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

Towards a comprehensive assessment of ichthyofaunal diversity in the Yangtze River estuary: Leveraging environmental DNA technology and bottom trawl surveys

The fishery resources in the Yangtze River Estuary (YRE) have declined drastically because of overfishing and environmental changes, leading to ecosystem degradation of the YRE, and bringing numerous rare fish species to the brink of extinction. As a new technology with great prospects for popularization and application, environmental DNA (eDNA) technology has been utilized and proven by many studies to have high potential in revealing the various species' biodiversity. In this study, we analyzed the species composition and diversity of the Yangtze River Estuary using a combination of eDNA technology and bottom trawling approaches, and later, the comparison of both methods. The results showed that combining eDNA technology and bottom trawling, 30 fish species from 7 orders and 11 families were identified. Among the 30 fish species, a total of six species of fish could be observed in catches from both methods. Perciformes were the most abundant and Coilia mystus was the dominant species. According to diversity indices, the eDNA technology reveals significant differences in fish community richness and diversity in the Yangtze River Estuary compared to the bottom trawl. In summary, the eDNA technology is feasible for monitoring fishery resources in the waters of the Yangtze River Estuary, thereby serving as a valuable supplementary tool for conducting comprehensive surveys in this region. Moreover, it holds significant implications and promising prospects for conserving the diverse ecosystem of the YRE in future conservation efforts.

Vertical and horizontal environmental DNA (eDNA) patterns of fish in a shallow and well-mixed North Sea area

The integration of eDNA metabarcoding into monitoring programs provides valuable information about fish community structures. Despite the growing body of evidence supporting the method's effectiveness in distinguishing fine-scale eDNA signals, there is a limited understanding of eDNA distribution in shallow, well-mixed environments, especially related to sampling depth. We analyzed 167 samples collected from the surface and bottom water at 17 locations of the Belgian Part of the North Sea (BPNS), where the deepest sampling point was 31 m, and compared this to beam trawl catch data collected simultaneously at the same locations. eDNA metabarcoding identified an additional 22 species compared to beam trawl catch data. Diversity measures and patterns were very similar between surface and bottom samples and revealed community patterns that were previously described by long-term beam trawl catch data. Surface and bottom samples had 39 fish species in common, while six and eight rare species were uniquely detected, respectively. Our results demonstrate that eDNA metabarcoding effectively identifies spatial community patterns of fishes in the highly dynamic environment of the BPNS regardless of sampling depth. Out of the six most common species tested, eDNA metabarcoding read abundances correlated strongly with catch-based abundance data for one species, but moderately for two others, indicating that inferring fish abundance and biomass via eDNA metabarcoding remains challenging.

Integrating microbial 16S rRNA sequencing and non-targeted metabolomics to reveal sexual dimorphism of the chicken cecal microbiome and serum metabolome

Background

The gut microbiome plays a key role in the formation of livestock and poultry traits via serum metabolites, and empirical evidence has indicated these traits are sex-linked.

Methods

We examined 106 chickens (54 male chickens and 52 female chickens) and analyzed cecal content samples and serum samples by 16S rRNA gene sequencing and non-targeted metabolomics, respectively.

Results

The cecal microbiome of female chickens was more stable and more complex than that of the male chickens. Lactobacillus and Family XIII UCG-001 were enriched in male chickens, while Eubacterium_nodatum_group, Blautia, unclassified_Anaerovoraceae, Romboutsia, Lachnoclostridium, and norank_Muribaculaceae were enriched in female chickens. Thirty-seven differential metabolites were identified in positive mode and 13 in negative mode, showing sex differences. Sphingomyelin metabolites possessed the strongest association with cecal microbes, while 11β-hydroxytestosterone showed a negative correlation with Blautia.

Conclusion

These results support the role of sexual dimorphism of the cecal microbiome and metabolome and implicate specific gender factors associated with production performance in chickens.

A new species of the genus Luciogobius Gill, 1859 (Teleostei, Oxudercidae) from Taiwan

A new species, Luciogobiusopisthoproctus sp. nov., is described based on 18 specimens collected from Daxi Creek (Yilan) and Babian Creek (Taitung) in Taiwan. The new species is characterized by having a yellowish body with scattered spots on the sides, a black blotch on the caudal fin, the absence of free pectoral-fin rays, and more than 40 vertebrae. The new species can be distinguished from congeners by the following combination of characters: AAA distance (anus to anal-fin origin) shorter than twice the body depth at anus, 4.2-7.2% of standard length (SL); pre-anus length 80.0-92.8% of pre-anal-fin length; snout length 39.7-62.7% of AAA distance; abdominal vertebrae 20-22; caudal vertebrae 20-22; first anal-fin pterygiophore usually inserted behind the second haemal spine.

Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems

Environmental DNA (eDNA) monitoring, a rapidly advancing technique for assessing biodiversity and ecosystem health, offers a noninvasive approach for detecting and quantifying species from various environmental samples. In this review, a comprehensive overview of current eDNA collection and detection technologies is provided, emphasizing the necessity for standardization and automation in aquatic ecological monitoring. Furthermore, the intricacies of water bodies, from streams to the deep sea, and the associated challenges they pose for eDNA capture and analysis are explored. The paper delineates three primary eDNA survey methods, namely, bringing back water, bringing back filters, and bringing back data, each with specific advantages and constraints in terms of labor, transport, and data acquisition. Additionally, innovations in eDNA sampling equipment, including autonomous drones, subsurface samplers, and in-situ filtration devices, and their applications in monitoring diverse taxa are discussed. Moreover, recent advancements in species-specific detection and eDNA metabarcoding are addressed, highlighting the integration of novel techniques such as CRISPR-Cas and nanopore sequencing that enable precise and rapid detection of biodiversity. The implications of environmental RNA and epigenetic modifications are considered for future applications in providing nuanced ecological data. Lastly, the review stresses the critical role of standardization and automation in enhancing data consistency and comparability for robust long-term biomonitoring. We propose that the amalgamation of these technologies represents a paradigm shift in ecological monitoring, aligning with the urgent call for biodiversity conservation and sustainable management of aquatic ecosystems.

Comparative analysis of bottom trawl and nanopore sequencing in fish biodiversity assessment: The sylt outer reef example

The assessment of fish diversity is crucial for effective conservation and management strategies, especially in ecologically sensitive regions such as marine protected areas. This study contrasts the effectiveness of environmental DNA (eDNA) metabarcoding analysis employing Nanopore technology with compare beam trawl surveys at the Sylt Outer Reef, a Natura 2000 site in the North Sea, Germany. Out of the 17 fish species caught in a bottom trawl (using a 3m beam trawl), 14 were also identified through eDNA extracted from water samples. The three species not detected in the eDNA results were absent because they lacked representation in public DNA databases. The eDNA method detected twice as many fish species as the beam trawl, totalling 36 species, of which 14 were also detected by the trawl. Additionally, the selection of primers (Mifish) facilitated the identification of one marine mammal species, the harbour porpoise. In conclusion, the findings underscore the potential of eDNA coupled with MinION sequencing (Long read technology) as a robust tool for biodiversity assessment, surpassing traditional methods in detecting species richness.

Species diversity of fish at the Wuzhizhou Island, South China Sea, based on environmental DNA

Background

Wuzhizhou Island (WZZ) is located in Haitang Bay in the northern region of Sanya, Hainan Island. The sea area surrounding WZZ represents a typical tropical marine ecosystem, characterised by diverse and complex habitats. Therefore, there is a rich variety of marine fish species at WZZ. The marine ecosystem of WZZ was seriously destroyed initially in the 1970s-1980s and recovered in the 1990s, then constructed as the first national tropical marine ranch demonstration area of China in 2019. As fish is an important high trophic vertebrate in the marine ecosystem, understanding the composition and distribution of fish species could help us to recognise the status of the ecosystem of WZZ and supply scientific data for construction of the national marine ranch demonstration area. This study used eDNA technology to investigate the composition of fish community surrounding WZZ and provided a scientific basis for realising and protecting the marine ecosystem of the South China Sea.

