Use Of Environmental DNA Research Articles

A Review of Next-Generation Wildlife Monitoring using Environmental DNA (eDNA) Detection and Next-Generation Sequencing in Malaysia

The use of environmental DNA (eDNA) as the genetic tool to monitor biodiversity has been increasing across the world, including Malaysia. Over a decade, the technique has become widely used in wildlife conservation with the technologies called next-generation sequencing (NGS). Unfortunately, as one of the top megadiverse countries, Malaysia is still behind in this field since eDNA methods outperform traditional surveys. Hence, in this study, we analyzed the paper related to eDNA studies in Malaysia, which focused on wildlife monitoring. We conducted a systematic bibliographic search and quantitative review of studies published before June 2021 from Google Scholar and Scopus database. Forty published eDNA studies were found, and each paper was classified based on five themes (species identification, diet assessment, health monitoring, resolve taxonomic, whole-genome sequencing) according to the study analysis. This study aims to identify gaps in eDNA in Malaysia, which can later be useful for future conservation actions and development by applying technology in wildlife monitoring.

Steps forward in biomonitoring 2.0: eDNA Metabarcoding and community-level modelling allow the assessment of complex drivers of Neotropical fish diversity.

The way we inventory and monitor biodiversity globally has been revolutionized by new molecular and ecological methods (Pawlowski et al 2021). Nonetheless, the Neotropical realm still represents a great challenge to our understanding of species distribution patterns and the role played by different drivers of biodiversity. The paper by Coutant et al. (2022) is a great advance towards a holistic approach to quantifying the contribution of environmental and anthropogenic factors that drive community assembly in the Amazon, and how we can apply such knowledge to guide future monitoring programmes. Disentangling the relative roles played by multiple drivers of biodiversity allowed them to also highlight hotspot areas hosting unique freshwater fish diversity and to pinpoint conservation priorities. Toward this end, the authors applied an innovative framework that included the use of environmental DNA (eDNA) to conduct fish inventories combined with community-level modelling. Their multifaceted approach accounting for taxonomic and functional measures of biodiversity allowed a thorough evaluation of ecological patterns. They reported a mismatch between functional and taxonomic biodiversity in their responses to geographical, environmental, and anthropogenic factors. Functional diversity was influenced by environmental and anthropogenic factors, while fish taxonomic diversity was determined by dispersal restrictions at both intra and inter-basin scales in the Guiana Shield. The role played by dispersal limitation and human activities in shaping fish diversity in large rivers is very relevant considering that Amazonian freshwater ecosystems are facing large-scale degradation due to human activities greatly impairing river connectivity (Castello & Macedo, 2016).

EnvironmentalDNAsurveys of African biodiversity: State of knowledge, challenges, and opportunities

AbstractEnvironmental DNA surveys have become a well‐established tool for detecting natural communities, showing excellent promise for supporting biodiversity monitoring, conservation, and management efforts. Africa is a continent of exceptional biodiversity, threatened not only by anthropogenic pressures but also by a general lack of research capacity and infrastructure, limiting evaluation and monitoring of ecosystems. This commentary explores the use of environmental DNA in surveying natural diversity, a rapidly moving field, within the context of capturing Africa's natural capital. Through an extensive literature search and filtering, 65 papers from 22 countries were identified, with research from Madagascar and Africa forming the bulk of the literature (~38%), with many countries only represented by one to three papers. There was a diverse range of studies, with more than half reporting on communities or diet analyses; freshwater and marine research are underrepresented, accounting for ~5% of studies. There were some papers on disease monitoring, particularly in freshwater. Disturbingly, representation of authors was highly skewed and highlights the ongoing inequality of scientific publishing and the extent of parachute science; one‐third of papers (n = 21) reported no African representation, in contrast with the 18 papers that had either first or senior authors affiliated with an institution in Africa. The remainder of the papers (n = 27) had at least one author affiliated with an African institution. In addition, less than half of papers reported appropriate sampling permits. Importantly and with a concerted global effort, building long‐term capacity, through meaningful and equitable relationships will help increase self‐sustaining science around technologies based on eDNA, thus ensuring not only biodiversity but also humanitarian benefits across Africa.

