrations were found to be crucial in shaping omnivorous and pelagic communities, respectively. This study highlights the role of SGD in enhancing nutrient conditions favorable for diverse fish communities and demonstrates the effectiveness of eDNA metabarcoding for rapid marine biodiversity assessment. These findings provide valuable insights for coastal ecosystem monitoring and management.

phyloBARCODER: A Web Tool for Phylogenetic Classification of Eukaryote Metabarcodes Using Custom Reference Databases

We developed phyloBARCODER (https://github.com/jun-inoue/phyloBARCODER), a new web tool that can identify short DNA sequences to the species level using metabarcoding. phyloBARCODER estimates phylogenetic trees based on the uploaded anonymous DNA sequences and reference sequences from databases. Without such phylogenetic contexts, alternative, similarity-based methods independently identify species names and anonymous sequences of the same group by pairwise comparisons between queries and database sequences, with the caveat that they must match exactly or very closely. By putting metabarcoding sequences into a phylogenetic context, phyloBARCODER accurately identifies (i) species or classification of query sequences and (ii) anonymous sequences associated with the same species or even with populations of query sequences, with clear and accurate explanations. Version 1 of phyloBARCODER stores a database comprising all eukaryotic mitochondrial gene sequences. Moreover, by uploading their own databases, phyloBARCODER users can conduct species identification specialized for sequences obtained from a local geographic region or those of nonmitochondrial genes, e.g. ITS or rbcL.

Marine eDNA sampling from submerged surfaces with paint rollers

Environmental DNA (eDNA) analyses of species present in marine environments is the most effective biological diversity measurement tool currently available. eDNA sampling methods are an intrinsically important part of the eDNA biodiversity analysis process. Identification and development of eDNA sampling methods that are as rapid, affordable, versatile and practical as possible will improve rates of detection of marine species. Optimal outcomes of eDNA biodiversity surveys come from studies employing high levels of sampling replication, so any methods that make sampling faster and cheaper will improve scientific outcomes. eDNA sampling methods that can be applied more widely will also enable sampling from a greater range of marine surface micro-habitats, resulting in detection of a wider range of organisms. In this study, we compared diversity detection by several methods for sampling eDNA from submerged marine surfaces: polyurethane foam, nylon swabs, microfibre paint rollers, and sediment scoops. All of the methods produced a diverse range of species identifications, with >250 multicellular species represented by eDNA at the study site. We found that widely-available small paint rollers were an effective, readily available and affordable method for sampling eDNA from underwater marine surfaces. This approach enables the sampling of marine eDNA using extended poles, or potentially by remotely operated vehicles, where surface sampling by hand is impractical.