New information

The WZZ is an offshore island in the South China Sea, harbouring abundant marine fish resources. Although previous research investigated fish species of WZZ, the data were, however, still incomplete due to limitation of sampling methods and survey seasons. In this study, we intended to take advantage of eDNA and supplement data of fish species at WZZ as much as possible. Based on eDNA, this study provided the data on 188 fish species (including nine undetermined species denoted by genus sp.) belonging to 17 orders, 63 families and 124 genera and they were the more comprehensive records of fish species surrounding WZZ. In addition, the information on Molecular Operational Taxonomic Units (MOTUs) for taxon identification was also provided, aiming to contribute to the establishment of a specific eDNA taxon database for fish of the South China Sea. This study included two datasets, which were occurrences of fish taxa at WZZ, as well as MOTUs sequences and geographical coordinate information of sampling sites. The "fish taxon occurrences" dataset presented records on taxonomic, distribution and habitat conditions of 188 fish species detected using eDNA, as well as the latitude and longitude information of the sampling sites, the "MOTUs information" dataset provided the MOTUs sequences, source of sequences, abundance of sequences for 188 fish species, also included the species matched in NCBI and the best NCBI BLAST sequence similarity.

Rapid, contamination-less, and efficient environmental DNA filtration system

Due to the sporadic distribution and trace amount of environmental DNA (eDNA) in deep-sea water, in the context of biodiversity monitoring, large volumes of filtration and multiple filtration replicates are required for eDNA metabarcoding. To address issues tied to the use of multiple filtration devices and large filtration volumes (e.g., contamination, time consumption, etc.), we have developed two systems for simple, rapid, and contamination-less filtration simultaneously that allow for the processing of multiple sample replicates from large volumes of water. First, the water from a Niskin bottle was filtered directly using a solenoid pump. Second, the pumped deep-sea water, using the siphon effect, was directly filtered by a filtration device driven by water pressure. This system can process 24 replicates simultaneously without the need for expensive equipment and active driving force. Compared with conventional filtering methods, e.g., peristaltic pumps, the proposed systems reduce filtration time, minimizing contamination, and enabling the simultaneous acquisition of multiple replicates. Overall, the systems presented here provide an effective approach for eDNA metabarcoding analysis, particularly for the filtration of large volumes of water containing small amounts of eDNA, such as deep-sea water. •The present systems reduce filtration time and contamination without water having to be transferred.•Simultaneous multiple replicates improve the efficiency and reliability of biodiversity assessments.

Relating target fish DNA concentration to community composition analysis in freshwater fish via metabarcoding

Metabarcoding has been widely accepted as a useful tool for biodiversity assessment based on eDNA. The method allows for the detection of entire groups of organisms in a single sample, making it particularly applicable in aquatic habitats. The high sensitivity of the molecular approaches is especially beneficial in detecting elusive and rare fish species, improving biodiversity assessments. Numerous biotic and abiotic factors that affect the persistence and availability of fish DNA in surface waters and therefore affecting species detectability, have been identified. However, little is known about the relationship between the total fish DNA concentration and the detectability of differential abundant species. In this study three controlled mock-community DNA samples (56 individual samples) were analyzed by (i) metabarcoding (MiSeq) of 12S rDNA (175 bp) and by (ii) total freshwater fish DNA quantification (via qPCR of 12S rDNA). We show that the fish DNA quantity affects the relative abundance of species-specific sequences and the detectability of rare species. In particular we found that samples with a concentration between 1000 pg/μL down to 10 pg/μL of total fish DNA revealed a stable relative frequency of DNA sequences obtained for a specific fish species, as well as a low variability between replicates. Additionally, we observed that even in complex mock-community DNA samples, a total fish DNA concentration of 23 pg/μL was sufficient to reliably detect all species in every replicate, including three rare species with proportions of ≤0.5 %. We also found that the DNA barcode similarity between species can affect detectability, if evenness is low. Our data suggest that the total DNA concentration of fish is an important factor to consider when analyzing and interpreting relative sequence abundance data. Therefore, the workflow proposed here will contribute to an ecologically and economically efficient application of metabarcoding in fish biodiversity assessment.

Environmental DNA: The next chapter

Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.

Utilizing environmental DNA and imaging to study the deep-sea fish community of Takuyo-Daigo Seamount

The increase in interest of mining at seamounts means there is a critical need to establish baseline inventories through environmental survey, with the aim of promoting the conservation and stewardship of these remote habitats. To efficiently evaluate fish biodiversity around a seamount, we compared environmental DNA (eDNA) methods using seawater and sponge samples against methods using imagery obtained with a remotely operated vehicle (ROV) and a free-fall deep-sea camera lander called the Edokko Mark I on the Takuyo-Daigo Seamount (153.0°E, 23.5°N) in the northwestern Pacific Ocean. We detected a total of 18 fish families by these methods. The fish fauna detected on the seamount included many families commonly found in deep-sea areas and were similar to the fish fauna of other seamounts located at similar latitudes in the northwestern Pacific. Significant differences in the patterns of detection of fish families between the eDNA and imaging methods is attributed to the differing powers of detection of some fish groups between methods (related to primer compatibility and fish size). For deep-sea fish, the difference in fish composition at the family level between seawater and sponge eDNA methods was not significant, but the difference between Edokko Mark I and ROV methods was significant; the latter difference is likely due to whether or not bait is used to attract fish. Although the eDNA workflow implemented here requires improvements, the use of eDNA and imaging methods in combination provided better insight into the biodiversity of deep-sea fishes in the deep-sea around a seamount, where our knowledge of the fish fauna has been extremely limited. Our recovery of eDNA from seawater and sponge samples around the seamount demonstrates the potential of these methods for facilitating environmental baseline surveys and impact assessments of mining activities to obtain results not previously possible with the use of visual methods only.

Development of environmental DNA metabarcoding primers for marine mollusks and comparison with published primers

Monitoring mollusk biodiversity is a great challenge due to their large diversity and broad distribution. Environmental DNA (eDNA) technology is increasingly applied for biodiversity monitoring, but relevant studies on marine mollusks are still limited. Although previous studies have developed several pairs of primers for mollusk eDNA analyses, most of them targeted only a small group of mollusks. In this study, seven primers were designed for the mollusk community and validated and compared with eight pairs of published primers to select the best candidates. After in silico test, MollCOI154 and MollCOI255 primers showed non-specific amplification, and same results were also obtained in published primers (COI204, Sepi, and veneroida). Moll12S100, Moll12S195 and Moll16S primers failed to amplify across all genomic DNA from selected mollusk. Except Moll16S, all developed and two published (unionoida and veneroida) primers were successfully amplified on four eDNA samples from Yangtze River estuary. After annotation of the amplified sequences, MollCOI253 showed higher annotation of the amplification results than the other primers. In conclusion, MollCOI253 had better performance in terms of amplification success and specificity, and can provide technical support for eDNA-based research, which will be beneficial for molluscan biodiversity investigation and conservation.