Cultivating epizoic diatoms provides insights into the evolution and ecology of both epibionts and hosts

Our understanding of the importance of microbiomes on large aquatic animals—such as whales, sea turtles and manatees—has advanced considerably in recent years. The latest observations indicate that epibiotic diatom communities constitute diverse, polyphyletic, and compositionally stable assemblages that include both putatively obligate epizoic and generalist species. Here, we outline a successful approach to culture putatively obligate epizoic diatoms without their hosts. That some taxa can be cultured independently from their epizoic habitat raises several questions about the nature of the interaction between these animals and their epibionts. This insight allows us to propose further applications and research avenues in this growing area of study. Analyzing the DNA sequences of these cultured strains, we found that several unique diatom taxa have evolved independently to occupy epibiotic habitats. We created a library of reference sequence data for use in metabarcoding surveys of sea turtle and manatee microbiomes that will further facilitate the use of environmental DNA for studying host specificity in epizoic diatoms and the utility of diatoms as indicators of host ecology and health. We encourage the interdisciplinary community working with marine megafauna to consider including diatom sampling and diatom analysis into their routine practices.

Detecting endangered pinto abalone (Haliotis kamtschatkana) using environmental DNA: Comparison of ddPCR, qPCR, and conventional diver surveys

AbstractAbalone populations along the Pacific Coast of North America are threatened. In the Salish Sea (Washington, USA), pinto abalone (Haliotis kamtschatkana) have failed to recover from intensive harvest after over 25 years of fishery closure, prompting a growing restoration effort. As these efforts expand, a persistent challenge is simply locating this rare and highly cryptic species in the field, limiting the ability to identify critical habitat and locate wild adults to serve as restoration broodstock. Here, we tested the use of environmental DNA (eDNA) to detect pinto abalone. Using a quantitative PCR (qPCR) assay previously developed for larval pinto abalone, we first evaluated its sensitivity to abalone eDNA in aquaria settings, finding a positive relationship between abalone biomass and the concentration of abalone DNA. We then tested abalone eDNA detection in the field by collecting replicate water samples from abalone restoration sites, using an occupancy model to estimate detection probability in relation to abalone biomass estimated via diver surveys. Both eDNA concentration and detection probability were positively associated with diver‐estimated abalone biomass. By modifying the assay for droplet digital PCR (ddPCR), detection probability increased by 32%–89% over qPCR. eDNA surveys using ddPCR had higher error (CV = 96.9%) than diver surveys (CV = 29.4%) but were more efficient, taking approximately 1/10th of the person‐hours per site of a diver survey. For the final phase of the study, we collected water samples at 80 sites throughout the region, obtaining positive abalone eDNA detections at 11 sites with qPCR and 19 additional sites with ddPCR. Our results provide novel survey data on abalone populations within the Salish Sea and show that eDNA is a viable tool for cost‐effective, efficient, and non‐invasive abalone detection.

Use of environmental DNA to detect the myxozoan endoparasite Tetracapsuloides bryosalmonae in large Norwegian lakes

AbstractEnvironmental DNA (eDNA) is an increasingly used noninvasive and cost‐effective method for species detections in surveillance studies. The myxozoan endoparasite Tetracapsuloides bryosalmonae is the causative agent of proliferative kidney disease (PKD) in salmonid fish. PKD is a potentially lethal disease of freshwater salmonids when water temperatures exceed 12–14°C for prolonged periods. Periodically, high mortality and decline in farmed and wild salmonid populations in Europe and North America have been reported in the last decades. The aim of this study was to use eDNA as a method to detect Tetracapsuloides bryosalmonae from large, deep, dimictic Norwegian lakes. Such habitats are expected to become increasingly important for cold‐water salmonids with global warming. Samples were collected from five lakes in southeastern Norway, and parasite DNA was detected by qPCR. eDNA from T. bryosalmonae was detected in four of the five lakes surveyed. These findings corresponded with the detection of T. bryosalmonae DNA in salmonid kidneys in four of the lakes in a previous survey. The detection of parasites from eDNA varied between years and stations within the same lake, revealing a changing and apparently stochastic spatial distribution of parasite DNA from year to year. Nonetheless, by sampling multiple sites throughout the lakes, we were able to detect T. bryosalmonae at the lake level in both survey years. Strategies for eDNA sampling in deep, dimictic lakes are discussed.

