Environmental DNA study on aquatic ecosystem monitoring and management: Recent advances and prospects

Passive acoustic monitoring of baleen whale seasonal presence across the New York Bight

The New York Bight is an ecologically and economically important marine region along the U.S. Atlantic Coast. Extensive assessments have characterized the habitats and biota in this ecosystem; however, most have focused on fishes, benthic habitats, and human impacts. To investigate the spatial and temporal occurrence of whales in this region, we conducted a three-year passive acoustic monitoring survey that documented the acoustic presence of five baleen whale species that occur within the New York Bight and are of conservation concern: North Atlantic right whales (Eubalaena glacialis), humpback whales (Megaptera novaeangliae), fin whales (Balaenoptera physalus), sei whales (Balaenoptera borealis), and blue whales (Balaenoptera musculus). Data were recorded with 14 bottom-mounted acoustic sensors across the continental shelf between 2017 and 2020. Right whales were detected across all seasons, with most detections in autumn closer to New York Harbor and spring detections at sites closer to the continental shelf edge. Humpbacks were detected during all months of the year with varying distribution of detections across the shelf. The year-round presence of right and humpback whales challenges previous hypotheses that this region is primarily a stopover location along their migration paths. Fin whales were detected at all sites on most days. Sei whales were detected primarily during the spring at offshore sites. Blue whales were detected in the winter at sites closer to the continental shelf edge, but were rare. These data improve our understanding of baleen whale seasonal occurrences in the New York Bight and can inform monitoring and mitigation efforts associated with the management and conservation of these species.

Combining chemical analysis and toxicological methods to access the ecological risk of complex contamination in Daye Lake

As one of the nine primary non-ferrous metal smelting bases in China, Daye Lake basin was polluted due to diverse human activities. But so far the pollution status and related ecological risks of this region have not been detailly investigated. In current study, pollutants including heavy metals, polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCPs) in eight sediment samples from Daye Lake were quantified. 18S rRNA gene sequencing was employed to profile the nematode community structure within these sediments. Model organism Caenorhabditis elegans (C. elegans) were further applied for a comprehensive ecological risk assessment of Daye Lake. Notably, Cadmium (Cd) was identified as a key driver of ecological risk, reaching an index of 1287.35. At sample point S4, OCPs particularly p,p'-DDT, displayed an extreme ecological risk with a value of 23.19. Cephalobidae and Mononchida showed strong sensitivity to pollutant levels, reinforcing their suitability as robust bioindicators. The composite pollutants in sampled sediments caused oxidative stress in C. elegans, with gene Vit-2 and Mtl-1 as sensitive biomarkers. By employing the multiple analysis methods, our data can offer valuable contributions to environmental monitoring and health risk assessment for composite polluted areas.

Freshwater megafauna shape ecosystems and facilitate restoration

Freshwater megafauna, such as sturgeons, giant catfishes, river dolphins, hippopotami, crocodylians, large turtles, and giant salamanders, have experienced severe population declines and range contractions worldwide. Although there is an increasing number of studies investigating the causes of megafauna losses in fresh waters, little attention has been paid to synthesising the impacts of megafauna on the abiotic environment and other organisms in freshwater ecosystems, and hence the consequences of losing these species. This limited understanding may impede the development of policies and actions for their conservation and restoration. In this review, we synthesise how megafauna shape ecological processes in freshwater ecosystems and discuss their potential for enhancing ecosystem restoration. Through activities such as movement, burrowing, and dam and nest building, megafauna have a profound influence on the extent of water bodies, flow dynamics, and the physical structure of shorelines and substrata, increasing habitat heterogeneity. They enhance nutrient cycling within fresh waters, and cross-ecosystem flows of material, through foraging and reproduction activities. Freshwater megafauna are highly connected to other freshwater organisms via direct consumption of species at different trophic levels, indirect trophic cascades, and through their influence on habitat structure. The literature documenting the ecological impacts of freshwater megafauna is not evenly distributed among species, regions, and types of ecological impacts, with a lack of quantitative evidence for large fish, crocodylians, and turtles in the Global South and their impacts on nutrient flows and food-web structure. In addition, population decline, range contraction, and the loss of large individuals have reduced the extent and magnitude of megafaunal impacts in freshwater ecosystems, rendering a posteriori evaluation more difficult. We propose that reinstating freshwater megafauna populations holds the potential for restoring key ecological processes such as disturbances, trophic cascades, and species dispersal, which will, in turn, promote overall biodiversity and enhance nature's contributions to people. Challenges for restoration actions include the shifting baseline syndrome, potential human-megafauna competition for habitats and resources, damage to property, and risk to human life. The current lack of historical baselines for natural distributions and population sizes of freshwater megafauna, their life history, trophic interactions with other freshwater species, and interactions with humans necessitates further investigation. Addressing these knowledge gaps will improve our understanding of the ecological roles of freshwater megafauna and support their full potential for facilitating the development of effective conservation and restoration strategies to achieve the coexistence of humans and megafauna.