An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding

Anthropogenically forced changes in global freshwater biodiversity demand more efficient monitoring approaches. Consequently, environmental DNA (eDNA) analysis is enabling ecosystem-scale biodiversity assessment, yet the appropriate spatio-temporal resolution of robust biodiversity assessment remains ambiguous. Here, using intensive, spatio-temporal eDNA sampling across space (five rivers in Europe and North America, with an upper range of 20-35 km between samples), time (19 timepoints between 2017 and 2018) and environmental conditions (river flow, pH, conductivity, temperature and rainfall), we characterise the resolution at which information on diversity across the animal kingdom can be gathered from rivers using eDNA. In space, beta diversity was mainly dictated by turnover, on a scale of tens of kilometres, highlighting that diversity measures are not confounded by eDNA from upstream. Fish communities showed nested assemblages along some rivers, coinciding with habitat use. Across time, seasonal life history events, including salmon and eel migration, were detected. Finally, effects of environmental conditions were taxon-specific, reflecting habitat filtering of communities rather than effects on DNA molecules. We conclude that riverine eDNA metabarcoding can measure biodiversity at spatio-temporal scales relevant to species and community ecology, demonstrating its utility in delivering insights into river community ecology during a time of environmental change.

Harnessing eDNA metabarcoding to investigate fish community composition and its seasonal changes in the Oslo fjord

In the face of global ecosystem changes driven by anthropogenic activities, effective biomonitoring strategies are crucial for mitigating impacts on vulnerable aquatic habitats. Time series analysis underscores a great significance in understanding the dynamic nature of marine ecosystems, especially amidst climate change disrupting established seasonal patterns. Focusing on Norway's Oslo fjord, our research utilises eDNA-based monitoring for temporal analysis of aquatic biodiversity during a one year period, with bi-monthly sampling along a transect. To increase the robustness of the study, a taxonomic assignment comparing BLAST+ and SINTAX approaches was done. Utilising MiFish and Elas02 primer sets, our study detected 63 unique fish species, including several commercially important species. Our findings reveal a substantial increase in read abundance during specific migratory cycles, highlighting the efficacy of eDNA metabarcoding for fish composition characterization. Seasonal dynamics for certain species exhibit clear patterns, emphasising the method's utility in unravelling ecological complexities. eDNA metabarcoding emerges as a cost-effective tool with considerable potential for fish community monitoring for conservation purposes in dynamic marine environments like the Oslo fjord, contributing valuable insights for informed management strategies.

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.

Environmental DNA unveils deep phylogeographic structure of a freshwater fish

Phylogeography bears an important part in ecology and evolution. However, current phylogeographic studies are largely constrained by limited numbers of individual samples. Using an environmental DNA (eDNA) assay for phylogeographic analyses, this study provides detailed information regarding the history of Siberian stone loach Barbatula toni, a primary freshwater fish across the whole range of Hokkaido, Japan. Based on an eDNA metabarcoding on 293 river water samples, we detected eDNA from B. toni in 189 rivers. A total of 51 samples, representing the entire island, were then selected from the B. toni eDNA-positive sample set for the subsequent analyses. To elucidate the phylogeographic structure of B. toni, newly developed eDNA metabarcoding primers (Barba-cytb-F/R) were applied to these samples, specifically targeting their haplotypic variation in cytochrome b. After a bioinformatic processing to mitigate haplotypic false positives, a total of 50 eDNA haplotypes were identified. Two regionally restricted, genetically distinct lineages of the species were revealed as a result of phylogeographic analyses on the haplotypes and tissue-derived DNA from B. toni. According to a molecular clock analysis, they have been genetically isolated for at least 1.5 million years, suggesting their ancient origin and colonisation of Hokkaido, presumably in the glacial periods. These results demonstrate how freshwater fishes can alter their distributions over evolutionary timescales and how eDNA assay can deepen our understanding of phylogeography.

An overlooked source of false positives in eDNA-based biodiversity assessment and management

Biodiversity conservation and management in urban aquatic ecosystems is crucial to human welfare, and environmental DNA (eDNA)-based methods have become popular in biodiversity assessment. Here we report a highly overlooked source of significant false positives for eDNA-based biodiversity assessment in urban aquatic ecosystems supplied with treated wastewater - eDNA pollution originating from treated wastewater represents a noteworthy source of false positives. To investigate whether eDNA pollution is specific to a certain treatment or prevalent across methods employed by wastewater treatment plants, we conducted tests on effluent treated using three different secondary processes, both before and after upgrades to tertiary treatment. We metabarcoded eDNA collected from effluent immediately after full treatment and detected diverse native and non-native, commercial and ornamental fishes (48 taxa) across all treatment processes before and after upgrades. Thus, eDNA pollution occurred irrespective of the treatment processes applied. Release of eDNA pollution into natural aquatic ecosystems could translate into false positives for eDNA-based analysis. We discuss and propose technical solutions to minimize these false positives in environmental nucleic acid-based biodiversity assessments and conservation programs.

Cost-effort analysis of Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) in monitoring marine ecological communities

Monitoring the diversity and distribution of species in an ecosystem is essential to assess the success of restoration strategies. Implementing biomonitoring methods, which provide a comprehensive assessment of species diversity and mitigate biases in data collection, holds significant importance in biodiversity research. Additionally, ensuring that these methods are cost-efficient and require minimal effort is crucial for effective environmental monitoring. In this study we compare the efficiency of species detection, the cost and the effort of two non-destructive sampling techniques: Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) metabarcoding to survey marine vertebrate species. Comparisons were conducted along the Sussex coast upon the introduction of the Nearshore Trawling Byelaw. This Byelaw aims to boost the recovery of the dense kelp beds and the associated biodiversity that existed in the 1980s. We show that overall BRUV surveys are more affordable than eDNA, however, eDNA detects almost three times as many species as BRUV. eDNA and BRUV surveys are comparable in terms of effort required for each method, unless eDNA analysis is carried out externally, in which case eDNA requires less effort for the lead researchers. Furthermore, we show that increased eDNA replication yields more informative results on community structure. We found that using both methods in conjunction provides a more complete view of biodiversity, with BRUV data supplementing eDNA monitoring by recording species missed by eDNA and by providing additional environmental and life history metrics. The results from this study will serve as a baseline of the marine vertebrate community in Sussex Bay allowing future biodiversity monitoring research projects to understand community structure as the ecosystem recovers following the removal of trawling fishing pressure. Although this study was regional, the findings presented herein have relevance to marine biodiversity and conservation monitoring programs around the globe.

A comparative study on eDNA-based detection of Siamese bat catfish (Oreoglanis siamensis) in wet and dry conditions

The use of environmental DNA (eDNA) analysis has demonstrated notable efficacy in detecting the existence of freshwater species, including those that are endangered or uncommon. This application holds significant potential for enhancing environmental monitoring and management efforts. However, the efficacy of eDNA-based detection relies on several factors. In this study, we assessed the impact of rainfall on the detection of eDNA for the Siamese bat catfish (Oreoglanis siamensis). Quantitative polymerase chain reaction (qPCR) analysis indicated that samples from days with average rainfall exceeding 35 mm (classified as heavy and very heavy rain) yielded negative results. While eDNA detection remains feasible on light or moderate rainy days, a noteworthy reduction in eDNA concentration and qPCR-positive likelihood was observed. Analysis across 12 sampling sites established a statistically significant negative relationship (p < 0.001) between eDNA detection and rainfall. Specifically, for each 1 mm increase in rainfall, there was an observed drop in eDNA concentration of 0.19 copies/mL (±0.14). The findings of this study provide definitive evidence that precipitation has a significant impact on the detection of eDNA in Siamese bat catfish. However, in the case of adverse weather conditions occurring on the day of sampling, our research indicates that it is acceptable to continue with the task, as long as the rainfall is not heavy or very heavy. To enhance the effectiveness of an eDNA survey, it is crucial to consider many factors related to climatic conditions. The aforementioned factor holds significant importance not only for the specific species under scrutiny but also for the broader dynamics of the climate.