The use of environmental DNA to monitor impacted coastal estuaries

Environmental DNA (eDNA) metabarcoding is increasingly being used to assess community composition in coastal ecosystems. In this study, we chose to examine temporal and spatial changes in the aquatic community of Manly Lagoon – one of the most heavily developed and polluted estuaries in eastern Australia. Based on metabarcoding of the 16S mitochondrial gene (for fish) and the 18S nuclear gene (for macroinvertebrates), we identified seasonal differences in fish and macroinvertebrate community composition as well as species richness, which correlated, in some cases, with the environmental parameters of sea surface temperature and freshwater input. Moreover, given the greater taxonomic resolution of fish versus macroinvertebrate assignments, we identified several known migratory fish species of management importance that contributed significantly to the overall patterns observed. Overall, our data support the use of eDNA metabarcoding to track fish assemblages shifting in response to environmental drivers in polluted estuaries with increased sampling and consultation with historical data.

Diversity, distribution and ecology of fungal communities present in Antarctic lake sediments uncovered by DNA metabarcoding

We assessed fungal diversity in sediments obtained from four lakes in the South Shetland Islands and James Ross Island, Antarctica, using DNA metabarcoding. We detected 218 amplicon sequence variants (ASVs) dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota and Chytridiomycota. In addition, the rare phyla Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Monoblepharomycota, Rozellomycota and Zoopagomycota as well as fungal-like Straminopila belonging to the phyla Bacillariophyta and Oomycota were detected. The fungal assemblages were dominated by unknown fungal taxa (Fungal sp. 1 and Fungal sp. 2), followed by Talaromyces rubicundus and Dactylonectria anthuriicola. In general, they displayed high diversity, richness and moderate dominance. Sequences representing saprophytic, pathogenic and symbiotic fungi were detected, including the phytopathogenic fungus D. anthuriicola that was abundant, in the relatively young Soto Lake on Deception Island. The lake sediments studied contained the DNA of rich, diverse and complex fungal communities, including both fungi commonly reported in Antarctica and other taxa considered to be rare. However, as the study was based on the use of environmental DNA, which does not unequivocally confirm the presence of active or viable organisms, further studies using other approaches such as shotgun sequencing are required to elucidate the ecology of fungi in these Antarctic lake sediments.

Environmental DNA reveals fine‐scale habitat associations for sedentary and resident marine species across a coastal mosaic of soft‐ and hard‐bottom habitats

AbstractAccurate knowledge on spatiotemporal distributions of marine species and their association with surrounding habitats is crucial to inform adaptive management actions responding to coastal degradation across the globe. Here, we investigate the potential use of environmental DNA (eDNA) to detect species–habitat associations in a patchy coastal area of the Baltic Sea. We directly compare species‐specific qPCR analysis of eDNA with baited remote underwater video systems (BRUVS), two non‐invasive methods widely used to monitor marine habitats. Four focal species (cod Gadus morhua, flounder Platichthys flesus, plaice Pleuronectes platessa, and goldsinny wrasse Ctenolabrus rupestris) were selected based on contrasting habitat associations (reef‐ vs. sand‐associated species), as well as differential levels of mobility and residency, to investigate whether these factors affected the detection of species–habitat associations from eDNA. To this end, a species‐specific qPCR assay for goldsinny wrasse is developed and made available herein. In addition, potential correlations between eDNA signals and abundance counts (MaxN) from videos were assessed. Results from Bayesian multilevel models revealed strong evidence for a sand association for sedentary flounder (98% posterior probability) and a reef association for highly resident wrasse (99% posterior probability) using eDNA, in agreement with BRUVS. However, contrary to BRUVS, eDNA sampling did not detect habitat associations for cod or plaice. We found a positive correlation between eDNA detection and MaxN for wrasse (posterior probability 95%), but not for the remaining species and explanatory power of all relationships was generally limited. Our results indicate that eDNA sampling can detect species–habitat associations on a fine spatial scale, yet this ability likely depends on the mobility and residency of the target organism, with associations for sedentary or resident species most likely to be detected. Combined sampling with conventional non‐invasive methods is advised to improve detection of habitat associations for mobile and transient species, or for species with low eDNA concentrations.

Effects of Harmful Algal Blooms on Fish and Shellfish Species: A Case Study of New Zealand in a Changing Environment.