New insights into the on-site monitoring of probiotics eDNA using biosensing technology for heat-stress relieving in coral reefs

Coral probiotics can improve the tolerance of corals to heat stress, thus mitigating the process of coral thermal bleaching. Sensitive and specific detection of coral probiotics at low abundances is highly desirable but remains challenging, especially for rapid and on-site detection of coral probiotics. Since the electrochemical biosensor has been recently used in the field of environmental DNA (eDNA) detection, herein, an efficient electrochemical biosensor was developed based on CoS2/CoSe2-NC HNCs electrode material with a specific DNA probe for the C. marina detection. After optimization, the lower limit of detection (LOD) values of such biosensors for the target DNA and genomic DNA were 1.58 fM and 6.5 pM, respectively. On this basis, a portable device was constructed for the practical detection of C. marina eDNA, and its reliability and accuracy were verified by comparison with the ddPCR method (P > 0.05). For each analysis, the average cost was only ∼ $1.08 and could be completed within 100 min with reliable sensitivity and specificity. Overall, the biosensor could reflect the protective effect of probiotics on coral heat stress, and the proposed technique will put new insights into the rapid and on-site detection of coral probiotics to assist corals against global warming.

Urban landscape-level biodiversity assessments of aquatic and terrestrial vertebrates by environmental DNA metabarcoding

Globally, expansive urbanization profoundly alters natural habitats and the associated biota. Monitoring biodiversity in cities can provide essential information for conservation management, but the complexity of urban landscapes poses serious challenges to conventional observational and capture-based surveys. Here we assessed pan-vertebrate biodiversity, including both aquatic and terrestrial taxa, using environmental DNA (eDNA) sampled from 109 water sites across Beijing, China. Using eDNA metabarcoding with a single primer set (Tele02), we detected 126 vertebrate species, including 73 fish, 39 birds, 11 mammals, and 3 reptiles belonging to 91 genera, 46 families, and 22 orders. The probability of detection from eDNA varied substantially among species and was related to their lifestyle, as shown by the greater detectability of fish compared to that of terrestrial and arboreal (birds and mammals) groups, as well as the greater detectability of water birds compared to that of forest birds (Wilcoxon rank-sum test p = 0.007). Furthermore, the eDNA detection probabilities across all vertebrates (Wilcoxon rank-sum test p = 0.009), as well as for birds (p < 0.001), were higher at lentic sites in comparison with lotic sites. Also, the detected biodiversity was positively correlated with lentic waterbody size for fish (Spearman p = 0.012), but not for other groups. Our results demonstrate the capacity of eDNA metabarcoding to efficiently surveil diverse vertebrate communities across an extensive spatial scale in heterogenous urban landscapes. With further methodological development and optimization, the eDNA approach has great potential for non-invasive, efficient, economic, and timely assessments of biodiversity responses to urbanization, thus guiding city ecosystem conservation management.

Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution

Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.

Evaluation and comparison of the benthic and microbial indices of biotic integrity for urban lakes based on environmental DNA and its management implications

With the intensification of human disturbance in urban lakes, the loss of eukaryotic biodiversity (macroinvertebrates, etc.) reduces the accuracy of the index of biotic integrity (IBI) assessment. Therefore, how to accurately evaluate the ecological status of urban lakes based on IBI has become an important issue. In this study, 17 sampling sites from four lakes in Wuhan City, China were selected to analyze the composition and diversity characteristics of benthic and microbial communities and their relationship with environmental factors based on eDNA high-throughput sequencing, and compare the application effects of the benthic index of biotic integrity (B-IBI) and the microbial index of biotic integrity (M-IBI). Canonical correspondence analysis showed that the key environmental factors affecting benthic family/genus composition were temperature, conductivity, total phosphorus (TP), and total nitrogen (TN). Redundancy analysis showed that pH, TP, conductivity, and ammonia nitrogen had the greatest impact on microbial phyla/genera. After screening, four and six core metrics were determined from candidate parameters to establish B-IBI and M-IBI. The B-IBI evaluation results showed that healthy, sub-heathy, and poor accounted for 58.8%, 35.3%, and 5.9%, respectively, in the sites. The results of the M-IBI evaluation showed that 29.4% of the sites were healthy, 47.1% were sub-healthy, and 23.5% were common. M-IBI was positively correlated with water quality (r = 0.74, P < 0.001), whereas B-IBI was not. Further results showed that M-IBI was negatively correlated with the relative abundance of bloom-forming cyanobacteria Planktothrix (r = -0.54, P < 0.05). Therefore, M-IBI is more sensitive than B-IBI and can better reflect the actual water pollution status. This study can provide a new perspective for ecological assessment and management of urban lakes strongly disturbed by human activities.

Compact and automated eDNA sampler for in situ monitoring of marine environments

Using environmental DNA (eDNA) to monitor biodiversity in aquatic environments is becoming an efficient and cost-effective alternative to other methods such as visual and acoustic identification. Until recently, eDNA sampling was accomplished primarily through manual sampling methods; however, with technological advances, automated samplers are being developed to make sampling easier and more accessible. This paper describes a new eDNA sampler capable of self-cleaning and multi-sample capture and preservation, all within a single unit capable of being deployed by a single person. The first in-field test of this sampler took place in the Bedford Basin, Nova Scotia, Canada alongside parallel samples taken using the typical Niskin bottle collection and post-collection filtration method. Both methods were able to capture the same aquatic microbial community and counts of representative DNA sequences were well correlated between methods with R[Formula: see text] values ranging from 0.71-0.93. The two collection methods returned the same top 10 families in near identical relative abundance, demonstrating that the sampler was able to capture the same community composition of common microbes as the Niskin. The presented eDNA sampler provides a robust alternative to manual sampling methods, is amenable to autonomous vehicle payload constraints, and will facilitate persistent monitoring of remote and inaccessible sites.