Biogenic manganese oxides promote metal(loid) remediation by shaping microbial communities in biological aqua crust

Biological aqua crust (biogenic aqua crust-BAC) is a potentially sustainable solution for metal(loid) bioremediation in global water using solar energy. However, the key geochemical factors and underlying mechanisms shaping microbial communities in BAC remain poorly understood. The current study aimed at determining the in situ metal(loid) distribution and the key geochemical factors related to microbial community structure and metal(loid)-related genes in BAC of a representative Pb/Zn tailing pond. Here we showed that abundant metal(loid)s (e.g. Pb, As) were co-distributed with Mn/Fe-rich minerals (e.g. biogenic Mn oxide, FeOOH) in BAC. Biogenic Mn oxide (i.e. Mn) was the most dominant factor in shaping microbial community structure in BAC and source tailings. Along with the fact that keystone species (e.g. Burkholderiales, Haliscomenobacter) have the potential to promote Mn ion oxidization and particle agglomeration, as well as Mn is highly associated with metal(loid)-related genes, especially genes related to As redox (e.g. arsC, aoxA), and Cd transport (e.g. zipB), biogenic Mn oxides thus effectively enhance metal(loid) remediation by accelerating the formation of organo-mineral aggregates in biofilm-rich BAC system. Our study indicated that biogenic Mn oxides may play essential roles in facilitating in situ metal(loid) bioremediation in BAC of mine drainage.

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.

Species distribution modeling combined with environmental DNA analysis to explore distribution of invasive alien mosquitofish (Gambusia affinis) in China

China has become one of the most serious countries suffering from biological invasions in the world. In the context of global climate change, invasive alien species (IAS) are likely to invade a wider area, posing greater ecological and economic threats in China. Western mosquitofish (Gambusia affinis), which is known as one of the 100 most invasive alien species, has distributed widely in southern China and is gradually spreading to the north, causing serious ecological damage and economic losses. However, its distribution in China is still unclear. Hence, there is an urgent need for a more convenient way to detect and monitor the distribution of G. affinis to put forward specific management. Therefore, we detected the distribution of G. affinis in China under current and future climate change by combing Maxent modeling prediction and eDNA verification, which is a more time-saving and reliable method to estimate the distribution of species. The Maxent modeling showed that G. affinis has a broad habitat suitability in China (especially in southern China) and would continue to spread in the future with ongoing climate change. However, eDNA monitoring showed that occurrences can already be detected in regions that Maxent still categorized as unsuitable. Besides temperature, precipitation and human influence were the most important environmental factors affecting the distribution of G. affinis in China. In addition, by environmental DNA analysis, we verified the presence of G. affinis predicted by Maxent in the Qinling Mountains where the presence of G. affinis had not been previously recorded.

Obtaining accurate population estimates with reduced workload and lower fish mortality in multi-mesh gillnet sampling of a large pre-alpine lake

The EU Water Framework Directive requires monitoring of the ecological status of lakes, with fish as a relevant class of biotic quality indicator, but monitoring fish populations in large lakes is demanding. This study evaluated use in Lake Constance of a novel multi-mesh gillnet modified to reduce catch numbers. In direct comparison with conventional European Committee for Standardization (CEN) nets we achieved 48% reduction in fish mortality with 38% less labour for tasks directly influenced by fish catch numbers, while maintaining comparable species composition and catch per unit effort. Comparison of mesh sizes indicated no significant reduction in species detection in area-reduced panels of the small mesh sizes, while total observed species richness was greater when using the modified nets. Differences in benthic species communities among depth strata were common, while those of pelagic zones were more homogeneous and did not differ significantly with depth. Catches of different net types from the same depth stratum did not exhibit significant differences. The dominance structure of the most common species, relevant to lake assessment, was similar in catches of both net types, suggesting overall superiority of the modified nets in Lake Constance. Sampling conducted according to standard European CEN protocol, while deploying 60% fewer nets, yielded sufficiently precise abundance estimates for monitoring shallow areas of the benthic zone. A 50% difference in the abundance of dominant species was detected among sampling events with a certainty of 95%. The sample did not provide comparable accuracy in deep benthic strata or the pelagic zone, but was adequate to record complete inventories of species present. Based on this trial data, a new stratified sampling design is proposed for monitoring large lake fish communities for ecological assessment. Depth-dependent fish communities were used to calculate the required number of nets, which resulted in a 69% reduction for the entire lake compared to the CEN calculation method. Using the modified nets increases the feasibility of performing WFD surveys, by reducing effort and cost, while the simultaneous halving of fish mortality minimises the negative impact of fish surveys.

Comparative Analysis and Phylogenetic Study of Dawkinsia filamentosa and Pethia nigrofasciata Mitochondrial Genomes

Smiliogastrinae are recognized for their high nutritional and ornamental value. In this study, we employed high-throughput sequencing technology to acquire the complete mitochondrial genome sequences of Dawkinsia filamentosa and Pethia nigrofasciata. The gene composition and arrangement order in these species were similar to those of typical vertebrates, comprising 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 non-coding region. The mitochondrial genomes of D. filamentosa and P. nigrofasciata measure 16,598 and 16,948 bp, respectively. Both D. filamentosa and P. nigrofasciata exhibit a significant preference for AT bases and an anti-G bias. Notably, the AT and GC skew values of the ND6 gene fluctuated markedly, suggesting that the selection and mutation pressures on this gene may differ from those affecting other genes. Phylogenetic analysis, based on the complete mitochondrial genomes of 23 Cyprinidae fishes, revealed that D. filamentosa is closely related to the sister group comprising Dawkinsia denisonii and Sahyadria chalakkudiensis. Similarly, P. nigrofasciata forms a sister group with Pethia ticto and Pethia stoliczkana.

Vertical eDNA distribution of cold-water fishes in response to environmental variables in stratified lake

In summer, the survival zones of cold-water species are predicted to narrow by both increasing water temperatures from the surface and by expanding hypoxic zones from the lake bottom. To examine how the abundance of cold-water fishes changes along environmental gradients, we assessed the vertical environmental DNA (eDNA) distributions of three salmonid species which may have different water temperature tolerances during both stratification and turnover periods using quantitative PCR (qPCR). In addition, we examined on the vertical distribution of diverse fish fauna using an eDNA metabarcoding assay. The results suggested that the kokanee salmon (Oncorhynchus nerka) eDNA were abundant in deep, cold waters. On the other hand, rainbow trout (O. mykiss) eDNA were distributed uniformly throughout the water column, suggesting that they may have high water-temperature tolerance compared with kokanee salmon. The eDNA concentrations of masu salmon (O. masou) were below the detection limit (i.e., <10 copies μL-1) at all stations and depths and hence could not be quantified during stratification. Together with the finding that the eDNA distributions of other prey fish species were also constrained vertically in species-specific ways, our results suggest that climate change will result in substantial changes in the vertical distributions of lake fish species and thus affect their populations and interactions.

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.