Harmful algal blooms (HABs) have wide-ranging environmental impacts, including on aquatic species of social and commercial importance. In New Zealand (NZ), strategic growth of the aquaculture industry could be adversely affected by the occurrence of HABs. This review examines HAB species which are known to bloom both globally and in NZ and their effects on commercially important shellfish and fish species. Blooms of Karenia spp. have frequently been associated with mortalities of both fish and shellfish in NZ and the sub-lethal effects of other genera, notably Alexandrium spp., on shellfish (which includes paralysis, a lack of byssus production, and reduced growth) are also of concern. Climate change and anthropogenic impacts may alter HAB population structure and dynamics, as well as the physiological responses of fish and shellfish, potentially further compromising aquatic species. Those HAB species which have been detected in NZ and have the potential to bloom and harm marine life in the future are also discussed. The use of environmental DNA (eDNA) and relevant bioassays are practical tools which enable early detection of novel, problem HAB species and rapid toxin/HAB screening, and new data from HAB monitoring of aquaculture production sites using eDNA are presented. As aquaculture grows to supply a sizable proportion of the world’s protein, the effects of HABs in reducing productivity is of increasing significance. Research into the multiple stressor effects of climate change and HABs on cultured species and using local, recent, HAB strains is needed to accurately assess effects and inform stock management strategies.

Development of a triplex droplet digital polymerase chain reaction assay for the detection of three New Zealand native freshwater mussels (Echyridella) in environmental samples

AbstractThe freshwater mussel Echyridella (also known as kākahi) is the only freshwater mussel found in New Zealand's lakes and rivers and is endemic to the country. They play a crucial role in freshwater ecosystems and have high cultural significance. The three putative species of Echyridella are all classified as at risk. Monitoring is required to enhance knowledge on their distribution and to provide management, but conventional approaches (diving, wading, or swimming and visually looking for mussels) are time‐consuming, costly, and require good visibility. The use of environmental DNA (eDNA) in combination with PCR techniques offer advantages over conventional methods. In this study, we developed a triplex droplet digital PCR assay, targeting a region of the mitochondrial cytochrome oxidase subunit 1 gene, that differentiates all three kākahi species. The limits of quantification using gblocks were 0.6 × 10−03–6 × 10−03 fg/µl, yielding 2–8 copies/reaction, and for tissue DNA 10,000–100,000 fg/µl, yielding 9–15 copies/reaction. The method was applied to water samples from 48 lakes, lagoons, or ponds and two samples from streams. A total of 58% of samples from lakes, lagoons, or ponds and all samples from the streams were positive for kākahi. Sediment samples (n = 15) were also tested. Only those collected in close proximity (<1 m) to living kākahi were positive highlighting the patchy distribution of eDNA in sediment. This new assay will assist in determining the current distribution of kākahi at large temporal and spatial scales and has the potential to be used for the assessment of historic distributions as well.

The Multiple States of Environmental DNA and What Is Known about Their Persistence in Aquatic Environments.

Increased use of environmental DNA (eDNA) analysis for indirect species detection has spurred the need to understand eDNA persistence in the environment. Understanding the persistence of eDNA is complex because it exists in a mixture of different states (e.g., dissolved, particle adsorbed, intracellular, and intraorganellar), and each state is expected to have a specific decay rate that depends on environmental parameters. Thus, improving knowledge about eDNA conversion rates between states and the reactions that degrade eDNA in different states is needed. Here, we focus on eukaryotic extraorganismal eDNA, outline how water chemistry and suspended mineral particles likely affect conversion among each eDNA state, and indicate how environmental parameters affect persistence of states in the water column. On the basis of deducing these controlling parameters, we synthesized the eDNA literature to assess whether we could already derive a general understanding of eDNA states persisting in the environment. However, we found that these parameters are often not being measured or reported when measured, and in many cases very few experimental data exist from which to draw conclusions. Therefore, further study of how environmental parameters affect eDNA state conversion and eDNA decay in aquatic environments is needed. We recommend analytic controls that can be used during the processing of water to assess potential losses of different eDNA states if all were present in a water sample, and we outline future experimental work that would help determine the dominant eDNA states in water.

Evaluating eDNA for Use within Marine Environmental Impact Assessments

In this review, the use of environmental DNA (eDNA) within Environmental Impact Assessment (EIA) is evaluated. EIA documents provide information required by regulators to evaluate the potential impact of a development project. Currently eDNA is being incorporated into biodiversity assessments as a complementary method for detecting rare, endangered or invasive species. However, questions have been raised regarding the maturity of the field and the suitability of eDNA information as evidence for EIA. Several key issues are identified for eDNA information within a generic EIA framework for marine environments. First, it is challenging to define the sampling unit and optimal sampling strategy for eDNA with respect to the project area and potential impact receptor. Second, eDNA assay validation protocols are preliminary at this time. Third, there are statistical issues around the probability of obtaining both false positives (identification of taxa that are not present) and false negatives (non-detection of taxa that are present) in results. At a minimum, an EIA must quantify the uncertainty in presence/absence estimates by combining series of Bernoulli trials with ad hoc occupancy models. Finally, the fate and transport of DNA fragments is largely unknown in environmental systems. Shedding dynamics, biogeochemical and physical processes that influence DNA fragments must be better understood to be able to link an eDNA signal with the receptor’s state. The biggest challenge is that eDNA is a proxy for the receptor and not a direct measure of presence. Nonetheless, as more actors enter the field, technological solutions are likely to emerge for these issues. Environmental DNA already shows great promise for baseline descriptions of the presence of species surrounding a project and can aid in the identification of potential receptors for EIA monitoring using other methods.

Dams in South Europe: socio-environmental approach and eDNA-metabarcoding to study dam acceptance and ecosystem health

Under current climate warming, dams and reservoirs are main options to ensure water supply in dry regions. However, the presence of these infrastructures encompasses impacts on ecosystem due to the alteration of connectivity and river habitat. We expect that as a result of the relation between water supply as a resource and the population will depend on their use or demand, so the benefits of dams compensate their negative impacts in regions with droughts while not having the same perception in zones where water supply is not a problem, so the public acceptance of dams is expected to change depending on the area. Here, we have employed a multidisciplinary approach to study dam acceptance and also measure ecosystem health in two dammed areas, Guadalhorce and Nalón rivers, Mediterranean dry south and Atlantic humid north of Spain, respectively. The methodology employed has included the use of Environmental DNA for phytoplankton inventory and surveys to stakeholders and ordinary citizens to measure dam’s acceptance. Worse bioindicators of water quality associated to dams were found in Guadalhorce than in Nalon River. However, stakeholders valued more the ecosystem services provided by Guadalhorce dams, especially of cultural nature, than those provided by Nalón dams. Most citizens consulted (N = 319 and 300 in Guadalhorce and Nalón regions) were favourable to the presence of dams and reservoirs. They would also increase their annual taxes to restore river connectivity, especially in Guadalhorce River, while dam demolition was the least supported. The generally positive views would help to identify actions for improvement of dammed rivers highlighting the importance of restoring river connectivity without dam demolition for local river users.

Assessing the presence and spread of Renibacterium salmoninarum between farmed and wild fish in Sweden.

Bacterial kidney disease (BKD) can be a devastating bacterial infection in salmonids, and it is present in aquaculture throughout the world. BKD is caused by the Gram‐positive facultative intracellular bacterium Renibacterium salmoninarum (R. salmoninarum) that is spread both horizontally and vertically. Disease signs include external ulcerations and blisters and internal signs such as organ swelling, granulomas, petechiae and ascites. In Sweden, BKD accounts for a significant income loss in aquacultures due to expensive decontamination of the facility and increased disease susceptibility for the immunocompromised fish leading to higher mortality rates. In addition, uncontrolled spread in aquaculture may threaten the survival of wild fish populations. The aim of our study was to investigate the prevalence of R. salmoninarum in wild salmonids caught in Swedish waters where net pen farms with a recent history of BKD are present. Four rivers with at least one BKD‐positive or recently BKD‐positive farm were selected. In addition, we evaluated the use of environmental DNA (eDNA) for surveillance and monitoring of ongoing infections at these locations. In total, 1058 fish were sampled from four different river systems, and of them 52 (4.9%) were positive for R. salmoninarum by antigen ELISA. Surprisingly, these fish were not evenly distributed between the four river systems, but 50 were caught in the same river (Ljungan). This accounts for an alarmingly high rate of 17% R. salmoninarum‐positive samples in wild salmonids in this area. This number is far above what was expected and clearly shows the risk with an open farming system as well as the importance of effective health monitoring programmes to avoid an uncontrolled spread of the disease. The use of eDNA for monitoring BKD is somewhat difficult to evaluate. Few of the water samples analysed were PCR positive for R. salmoninarum (2 of 38) and those were collected where no ELISA positive fish were identified. In addition to water, sediment samples were collected under a net pen farm that had recently slaughtered all fish due to ongoing R. salmoninarum infections. Sediment samples are more promising than water as 4 of 5 samples at one farming facility where positive for R. salmoninarum. Thus, sediment samples may be valuable for monitoring potential ongoing BKD in farms, without the need to sacrifice valuable fish.