Detecting kelp-forest associated metazoan biodiversity with eDNA metabarcoding

Environmental DNA (eDNA) metabarcoding is a promising tool for monitoring marine biodiversity, but remains underutilised in Africa. In this study, we evaluated the ability of aquatic eDNA metabarcoding as a tool for detecting biodiversity associated with a South African kelp forest, an ecosystem that harbours high diversity of species, many of which are endemic, but are also sensitive to changing environmental conditions and anthropogenic pressures. Using fine-scale spatial (1 m and 8 m) and temporal (every four hours for 24 h) sampling of aquatic environmental DNA and targeting two gene regions (mtDNA COI and 12S rRNA), metabarcoding detected 880 OTUs representing 75 families in the broader metazoan community with 44 OTUs representing 24 fish families. We show extensive variability in the eDNA signal across space and time and did not recover significant spatio-temporal structure in OTU richness and community assemblages. Metabarcoding detected a broad range of taxonomic groups, including arthropods, ascidians, cnidarians, echinoderms, ctenophores, molluscs, polychaetes, ichthyofauna and sponges, as well as Placozoa, previously not reported from South Africa. Fewer than 3% of OTUs could be identified to species level using available databases (COI = 19 OTUs, 12S = 11 OTUs). Our study emphasizes that kelp-forest associated biodiversity in South Africa is understudied, but that with careful consideration for sampling design in combination with increased barcoding efforts and the construction of regional databases, eDNA metabarcoding will become a powerful biomonitoring tool of kelp-forest associated biodiversity.

Using eDNA to survey amphibians: Methods, applications, and challenges

In recent years, environmental DNA (eDNA) has received attention from biologists due to its sensitivity, convenience, labor and material efficiency, and lack of damage to organisms. The extensive application of eDNA has opened avenues for the monitoring and biodiversity assessment of amphibians, which are frequently small and difficult to observe in the field, in areas such as biodiversity survey assessment and detection of specific, rare and threatened, or alien invasive species. However, the accuracy of eDNA can be influenced by factors such as ambient temperature, pH, and false positives or false negatives, which makes eDNA an adjunctive tool rather than a replacement for traditional surveys. This review provides a concise overview of the eDNA method and its workflow, summarizes the differences between applying eDNA for detecting amphibians and other organisms, reviews the research progress in eDNA technology for amphibian monitoring, identifies factors influencing detection efficiency, and discusses the challenges and prospects of eDNA. It aims to serve as a reference for future research on the application of eDNA in amphibian detection.

Associations between impulsivity and fecal microbiota in individuals abstaining from methamphetamine

INTRODUCTION

Methamphetamine (MA) abuse is a major public problem, and impulsivity is both a prominent risk factor and a consequence of addiction. Hence, clarifying the biological mechanism of impulsivity may facilitate the understanding of addiction to MA. The microbiota-gut-brain axis was suggested to underlie a biological mechanism of impulsivity induced by MA.

METHODS

We therefore recruited 62 MA addicts and 50 healthy controls (HCs) to investigate the alterations in impulsivity and fecal microbiota and the associations between them in the MA group. Thereafter, 25 MA abusers who abstained from MA for less than 3 months were followed up for 2 months to investigate the relationship between impulsivity and microbiota as abstinence became longer. 16S rRNA sequencing was conducted for microbiota identification.

RESULTS

Elevated impulsivity and dysbiosis characterized by an increase in opportunistic pathogens and a decrease in probiotics were identified in MA abusers, and both the increased impulsivity and disrupted microbiota tended to recover after longer abstinence from MA. Impulsivity was related to microbiota, and the effect of MA abuse on impulsivity was mediated by microbiota.

CONCLUSION

Our findings potentially highlighted the importance of abstention and implicated the significant role of the microbiota-gut-brain axis in the interrelationship between microbiota and behaviors, as well as the potential of microbiota as a target for intervention of impulsivity.

Assessing the impact of river connectivity on fish biodiversity in the Yangtze River Basin using a multi-index evaluation framework

The Yangtze River Basin, the world's third-largest river basin and a hot spot for global biodiversity conservation, is facing biodiversity crisis caused by reduced river connectivity. The deterioration arises from four dimensions: longitudinal, lateral, vertical and temporal. However, limited research has quantified the spatiotemporal connectivity of the Yangtze River Basin and further evaluated the consequent impact on fish biodiversity. In our study, a multi-index evaluation framework was developed to assess the variations in the four-dimensional connectivity of the Yangtze River Basin from 1980 to 2020, and fish biodiversity affected by reduced connectivity was detected by environmental DNA metabarcoding. Our results showed that the Yangtze River Basin suffers from a pronounced connectivity reduction, with 67% of assessed rivers experiencing deteriorated connectivity in recent years. The lost fish biodiversity along the river reaches with the worst connectivity was likely attributed to the construction of hydropower plants. The headwaters and the downstreams of most hydropower plants had a higher fish biodiversity compared with reservoirs. The free-flowing reaches in the downstream of the lowest hydropower station, had higher lotic fish abundance compared with that in the upstream. As for the entire Yangtze River Basin, 67% of threatened fish species, with 70% endemic species, were threatened by reduced river connectivity. Our result indicates that the massive loss of river connectivity changes the spatiotemporal patterns of fish community and threatens protected fish. More effective measures to restore the populations of affected fish in rivers with reduced river connectivity are required.

Plumage microorganism communities of tidal marsh sparrows

Microorganism communities can shape host phenotype evolution but are often comprised of thousands of taxa with varied impact on hosts. Identification of taxa influencing host evolution relies on first describing microorganism communities and acquisition routes. Keratinolytic (keratin-degrading) microorganisms are hypothesized to be abundant in saltmarsh sediments and to contribute to plumage evolution in saltmarsh-adapted sparrows. Metabarcoding was used to describe plumage bacterial (16S rRNA) and fungal (ITS) communities in three sparrow species endemic to North America's Atlantic coast saltmarshes. Results describe limited within-species variability and moderate host species-level patterns in microorganism diversity and community composition. A small percentage of overall microorganism diversity was comprised of potentially keratinolytic microorganisms, warranting further functional studies. Distinctions between plumage and saltmarsh sediment bacteria, but not fungal, communities were detected, suggesting multiple bacterial acquisition routes and/or vertebrate host specialization. This research lays groundwork for future testing of causal links between microorganisms and avian host evolution.

Use of passive sampling in environmental DNA metabarcoding technology: Monitoring of fish diversity in the Jiangmen coastal waters

Environmental DNA (eDNA) metabarcoding technology is proving to be the most up-to-date and promising method for monitoring marine fish diversity. Fish eDNA is usually collected on a filter membrane after the filtration of water. Not only does this require the use of specialized equipment, but the amount of filtered water needed is also difficult to meet. The recently proposed passive eDNA collection method can expand the sampling scale, providing new perspectives for monitoring marine biodiversity. The role of collection methods in eDNA surveys, however, remains unclear. In this study, a low-cost custom framework with two types of filter membrane materials was used to conduct passive submersion samplings at the north and south ends of Shangchuan Island, Jiangmen, China. After defined periods of submersion, the filter membranes were recovered and eDNA extracted. Metabarcoding techniques were applied to detect fish species information in the eDNA samples. A total of 106 marine fish species from 27 orders, 53 families, and 92 genera, including one cartilaginous fish, were identified in the samples. The majority of fish detected by active filtration were also found in the passively collected samples, within the same location. Both sampling methods, therefore, showed similar species richness. Passive sampling was effective in identifying fish species diversity and provided a higher spatial resolution owing to the sample replicates. Passive sampling was also more sensitive in detecting species that differ significantly in abundance (biomarkers) between different sampling depths. When active filtration is not possible, or when large-scale sampling is the purpose of the study, passive sampling methods certainly provide a promising alternative. The findings of our study provide guidance for fish surveys and continuous bio-stereoscopic monitoring in coastal waters.

rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R

The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of both DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa then are currently curated by professional staff. Thus there is a growing need for an easy to implement computational tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R which, like it's predecessor, relies on sequence homology and PCR primer compatibility instead of keyword-searches to avoid limitations of user-defined metadata. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire a set of sequences analogous to PCR products containing a user-defined set of primer sequences. Next, these seeds are used to iteratively blast search seed sequences against a local copy of the National Center for Biotechnology Information (NCBI) formatted nt database using a taxonomic-rank based stratified random sampling approach ( blast_seeds() ). This results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer-specific reference barcode sequences from NCBI. Databases can then be compared (compare_db()) to determine read and taxonomic overlap. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, fungal ITS, and Leray CO1 loci than CRABS, MetaCurator, RESCRIPt, and ecoPCR reference databases. We then further demonstrate the utility of rCRUX by generating 24 reference databases for 20 metabarcoding loci, many of which lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.

DNA metabarcoding reveals spatial and temporal variation of fish eye fluke communities in lake ecosystems

Eye flukes (Diplostomidae) are diverse and abundant trematode parasites that form multi-species communities in fish with negative effects on host fitness and survival. However, the environmental factors and host-related characteristics that determine species diversity, composition, and coexistence in such communities remain poorly understood. Here, we developed a cost-effective cox1 region-specific DNA metabarcoding approach to characterize parasitic diplostomid communities in two common fish species (Eurasian perch and common roach) collected from seven temperate lakes in Estonia. We found considerable inter- and intra-lake, as well as inter-host species, variation in diplostomid communities. Sympatric host species characterization revealed that parasite communities were typically more diverse in roach than perch. Additionally, we detected five positive and two negative diplostomid species associations in roach, whereas only a single negative association was observed in perch. These results indicate that diplostomid communities in temperate lakes are complex and dynamic systems exhibiting both spatial and temporal heterogeneity. They are influenced by various environmental factors and by host-parasite and inter-parasite interactions. We expect that the described methodology facilitates ecological and biodiversity research of diplostomid parasites. It is also adaptable to other parasite groups where it could serve to improve current understanding of diversity, distribution, and interspecies interactions of other understudied taxa.

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.

Taxonomic profiling of Nasutitermes takasagoensis microbiota to investigate the role of termites as vectors of bacteria linked to ironwood tree decline in Guam

The ironwood tree (Casuarina equisetifolia, family Casuarinaceae), an indigenous agroforestry species in Guam, has been threatened by ironwood tree decline (IWTD) since 2002. Formation of bacterial ooze by the wilt pathogen from the Ralstonia solanacearum species complex and wetwood bacteria (primarily Klebsiella species) has been linked to IWTD. In addition, termite infestation of trees was statistically associated with IWTD. Termites are known carriers of a diverse microbiome. Therefore, we hypothesized that termites could be vectors of bacteria linked to IWTD. To investigate the potential role of termites as pathogen vectors, we employed next-generation 16S rRNA gene sequencing to describe the bacteria diversity of Nasutitermes takasagoensis (Family Termitidae) workers collected from 42 ironwood trees of different disease stages in Guam in association with tree-, plot-, and location-related factors. Nasutitermes takasagoensis workers account for the majority of termite infestations of ironwood trees. The bacterial phyla composition of N. takasagoensis workers was typical for wood-feeding higher termites consisting mainly of Spirochaetes and Fibrobacteres. However, Ralstonia species were not detected and Klebsiella species were rare even in termites collected from trees infected with Ralstonia and wetwood bacteria. Feeding experiments suggested that termites prefer to consume wood with low pathogen content over wood with high pathogen load. Termites were able to ingest Ralstonia but Ralstonia could not establish itself in healthy termite bodies. We concluded that N. takasagoensis workers are not vectors for Ralstonia spp. or the bacterial endophytes associated with wetwood (Klebsiella, Pantoea, Enterobacter, Citrobacter, and Erwinia) that were previously observed in IWTD-infested trees. The bacterial diversity in termite samples was significantly influenced by various factors, including Tree Health, Site Management, Plot Average Decline Severity, Proportion of Dead Trees in the Plot, Proportion of Trees with Termite Damage in the Plot, Presence of Ralstonia, and Altitude.

Environmental DNA unveiling the fish community structure and diversity features in the Yangtze River basin

Fish, as top predators in aquatic ecosystems, play an important role in maintaining the structure and functioning of these ecosystems, making their diversity a topic of great interest. This study focused on the Yangtze River Basin to investigate the fish community structure and diversity using environmental DNA (eDNA) technology. The results showed that a total of 71616 fish operational taxonomic units (OTUs) and 90 fish belonging to 23 families were detected, with the Cyprinidae family being the dominant group, followed by the Cobitidae, Amblycipitidae, etc. Compared to historical traditional morphological fish surveys, the quantity of fish detected using eDNA was relatively low, but the overall distribution pattern of fish communities was generally consistent. The highest fish Shannon-Wiener diversity index in the Yangtze River Basin sites reaches 2.60 with an average value of 1.25. The fish diversity index was higher in the downstream compared to the middle and upstream regions, and there were significant differences among different sampling sites. Significant environmental factors influencing α-diversity included chlorophyll-a, chemical oxygen demand, dissolved oxygen, total nitrogen, and elevation. Non-metric multidimensional scaling (NMDS) analysis revealed significant differences in fish community composition between the upstream and middle/lower reaches of the Yangtze River, while the composition of fish communities in the middle and lower reaches was more similar. Redundancy analysis (RDA) indicated that total organic carbon (TOC) was positively correlated with fish community distribution in the upstream, while water temperature and NO3-N were negatively correlated with fish distribution in the upstream. NH3-N and CODMn were negatively correlated with fish distribution in the middle and downstream regions, indicating a relatively severe water pollution in these areas. Additionally, fish communities in the Yangtze River displayed a typical distance decay pattern.

Quantifying impacts of an environmental intervention using environmental DNA

Environmental laws around the world require some version of an environmental-impact assessment surrounding construction projects and other discrete instances of human development. Information requirements for these assessments vary by jurisdiction, but nearly all require an analysis of the biological elements of ecosystems. Amplicon-sequencing-also called metabarcoding-of environmental DNA (eDNA) has made it possible to sample and amplify the genetic material of many species present in those environments, providing a tractable, powerful, and increasingly common way of doing environmental-impact analysis for development projects. Here, we analyze an 18-month time series of water samples taken before, during, and after two culvert removals in a salmonid-bearing freshwater stream. We also sampled multiple control streams to develop a robust background expectation against which to evaluate the impact of this discrete environmental intervention in the treatment stream. We generate calibrated, quantitative metabarcoding data from amplifying the 12s MiFish mtDNA locus and complementary species-specific quantitative PCR data to yield multispecies estimates of absolute eDNA concentrations across time, creeks, and sampling stations. We then use a linear mixed effects model to reveal patterns of eDNA concentrations over time, and to estimate the effects of the culvert removal on salmonids in the treatment creek. We focus our analysis on four common salmonid species: cutthroat trout (Oncorhynchus clarkii), coho salmon (Oncorhynchus kisutch), rainbow trout (Oncorhynchus mykiss), and sockeye salmon (Oncorhynchus nerka). We find that one culvert in the treatment creek seemed to have no impact while the second culvert had a large impact on fish passage. The construction itself seemed to have only transient effects on salmonid species during the two construction events. In the context of billions of dollars of court-mandated road culvert replacements taking place in Washington State, USA, our results suggest that culvert replacement can be conducted with only minimal impact of construction to key species of management concern. Furthermore, eDNA methods can be an effective and efficient approach for monitoring hundreds of culverts to prioritize culverts that are required to be replaced. More broadly, we demonstrate a rigorous, quantitative method for environmental-impact reporting using eDNA that is widely applicable in environments worldwide.