Use of environmental DNA in early detection of Mnemiopsis leidyi in UK coastal waters

Use of environmental DNA in early detection of Mnemiopsis leidyi in UK coastal waters

Capture by hybridization for full-length barcode-based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems.

Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future biodiversity research and biomonitoring tool. However, in poorly understood ecosystems, eDNA results remain difficult to interpret due to large gaps in reference databases and PCR bias limiting the detection of some major phyla. Here, we aimed to circumvent these limitations by avoiding PCR and recollecting larger DNA fragments to improve assignment of detected taxa through phylogenetic reconstruction. We applied capture by hybridization (CBH) to enrich DNA from deep-sea sediment samples and compared the results with those obtained through an up-to-date metabarcoding PCR-based approach (MTB). Originally developed for bacterial communities and targeting 16S rDNA, the CBH approach was applied to 18S rDNA to improve the detection of species forming benthic communities of eukaryotes, with a particular focus on metazoans. The results confirmed the possibility of extending CBH to metazoans with two major advantages: (i) CBH revealed a broader spectrum of prokaryotic, eukaryotic, and particularly metazoan diversity, and (ii) CBH allowed much more robust phylogenetic reconstructions of full-length barcodes with up to 1900 base pairs. This is particularly important for taxa whose assignment is hampered by gaps in reference databases. This study provides a database and probes to apply 18S CBH to diverse marine systems, confirming this promising new tool to improve biodiversity assessments in data-poor ecosystems such as those in the deep sea.

Use of environmental DNA in assessment of fish functional and phylogenetic diversity.

Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long-term remote video to assess species' phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded.

Assessing the in situ bacterial diversity and composition at anthropogenically active sites using the environmental DNA (eDNA)

In this study, we identified the in situ bacterial groups and their community structure in coastal waters influenced by anthropogenic inputs. The use of environmental DNA (eDNA) and high throughput sequencing (HTS) were employed to derive accurate and reliable information on bacterial abundance. The V3 and V4 hypervariable regions of the 16S rRNA gene were amplified and the sequences were clustered into operational taxonomic units to analyze the site-specific variations in community composition. The percentage composition within the bacterial orders varied significantly among nearshore anthropogenic hotspots and offshore (5 km) samples. The microbial network constructed taking the bacterial abundance as nodes displayed strong positive and negative correlations within the bacterial families. Overall, the use of eDNA coupled with HTS is an incredible means for monitoring and assessing the abundance of bacterial communities and also serves as a biomonitoring tool to understand the degree of anthropogenic contamination in coastal waters.

Observing Life in the Sea Using Environmental DNA

The use of environmental DNA (eDNA) for studying the ecology and variability of life in the sea is reviewed here in the context of US interagency Marine Biodiversity Observation Network (MBON) projects. Much of the information in this paper comes from samples collected within US National Marine Sanctuaries. The field of eDNA is relatively new but growing rapidly, and it has the potential to disrupt current paradigms developed on the basis of existing measurement methods. After a general review of the field, we provide specific examples of the type of information that eDNA provides regarding the changing distribution of life in the sea over space (horizontally and vertically) and time. We conclude that eDNA analyses yield results that are similar to those collected using traditional observation methods, are complementary to them, and because of the breadth of information provided, have the potential to improve conservation and management practices. Moreover, through technology development and standardization of methods, eDNA offers a means to scale biological observations globally to a level similar to those currently made for ocean physics and biogeochemistry. This scaling can ultimately result in a far better understanding of global marine biodiversity and contribute to better management and sustainable use of the world ocean. Improved information management systems that track methods and associated metadata, together with international coordination, will be needed to realize a global eDNA observation network.