Collection of environmental DNA from stemflow for monitoring arboreal biodiversity: Preliminary validation using lichens

The forest canopy harbors a diverse array of organisms. However, monitoring their biodiversity poses challenges due to limited accessibility and the vast taxonomic diversity. To address these challenges, we present a novel method for capturing arboreal biodiversity by harnessing stemflow as a source of DNA from organisms inhabiting trees. Our method involves encircling the tree trunk with gauze, directing the stemflow along the gauze into a funnel, and collecting it in a plastic bag. We employed dual collection systems to retrieve environmental DNA (eDNA) from the stemflow: the gauze trap, designed to capture macroscopic biological fragments, and the plastic bag trap, which collected the stemflow itself. The trapped fragments and stemflow were separately filtered, and eDNA was subsequently extracted from the filter membranes. To validate our method, we focused on foliose lichens, which are easily observable on tree surfaces. We performed eDNA metabarcoding and successfully detected a majority of the observed foliose lichen species, including those not identified through visual observation alone.•We have developed a non-invasive and straightforward method for monitoring arboreal biodiversity by collecting eDNA from stemflow, which has been validated using lichens for its efficacy.•This cost-effective approach minimizes disruptions to tree ecosystems and is expected to provide an efficient means of sampling and monitoring arboreal organisms.

Environmental DNA-based biomonitoring of Cuban Crocodylus and their accompanying vertebrate fauna from Zapata Swamp, Cuba

Crocodylians globally face considerable challenges, including population decline and extensive habitat modification. Close monitoring of crocodylian populations and their habitats is imperative for the timely detection of population trends, especially in response to management interventions. Here we use eDNA metabarcoding to identify the Critically Endangered Crocodylus rhombifer and the Vulnerable C. acutus, as well as vertebrate community diversity, in Cuba's Zapata Swamp. We tested four different primer sets, including those used previously in Crocodylus population genetic and phylogenetic research, for their efficiency at detecting crocodylian eDNA. We detected C. rhombifer eDNA in 11 out of 15 sampled locations within its historical geographic distribution. We found that data analyses using the VertCOI primers and the mBRAVE bioinformatics pipeline were the most effective molecular marker and pipeline combination for identifying this species from environmental samples. We also identified 55 vertebrate species in environmental samples across the four bioinformatics pipelines- ~ 85% known to be present in the Zapata ecosystem. Among them were eight species previously undetected in the area and eight alien species, including known predators of hatchling crocodiles (e.g., Clarias sp.) and egg predators (e.g., Mus musculus). This study highlights eDNA metabarcoding as a powerful tool for crocodylian biomonitoring within fragile and diverse ecosystems, particularly where fast, non-invasive methods permit detection in economically important areas and will lead to a better understanding of complex human-crocodile interactions and evaluate habitat suitability for potential reintroductions or recovery programs for threatened crocodylian species.

Validating post-enrichment steps in environmental RNA analysis for improving its availability from water samples

Environmental RNA (eRNA) analysis is expected to inclusively provide the physiological information of a population and community without individual sampling, having the potential for the improved monitoring of biodiversity and ecosystem function. Protocol development for maximizing eRNA availability is crucial to interpret its detection and quantification results with high accuracy and reliability, but the methodological validation and improvement of eRNA collection and processing methods are scarce. In this study, the technical steps after eRNA extraction, including genomic DNA (gDNA) removal and reverse transcription, were focused on and their performances were compared by zebrafish (Danio rerio) aquarium experiments. Additionally, this study also focused on the eRNA quantification variabilities between replicates and compared them between the PCR and sample levels. Results showed that (i) there was a trade-off between gDNA removal approaches and eRNA yields and an excess gDNA removal could lead to the false-negative eRNA detection, (ii) the use of the gene-specific primers for reverse transcription could increase the eRNA yields for multiple mitochondrial and nuclear genes compared with the random hexamer primers, and (iii) the coefficient of variation (CV) values of eRNA quantifications between PCR replicates were substantially lower for those between samples. Including the study, further knowledge for the sensitive and precise detection of macro-organismal eRNA should be needed for increasing the reliability and robustness of eRNA-based biomonitoring.

DNA metabarcoding reveals the dietary profiles of a benthic marine crustacean, Nephrops norvegicus

Norwegian lobster, Nephrops norvegicus, are a generalist scavenger and predator capable of short foraging excursions but can also suspension feed. Existing knowledge about their diet relies on a combination of methods including morphology-based stomach content analysis and stable isotopes, which often lack the resolution to distinguish prey items to species level particularly in species that thoroughly masticate their prey. DNA metabarcoding overcomes many of the challenges associated with traditional methods and it is an attractive approach to study the dietary profiles of animals. Here, we present the diet of the commercially valuable Nephrops norvegicus using DNA metabarcoding of gut contents. Despite difficulties associated with host amplification, our cytochrome oxidase I (COI) molecular assay successfully achieves higher resolution information than traditional approaches. We detected taxa that were likely consumed during different feeding strategies. Dinoflagellata, Chlorophyta and Bacillariophyta accounted for almost 50% of the prey items consumed, and are associated with suspension feeding, while fish with high fisheries discard rates were detected which are linked to active foraging. In addition, we were able to characterise biodiversity patterns by considering Nephrops as natural samplers, as well as detecting parasitic dinoflagellates (e.g., Hematodinium sp.), which are known to influence burrow related behaviour in infected individuals in over 50% of the samples. The metabarcoding data presented here greatly enhances a better understanding of a species' ecological role and could be applied as a routine procedure in future studies for proper consideration in the management and decision-making of fisheries.

Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA

Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information-especially sequence information that includes intraspecific variation-creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial 'barcode' regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.

Identification and functional characterization of a novel TRPA1 gene from sea cucumber Apostichopus japonicus and interaction with miR-2013 in response to salt stress

Salinity is important abiotic factor influencing sea cucumber aquaculture. This study aimed to identify and functional study of a novel transient receptor potential cation channel subfamily A member 1 (TRPA1) involved in salinity stress through interaction with miR-2013 in the sea cucumber. The full-length cDNA sequence was 1369 bp in length and encoded 138 amino acids. The TRPA1 homolog protein was a hydrophilic protein without a signal peptide and was predicted to a spatial structure of seven helices and eight random coils and two major ANK functional domains. Bioinformatic analysis and luciferase reporter assays confirmed TRPA1 as a target gene of miR-2013. Quantitative PCR revealed that miR-2013 was induced upregulation after salinity stress, while TRPA1 showed upregulated expression with maximum expression at 24 h. The expression of miR-2013 and TRPA1 was negatively regulated. Transfection experiments were conducted to validate the role of miR-2013 and TRPA1 in salinity response. The results showed that miR-2013 was upregulated and TRPA1 was downregulated after transfection with miR-2013 mimics, while miR-2013 was downregulated and TRPA1 was upregulated after transfection with miR-2013 inhibitor. Transfection with si-TRPA1 homolog resulted in upregulation of miR-2013 and downregulation of TRPA1 homolog. These findings suggest that miR-2013 can regulate the expression of TRPA1 under salt stress, and highlight the importance of miR-2013 and TRPA1 in salt stress response. miR-2013 mimics improved the survival rate, while miR-2013 inhibitor and si-TRPA1 reduced it. These findings suggest that miR-2013 and TRPA1 play important roles in sea cucumbers adaptation to salinity changes.

First pelagic fish biodiversity assessment of Cosmonaut Sea based on environmental DNA

The Cosmonaut Sea is a typical marginal sea in East Antarctica that has not yet been greatly impacted by climate change. As one of the least explored areas in the Southern Ocean, our knowledge regarding its fish taxonomy and diversity has been sparse. eDNA metabarcoding, as an emerging and promising tool for marine biodiversity research and monitoring, has been widely used across taxa and habitats. During the 38th Chinese Antarctic Research Expedition (CHINARE-38), we collected seawater and surface sediment samples from 38 stations in the Cosmonaut Sea and performed the first, to our knowledge, eDNA analysis of fish biodiversity in the Southern Ocean based on the molecular markers of 12S rRNA and 16S rRNA. There were 48 fish species detected by the two markers in total, with 30 and 34 species detected by the 12S rRNA and 16S rRNA marker, respectively. This was more than the trawling results (19 species) and historical survey records (16 species, "BROKE-West" cruise). With some nonsignificant differences between the Gunnerus Ridge and the Oceanic Area of Enderby Land, the Cosmonaut Sea had a richer fish biodiversity in this research compared with previous studies, and its overall composition and distribution patterns were consistent with what we know in East Antarctica. We also found that the eDNA composition of fish in the Cosmonaut Sea might be related to some environmental factors. Our study demonstrated that the use of the eDNA technique for Antarctic fish biodiversity research is likely to yield more information with less sampling effort than traditional methods. In the context of climate change, the eDNA approach will provide a novel and powerful tool that is complementary to traditional methods for polar ecology research.

Environmental DNA metabarcoding of water samples as a tool for monitoring Iberian freshwater fish composition

Environmental DNA (eDNA) metabarcoding has been increasingly used to monitor the community assemblages of a wide variety of organisms. Here, we test the efficacy of eDNA metabarcoding to assess the composition of Iberian freshwater fishes, one of the most endangered groups of vertebrates in Spain. For this purpose, we sampled 12 sampling sites throughout one of Spain's largest basins, the Duero, which is home to approximately 70% of the genera and 30% of the primary freshwater fish in Spain. We sampled these sampling sites in the summer by using electrofishing, a traditional sampling method, and eDNA metabarcoding of river water samples using the mitochondrial 12S rRNA gene (12S) as a marker. We also resampled four of these sampling sites in autumn by eDNA. We compared the results obtained through eDNA metabarcoding with those of electrofishing surveys (ones conducted for the present study and past ones) and assessed the suitability of 12S as an eDNA metabarcoding marker for this group of freshwater fishes. We found that the 12S fragment, analysed for 25 Iberian species, showed sufficient taxonomic resolution to be useful for eDNA approaches, and even showed population-level differences in the studied populations across the tissue samples for Achondrostoma arcasii. In most cases, a greater number of species was detected through eDNA metabarcoding than through electrofishing. Based on our results, eDNA metabarcoding is a powerful tool to study the freshwater fish composition in the Iberian Peninsula and to unmask cryptic diversity. However, we highlight the need to generate a local genetic database for 12S gene for such studies and to interpret the results with caution when studying only mitochondrial DNA. Finally, our survey shows that the high detection sensitivity of eDNA metabarcoding and the non-invasiveness of this method allows it to act as a detection system for species of low abundance, such as early invasive species or species in population decline, two key aspects of conservation management of Spanish freshwater fishes.

Environmental DNA metabarcoding reveals distinct fish assemblages supported by seagrass (Zostera marina and Zostera pacifica) beds in different geographic settings in Southern California

Seagrass beds are disappearing at a record pace despite their known value to our oceans and coastal communities. Simultaneously, our coastlines are under the constant pressure of climate change which is impacting their chemical, physical and biological characteristics. It is thus pertinent to evaluate and record habitat use so we can understand how these different environments contribute to local biodiversity. This study evaluates the assemblages of fish found at five Zostera beds in Southern California using environmental DNA (eDNA) metabarcoding. eDNA is a powerful biodiversity monitoring tool that offers key advantages to conventional monitoring. Results from our eDNA study found 78 species of fish that inhabit these five beds around Southern California representing embayment, open coastal mainland and open coastal island settings. While each bed had the same average number of species found throughout the year, the composition of these fish assemblages was strongly site dependent. There were 35 fish that were found at both open coast and embayment seagrass beds, while embayment seagrass sites had 20 unique fish and open coast sites had 23 unique fish. These results demonstrate that seagrass fish assemblages are heterogenous based on their geographic positioning and that marine managers must take this into account for holistic conservation and restoration efforts.

DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker-dependent

The study of ichthyoplankton is paramount to understanding fish assemblages' reproductive dynamics. DNA metabarcoding has been applied as a rapid, cost-effective, and accurate taxonomy tool, allowing the identification of multiple individuals simultaneously. However, there remain significant challenges when using DNA metabarcoding, such as molecular marker choice according to the taxonomic resolution and length of the fragment to be sequenced, primer bias, incomplete reference databases, and qualitative inference incongruences. Here, 30 ichthyoplankton pools collected from a Neotropical river were identified at a molecular level using DNA metabarcoding to compare the resolution, sensibility, specificity, and relative read abundance (RRA) recovery of three molecular markers: the standard COI fragment (650 pb, with each end analyzed individually) and two short 12S rRNA genes markers (≅200 bp - NeoFish and MiFish markers). The combined use of the three markers increased the genera detection rates by 25%-87.5%, allowing an increased taxonomic coverage and robust taxonomic identification of complex Neotropical ichthyoplankton communities. RRA is marker-dependent, indicating caution is still needed while inferring species abundance based on DNA metabarcoding data when using PCR-dependent protocols.

Merging two eDNA metabarcoding approaches and citizen-science-based sampling to facilitate fish community monitoring along vast Sub-Saharan coastlines

The coastline of Sub-Saharan Africa hosts highly diverse fish communities of great conservation value, which are also key resources for local livelihoods. However, many costal ecosystems are threatened by overexploitation and their conservation state is frequently unknown due to their vast spatial extent and limited monitoring budgets. Here, we evaluated the potential of citizen science-based eDNA surveys to alleviate such chronic data deficiencies and assessed fish communities in Mozambique using two 12S metabarcoding primer sets. Samples were either collected by scientific personnel or trained community members and results from the two metabarcoding primers were combined using a new data merging approach. Irrespective of the background of sampling personnel, a high average fish species richness was recorded (38 ± 20 OTUs per sample). Individual sections of the coastline largely differed in the occurrence of threatened and commercially important species, highlighting the need for regionally differentiated management strategies. A detailed comparison of the two applied primer sets revealed an important trade-off in primer choice with MiFish primers amplifying a higher number of species but Riaz primers performing better in the detection of threatened fish species. This trade-off could be partly resolved by applying our new data-merging approach, which was especially designed to increase the robustness of multiprimer assessments in regions with poor reference libraries. Overall, our study provides encouraging results but also highlights that eDNA-based monitoring will require further improvements of, for example, reference databases and local analytical infrastructure to facilitate routine applications in Sub-Saharan Africa.

Supporting ecosystem services of habitat and biodiversity in temperate seaweed (Saccharina spp.) farms

Habitat provisioning, and the biodiversity within, is considered a type of "supporting" ecosystem service. Ecosystem services are the benefits humans receive from healthy ecosystems. We assess whether kelp (Saccharina spp.) farms provide seasonal habitat for wild organisms. Contrary to other studies conducted in tropic seaweed farms, we did not observe habitat provisioning or increased biodiversity at seasonal temperate seaweed farm sites compared to neighboring non-farm sites, which is encouraging news for the aquaculture industry given that most farm gear is removed from the water after the spring harvest. We quantified fish and crustaceans interacting with kelp farms using GoPro cameras. We also assessed small (<5 mm) invertebrates using mesh settling devices suspended at the same depth as kelp lines (2m). Visual surveys were paired with eDNA. There was coherence in the conclusions drawn from observational and eDNA methods, despite weak coherence in the specific species identified between the methods. Both farm and non-farm sites exhibited higher species richness and biodiversity in the summer non-growing season compared to the winter growing season, attributed to expected seasonal species movements.